diff --git a/.gitignore b/.gitignore index f89832908..fd3b5e9ba 100644 --- a/.gitignore +++ b/.gitignore @@ -8,4 +8,6 @@ resources/ public/ CLAUDE.md -.claude/ \ No newline at end of file +.claude/ +# Editor local history +.history/ diff --git a/.history/config/_default/menus_20210412141120.toml b/.history/config/_default/menus_20210412141120.toml deleted file mode 100644 index 68b8ee7e3..000000000 --- a/.history/config/_default/menus_20210412141120.toml +++ /dev/null @@ -1,199 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "SBOL Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "SBOL Libraries" - url = "/libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "SBOL Ontology" - url = "/ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "SBOL Converter" - url = "https://converter.sbolstandard.org/" - weight = 25 - parent = "dom-id" - -[[main]] - name = "SBOL Validator" - url = "https://validator.sbolstandard.org/" - weight = 30 - parent = "dom-id" - -[[main]] - name = "SBOL Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Ontology" - url = "/sbol-visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples from papers" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples from specification" - url = "/visual-spec-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "/publication" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "Help" - url = "/faq" - weight = 60 - identifier = "help-id" - -[[main]] - name = "FAQ" - url = "/faq" - weight = 62 - parent = "help-id" - -[[main]] - name = "StackExchange" - url = "https://bioinformatics.stackexchange.com/questions/tagged/sbol" - weight = 64 - parent = "help-id" - -[[main]] - name = "About" - url = "/about" - weight = 70 - identifier = "about-id" - -[[main]] - name = "View Source" - url = "https://synbiodex.github.io/SbolStandardWebsite/" - weight = 75 - parent = "about-id" - -[[main]] - name = "Community Media" - url = "https://github.com/SynBioDex/Community-Media" - weight = 80 - parent = "about-id" - -[[main]] - name = "Report an Issue" - url = "https://github.com/SynBioDex/SbolStandardWebsite/issues" - weight = 85 - parent = "about-id" - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/config/_default/params_20210124122229.toml b/.history/config/_default/params_20210124122229.toml deleted file mode 100644 index cb3ed9b6c..000000000 --- a/.history/config/_default/params_20210124122229.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "square" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/config/_default/params_20210419123423.toml b/.history/config/_default/params_20210419123423.toml deleted file mode 100644 index d44bde411..000000000 --- a/.history/config/_default/params_20210419123423.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = false - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "square" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/content/DataModel-Specification/_index_20210124122229.md b/.history/content/DataModel-Specification/_index_20210124122229.md deleted file mode 100644 index 1a8c2204e..000000000 --- a/.history/content/DataModel-Specification/_index_20210124122229.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-Specification/_index_20210813150230.md b/.history/content/DataModel-Specification/_index_20210813150230.md deleted file mode 100644 index c7401bffc..000000000 --- a/.history/content/DataModel-Specification/_index_20210813150230.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.1**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0.1specification.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-Specification/_index_20210813151018.md b/.history/content/DataModel-Specification/_index_20210813151018.md deleted file mode 100644 index 420bdfdfb..000000000 --- a/.history/content/DataModel-Specification/_index_20210813151018.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.1**
An updated version of SBOL 3.0.0 data model to refine naming conventions, and add the hasNamespace property to a TopLevel object.| {{% staticref "docs/SBOL3.0.1specification.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-Specification/_index_20210813151717.md b/.history/content/DataModel-Specification/_index_20210813151717.md deleted file mode 100644 index 1a8c2204e..000000000 --- a/.history/content/DataModel-Specification/_index_20210813151717.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-Specification/_index_20211027093435.md b/.history/content/DataModel-Specification/_index_20211027093435.md deleted file mode 100644 index 80c9a4932..000000000 --- a/.history/content/DataModel-Specification/_index_20211027093435.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-Specification/_index_20211027162304.md b/.history/content/DataModel-Specification/_index_20211027162304.md deleted file mode 100644 index 113b1529b..000000000 --- a/.history/content/DataModel-Specification/_index_20211027162304.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.1**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-Specification/_index_20211027162918.md b/.history/content/DataModel-Specification/_index_20211027162918.md deleted file mode 100644 index 22f0de109..000000000 --- a/.history/content/DataModel-Specification/_index_20211027162918.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.1**
An extension of version 3.0.0 data model to allow flexibility and extendibility of the following: move declaration of SBOL namespace from serialization to identifiers, change all identifiers.org URLs to short form, add serialization recommendation, use best practices in URI examples, change of logos, added compact validation rules, add extension of SBOL classes to extension options, improve complementary standards section, explain closure assumptions and document composition implications, use RDF cardinality terminology, add combinatorial derivation & validation rules amongst other fixes and updates | {{% staticref "docs/SBOL3.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-Specification/_index_20211027163614.md b/.history/content/DataModel-Specification/_index_20211027163614.md deleted file mode 100644 index a448c8d98..000000000 --- a/.history/content/DataModel-Specification/_index_20211027163614.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.1**
An extension of version 3.0.0 data model to allow flexibility and extendibility of the following: move declaration of SBOL namespace from serialization to identifiers, change all identifiers.org URLs to short form, add serialization recommendation, use best practices in URI examples, change of logos, added compact validation rules, add extension of SBOL classes to extension options, improve complementary standards section, explain closure assumptions and document composition implications, use RDF cardinality terminology, add combinatorial derivation & validation rules amongst other fixes and updates. | {{% staticref "docs/SBOL3.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/content/DataModel-about/_index_20210208150703.md b/.history/content/DataModel-about/_index_20210208150703.md deleted file mode 100644 index ab29cd22b..000000000 --- a/.history/content/DataModel-about/_index_20210208150703.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173742.md b/.history/content/DataModel-about/_index_20210208173742.md deleted file mode 100644 index 2869b38b0..000000000 --- a/.history/content/DataModel-about/_index_20210208173742.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173758.md b/.history/content/DataModel-about/_index_20210208173758.md deleted file mode 100644 index 75e767050..000000000 --- a/.history/content/DataModel-about/_index_20210208173758.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173810.md b/.history/content/DataModel-about/_index_20210208173810.md deleted file mode 100644 index 616e6cbe5..000000000 --- a/.history/content/DataModel-about/_index_20210208173810.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="...\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173827.md b/.history/content/DataModel-about/_index_20210208173827.md deleted file mode 100644 index b69360934..000000000 --- a/.history/content/DataModel-about/_index_20210208173827.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="..\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173837.md b/.history/content/DataModel-about/_index_20210208173837.md deleted file mode 100644 index 1e3aab617..000000000 --- a/.history/content/DataModel-about/_index_20210208173837.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src=".\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173902.md b/.history/content/DataModel-about/_index_20210208173902.md deleted file mode 100644 index 71a70be60..000000000 --- a/.history/content/DataModel-about/_index_20210208173902.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="content\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173944.md b/.history/content/DataModel-about/_index_20210208173944.md deleted file mode 100644 index 5b4e050c8..000000000 --- a/.history/content/DataModel-about/_index_20210208173944.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="\content\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208173955.md b/.history/content/DataModel-about/_index_20210208173955.md deleted file mode 100644 index efafb5807..000000000 --- a/.history/content/DataModel-about/_index_20210208173955.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="...\content\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174006.md b/.history/content/DataModel-about/_index_20210208174006.md deleted file mode 100644 index d43f8bd7e..000000000 --- a/.history/content/DataModel-about/_index_20210208174006.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="..\content\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174013.md b/.history/content/DataModel-about/_index_20210208174013.md deleted file mode 100644 index 8f6baf812..000000000 --- a/.history/content/DataModel-about/_index_20210208174013.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src=".\content\static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174029.md b/.history/content/DataModel-about/_index_20210208174029.md deleted file mode 100644 index 2869b38b0..000000000 --- a/.history/content/DataModel-about/_index_20210208174029.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="static\img\Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174409.md b/.history/content/DataModel-about/_index_20210208174409.md deleted file mode 100644 index ff2aa2b49..000000000 --- a/.history/content/DataModel-about/_index_20210208174409.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="static\img\Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174504.md b/.history/content/DataModel-about/_index_20210208174504.md deleted file mode 100644 index 8e6ec939a..000000000 --- a/.history/content/DataModel-about/_index_20210208174504.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="img\Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174526.md b/.history/content/DataModel-about/_index_20210208174526.md deleted file mode 100644 index 10cbb35fa..000000000 --- a/.history/content/DataModel-about/_index_20210208174526.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="\img\Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174606.md b/.history/content/DataModel-about/_index_20210208174606.md deleted file mode 100644 index 89340c747..000000000 --- a/.history/content/DataModel-about/_index_20210208174606.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure src="\img\Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174625.md b/.history/content/DataModel-about/_index_20210208174625.md deleted file mode 100644 index da38475bb..000000000 --- a/.history/content/DataModel-about/_index_20210208174625.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure src="static\img\Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210208174644.md b/.history/content/DataModel-about/_index_20210208174644.md deleted file mode 100644 index ff2aa2b49..000000000 --- a/.history/content/DataModel-about/_index_20210208174644.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="static\img\Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210209104111.md b/.history/content/DataModel-about/_index_20210209104111.md deleted file mode 100644 index a3c8d2083..000000000 --- a/.history/content/DataModel-about/_index_20210209104111.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210209104310.md b/.history/content/DataModel-about/_index_20210209104310.md deleted file mode 100644 index 4f5ba0ac7..000000000 --- a/.history/content/DataModel-about/_index_20210209104310.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLlogo.png" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210209104340.md b/.history/content/DataModel-about/_index_20210209104340.md deleted file mode 100644 index ab29cd22b..000000000 --- a/.history/content/DataModel-about/_index_20210209104340.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210209105323.md b/.history/content/DataModel-about/_index_20210209105323.md deleted file mode 100644 index c9f2e34cf..000000000 --- a/.history/content/DataModel-about/_index_20210209105323.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210209110645.md b/.history/content/DataModel-about/_index_20210209110645.md deleted file mode 100644 index fd53df0d0..000000000 --- a/.history/content/DataModel-about/_index_20210209110645.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- -{{< figure width="600px" library="true" src="Logos/SBOLlogo.png" title="" lightbox="true" >}} - - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210209110652.md b/.history/content/DataModel-about/_index_20210209110652.md deleted file mode 100644 index 9f40c332a..000000000 --- a/.history/content/DataModel-about/_index_20210209110652.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- -{{< figure width="600px" library="true" src="Logos/SBOLlogo.svg" title="" lightbox="true" >}} - - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/DataModel-about/_index_20210209110711.md b/.history/content/DataModel-about/_index_20210209110711.md deleted file mode 100644 index fbee12fac..000000000 --- a/.history/content/DataModel-about/_index_20210209110711.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- -{{< figure width="600px" library="true" src="Logos/SBOLlogo.svg" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/applications/_index_20210209104909.md b/.history/content/applications/_index_20210209104909.md deleted file mode 100644 index 26417dd93..000000000 --- a/.history/content/applications/_index_20210209104909.md +++ /dev/null @@ -1,24 +0,0 @@ ---- -title: Applications - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 2 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks. Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs. - - - - -### Feature Your Application Here! - -If you would like us to feature your application here, please fill out this [survey](https://docs.google.com/forms/d/e/1FAIpQLScOTJLCoTniVPrMh88eg74Eaubh1bFMjncbyG6yt8q4cFLQ-Q/viewform). diff --git a/.history/content/applications/_index_20210209111529.md b/.history/content/applications/_index_20210209111529.md deleted file mode 100644 index 294676105..000000000 --- a/.history/content/applications/_index_20210209111529.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: Applications - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 2 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks. Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs. - -< figure width="600px" library="true" src="/img/SBOL_2_demo_workflow_chris.png" title="" lightbox="true" > - -### Feature Your Application Here! - -If you would like us to feature your application here, please fill out this [survey](https://docs.google.com/forms/d/e/1FAIpQLScOTJLCoTniVPrMh88eg74Eaubh1bFMjncbyG6yt8q4cFLQ-Q/viewform). diff --git a/.history/content/applications/_index_20210209112508.md b/.history/content/applications/_index_20210209112508.md deleted file mode 100644 index 380207cf7..000000000 --- a/.history/content/applications/_index_20210209112508.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: Applications - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 2 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks. Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs. - -{{< figure width="600px" library="true" src="/img/SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -### Feature Your Application Here! - -If you would like us to feature your application here, please fill out this [survey](https://docs.google.com/forms/d/e/1FAIpQLScOTJLCoTniVPrMh88eg74Eaubh1bFMjncbyG6yt8q4cFLQ-Q/viewform). diff --git a/.history/content/applications/_index_20210209113122.md b/.history/content/applications/_index_20210209113122.md deleted file mode 100644 index a494f41b7..000000000 --- a/.history/content/applications/_index_20210209113122.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: Applications - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 2 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks. Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs. - -{{< figure width="600px" library="true" src="SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -### Feature Your Application Here! - -If you would like us to feature your application here, please fill out this [survey](https://docs.google.com/forms/d/e/1FAIpQLScOTJLCoTniVPrMh88eg74Eaubh1bFMjncbyG6yt8q4cFLQ-Q/viewform). diff --git a/.history/content/applications/_index_20210209122315.md b/.history/content/applications/_index_20210209122315.md deleted file mode 100644 index a494f41b7..000000000 --- a/.history/content/applications/_index_20210209122315.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: Applications - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 2 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -If you are a synthetic biologist, you may not be aware that there are already many software tools available that support different aspects of the synthetic biology workflow, such as optimizing DNA assembly or simulating gene networks. Each of the software tools listed here supports exchange of genetic designs in the SBOL file format (SBOL core) or supports display of genetic designs using standard SBOL Visual glyphs. - -{{< figure width="600px" library="true" src="SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -### Feature Your Application Here! - -If you would like us to feature your application here, please fill out this [survey](https://docs.google.com/forms/d/e/1FAIpQLScOTJLCoTniVPrMh88eg74Eaubh1bFMjncbyG6yt8q4cFLQ-Q/viewform). diff --git a/.history/content/authors/admin/_index_20210124122229.md b/.history/content/authors/admin/_index_20210124122229.md deleted file mode 100644 index f26c5523c..000000000 --- a/.history/content/authors/admin/_index_20210124122229.md +++ /dev/null @@ -1,83 +0,0 @@ ---- -# Display name -title: Synthetic Biology Open Language - -# Username (this should match the folder name) -authors: -- admin - -# Is this the primary user of the site? -superuser: true - -# Role/position -#role: Professor of Artificial Intelligence - -# Organizations/Affiliations -#organizations: -#- name: Stanford University -# url: "" - -# Short bio (displayed in user profile at end of posts) -# bio: My research interests include distributed robotics, mobile computing and programmable matter. - -# interests: -# - Artificial Intelligence -# - Computational Linguistics -# - Information Retrieval - -# education: -# courses: -# - course: PhD in Artificial Intelligence -# institution: Stanford University -# year: 2012 -# - course: MEng in Artificial Intelligence -# institution: Massachusetts Institute of Technology -# year: 2009 -# - course: BSc in Artificial Intelligence -# institution: Massachusetts Institute of Technology -# year: 2008 - -# Social/Academic Networking -# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons -# For an email link, use "fas" icon pack, "envelope" icon, and a link in the -# form "mailto:your-email@example.com" or "#contact" for contact widget. -social: -#- icon: envelope -# icon_pack: fas -# link: '#contact' # For a direct email link, use "mailto:test@example.org". -#- icon: google-scholar -# icon_pack: ai -# link: https://scholar.google.co.uk/citations?user=sIwtMXoAAAAJ -- icon: github - icon_pack: fab - link: https://github.com/SynBioDex -- icon: twitter - icon_pack: fab - link: https://twitter.com/SBOLstandard -- icon: facebook - icon_pack: fab - link: https://www.facebook.com/SBOLstandards/ -- icon: youtube - icon_pack: fab - link: https://www.youtube.com/channel/UCrxKZNvDVabwGoxEOMZt_Qg -# Link to a PDF of your resume/CV from the About widget. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# - icon: cv -# icon_pack: ai -# link: files/cv.pdf - -# Enter email to display Gravatar (if Gravatar enabled in Config) -email: "" - -# Organizational groups that you belong to (for People widget) -# Set this to `[]` or comment out if you are not using People widget. -user_groups: -- Researchers -- Visitors ---- - - -* SBOL is an open standard for the representation of in silico biological designs. -* SBOL provides a data format composed of genetic vocabulary terms called SBOL Data. -* SBOL also provides schematic glyphs to graphically depict genetic designs called SBOL Visual. -* SBOL standardises data used by synthetic biology practitioners, from users to software developers to wet lab biologists. \ No newline at end of file diff --git a/.history/content/authors/admin/_index_20210412140344.md b/.history/content/authors/admin/_index_20210412140344.md deleted file mode 100644 index 75a7d4d60..000000000 --- a/.history/content/authors/admin/_index_20210412140344.md +++ /dev/null @@ -1,80 +0,0 @@ ---- -# Display name -title: Synthetic Biology Open Language - -# Username (this should match the folder name) -authors: -- admin - -# Is this the primary user of the site? -superuser: true - -# Role/position -#role: Professor of Artificial Intelligence - -# Organizations/Affiliations -#organizations: -#- name: Stanford University -# url: "" - -# Short bio (displayed in user profile at end of posts) -# bio: My research interests include distributed robotics, mobile computing and programmable matter. - -# interests: -# - Artificial Intelligence -# - Computational Linguistics -# - Information Retrieval - -# education: -# courses: -# - course: PhD in Artificial Intelligence -# institution: Stanford University -# year: 2012 -# - course: MEng in Artificial Intelligence -# institution: Massachusetts Institute of Technology -# year: 2009 -# - course: BSc in Artificial Intelligence -# institution: Massachusetts Institute of Technology -# year: 2008 - -# Social/Academic Networking -# For available icons, see: https://sourcethemes.com/academic/docs/page-builder/#icons -# For an email link, use "fas" icon pack, "envelope" icon, and a link in the -# form "mailto:your-email@example.com" or "#contact" for contact widget. -social: -#- icon: envelope -# icon_pack: fas -# link: '#contact' # For a direct email link, use "mailto:test@example.org". -#- icon: google-scholar -# icon_pack: ai -# link: https://scholar.google.co.uk/citations?user=sIwtMXoAAAAJ -- icon: github - icon_pack: fab - link: https://github.com/SynBioDex -- icon: twitter - icon_pack: fab - link: https://twitter.com/SBOLstandard -- icon: youtube - icon_pack: fab - link: https://www.youtube.com/channel/UCrxKZNvDVabwGoxEOMZt_Qg -# Link to a PDF of your resume/CV from the About widget. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# - icon: cv -# icon_pack: ai -# link: files/cv.pdf - -# Enter email to display Gravatar (if Gravatar enabled in Config) -email: "" - -# Organizational groups that you belong to (for People widget) -# Set this to `[]` or comment out if you are not using People widget. -user_groups: -- Researchers -- Visitors ---- - - -* SBOL is an open standard for the representation of in silico biological designs. -* SBOL provides a data format composed of genetic vocabulary terms called SBOL Data. -* SBOL also provides schematic glyphs to graphically depict genetic designs called SBOL Visual. -* SBOL standardises data used by synthetic biology practitioners, from users to software developers to wet lab biologists. \ No newline at end of file diff --git a/.history/content/community-governance/_index_20210823152014.md b/.history/content/community-governance/_index_20210823152014.md deleted file mode 100644 index 553aaf200..000000000 --- a/.history/content/community-governance/_index_20210823152014.md +++ /dev/null @@ -1,181 +0,0 @@ ---- -title: Governance - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: - -* SBOL should be free and open standard, developed by an open and inclusive processes. -* SBOL is a community that believes in fostering, cultivating and preserving a culture of diversity and inclusion. -* Leaders of the SBOL community are expected to actively foster a safe environment where all participants feel comfortable making their voices heard. -* Leadership from new and diverse voices should be actively developed, including by participation in working groups and by public speaking at workshops. - -## SBOL Organization -The SBOL community has the following organization: - -* SBOL Development Group: general body comprising all members of the SBOL community, and ultimate authority -* Ad-Hoc Subgroups: portions of the general development group focused on particular aspects of SBOL development. -* SBOL Editors: operational executives for the community -* SBOL Chair and Steering Committee: strategic planning and guidance for the community -* SBOL Industrial Consortium: a pre-competitive organization of companies (or similar) investing in the SBOL community - -## SBOL Development Group -Membership in the SBOL Development Group is open to all interested parties. Individuals interested in joining the group should contact [the editors](mailto:sbol-editors@googlegroups.com). - -The SBOL Development Group as a whole is the ultimate authority and source of legitimacy for SBOL standards decisions. All elections, standards changes, and governance changes are voted on by the SBOL Development Group according to the procedures below. - -The primary means of communication for the SBOL Development Group is via the sbol-dev Google Group. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list. - -SBOL workshops should be held twice per year. These may be stand-alone workshops or in combination with another event, but must provide ample time for attending members to hold focused discussions on the development of SBOL. - -All members of the SBOL Development Group are encouraged (but not required) to: - -* Attend the SBOL Workshops and other meetings -* Participate in discussions on SBOL mailing lists -* Support the SBOL standard in any tools and systems they work on -* Provide constructive feedback for improving the standard - -## Ad-Hoc Subgroups -Certain activities of the SBOL community are expected to either generate noticeably higher volumes of communication (e.g., software development and support) or to address topics expected to be of interest only to certain special interest groups. When deemed appropriate, ad-hoc subgroups may be created for addressing such topics. - -Subgroups must communicate via open lists that may be readily accessed and joined by any member of the SBOL Development Group. Any communication regarding standards changes, however, should be migrated back to the SBOL Development Group mailing list. - -## SBOL editors -As a matter of pragmatism, many organizational decisions and actions are delegated to an elected group of SBOL Editors, so named because their primary responsibility is ensuring the effective curation of documents for the community. - -The responsibilities of the SBOL Editors are: - -* Equitably representing the community in voting, documents, and guidance of discussion. -* Curation and dissemination of the SBOL standards and related documents (including writing, editing, and coordinating changes). -* Maintaining an open and structured process by which members of the SBOL Development Group can modify and improve SBOL standards (including timely implementation of tracking, processing, responding to, and organizing voting on change proposals). -* Ensuring effective development and maintenance of official SBOL software libraries and associated documentation and tutorials. -* Coordinating scholarly publications and ensuring proper attribution of contributions. -* Running elections and other community votes. -* Organization (or delegation) of SBOL Workshops and other events. -* Maintaining community infrastructure, including: the SBOL web site, source code repositories, mailing lists - -The SBOL Editors shall hold weekly meetings to coordinate their execution of these responsibilities. These meetings should be open, and their minutes should be reported to the SBOL Development Group. - -The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. - -SBOL Editors are elected by a community vote, following the process below. Editors serve initially for a two-year term, and upon unanimous approval of the editors and chair, an editor's term can be extended for an additional third year. After completing their term as editor, a person may not run for editor again for at least one year. To maximize continuity, editors' terms should be de-synchronized. There are 5 editorial positions, currently held by: - -* Pedro Fontanarrosa, University of Utah -* James Scott-Brown, University of Oxford -* Prashant Vaidyananthan, Microsoft Research -* Gonzalo Vidal Peña, Pontificia Universidad Católica de Chile -* Tom Mitchell, Raytheon BBN Technologies - -Previous SBOL Editors include: Hasan Baig (University of Connecticut), Vishwesh Kulkarni (University of Warwick), Zach Palchik (Zymergen), Curtis Madsen (Sandia National Labs), Nicholas Roehner (BBN Technologies), Angel Goñi Moreno (Newcastle University), Umesh P (Kerala Technological University), Tramy Nguyen (University of Utah), James McLaughlin (Newcastle University), Robert Sidney Cox (Kobe University), Raik Grunberg (University of Montreal), Jacob Beal (BBN Technologies), Bryan Bartley (University of Washington), Kevin Clancy (ThermoFisher), Michal Galdzicki (University of Washington), Goksel Misirli (Newcastle University), Ernst Oberortner (Boston University), Matthew Pocock, (Newcastle University), Jacqueline Quinn (Google), Cesar Rodriguez (Autodesk), Mandy Wilson (Virginia Bioinformatics Institute). - -## SBOL Chair and Steering Committee -The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. - -The SBOL Chair is the head of the SBOL Steering Committee. The SBOL Chair is responsible for ensuring regular steering committee meetings are held, for effective moderation of these meetings, and for being an advertised public point of contact for outside organizations. - -The SBOL Chair is elected by a community vote, following the process below. Chairs serve for a four year term. In order to ensure a smooth working relationship between the SBOL Chair and SBOL Editors, the SBOL Editors can remove a chair by a no-confidence vote amongst the SBOL Editors at any time. - -The rest of the SBOL Steering Committee are appointed (and removed) by the SBOL Chair. The Steering Committee has no fixed size or fixed term, but should generally comprise the set of PI-level members who are strongly active, have a strong stake in SBOL, and are willing to assume community leadership responsibilities. - -The SBOL Steering Committee shall hold monthly meetings to coordinate around strategic issues for the community (e.g., funding, setting key priorities and goals). These meetings should be open, and their minutes should be reported to the SBOL Development Group. The SBOL Steering Committee should also convene an external advisory board to help maintain strategic links with other communities and to obtain useful advice in guiding the community. - -The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. - -The SBOL current chair: - -**Chris Myers (May, 2019-), University of Colorado, Boulder** - -Previous Chairs: - -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Kevin Clancy, Synthetic Genomics, Inc. -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Utah -* Ernst Oberortner, DOE Joint Genome Institute (JGI) -* Timothy Rudge, Newcastle University -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University - - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Panel is currently (listed alphabetically): - -* Prof. Matthew Chang, National University of Singapore -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Traci Haddock, iGEM Foundation -* Prof. Richard Kitney, Imperial College London -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University -* Prof. Chris Voigt, Massachusetts Institute of Technology - -## SBOL Industrial Consortium -The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. -As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium shall be free, open, and support the core values of the SBOL community. - -The SBOL Industrial Consortium will organize an Industrial Advisory Board to provide an industrial perspective on SBOL. The SBOL Chair shall hold quarterly meetings with the Industrial Advisory Board. These meetings (which may co-occur with Steering Committee Meetings) should be open and their minutes should be reported to the SBOL Development Group. - -Subject to these constraints, the SBOL Industrial Consortium is otherwise organized independently and operates under its own internal governance. Similarly, membership in the SBOL Industrial Consortium neither implies nor impairs membership in the SBOL Development Group. - -## Voting Procedures - -#### Elections Process: -Before any election, there is a nomination period of 5 working days. -All members of the SBOL Development Group are eligible for all offices (except those that are term-limited). -Any member can self-nominate or can nominate any other member. -Voting runs for 5 working days, starting at the end of the nomination period. All members of the SBOL Development Group are eligible to vote. -Candidates are elected by plurality. - -#### Voting process: -1. Any member of the SBOL Developers Group can submit an SBOL Enhancement Proposal (SEP) to the editors and/or to the community at large. See [SEP #1](https://github.com/SynBioDex/SEPs/issues/1) for a description of when and how to write and submit an SEP. - -2. SBOL editors are expected to move a given SEP draft to a vote once they agree that there has been sufficient debate. However, any member of the SBOL Developers Group can initiate the vote as long as one other member of the group seconds the motion. - -3. SBOL Editors post a voting form (see below), for a final discussion period of 2 working days. - -4. Voting runs for 5 working days, starting at the end of the discussion period. All members of the SBOL Development Group are eligible to vote. - -5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. - -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. - 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. - 2. The reasons for decisions must be recorded with the results of the vote. - 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. - - -#### Voting form must: - -1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” -3. Provide the following options for the vote: - * accept — vote to accept the SEP - * reject — vote to reject the SEP - * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). - -#### Ground-rules for moderating discussions in SBOL breakout sessions - -1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. -2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. -4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” -5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. -6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/.history/content/community-governance/_index_20210823160210.md b/.history/content/community-governance/_index_20210823160210.md deleted file mode 100644 index 6daa939dd..000000000 --- a/.history/content/community-governance/_index_20210823160210.md +++ /dev/null @@ -1,181 +0,0 @@ ---- -title: Governance - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: - -* SBOL should be free and open standard, developed by an open and inclusive processes. -* SBOL is a community that believes in fostering, cultivating and preserving a culture of diversity and inclusion. -* Leaders of the SBOL community are expected to actively foster a safe environment where all participants feel comfortable making their voices heard. -* Leadership from new and diverse voices should be actively developed, including by participation in working groups and by public speaking at workshops. - -## SBOL Organization -The SBOL community has the following organization: - -* SBOL Development Group: general body comprising all members of the SBOL community, and ultimate authority -* Ad-Hoc Subgroups: portions of the general development group focused on particular aspects of SBOL development. -* SBOL Editors: operational executives for the community -* SBOL Chair and Steering Committee: strategic planning and guidance for the community -* SBOL Industrial Consortium: a pre-competitive organization of companies (or similar) investing in the SBOL community - -## SBOL Development Group -Membership in the SBOL Development Group is open to all interested parties. Individuals interested in joining the group should contact [the editors](mailto:sbol-editors@googlegroups.com). - -The SBOL Development Group as a whole is the ultimate authority and source of legitimacy for SBOL standards decisions. All elections, standards changes, and governance changes are voted on by the SBOL Development Group according to the procedures below. - -The primary means of communication for the SBOL Development Group is via the sbol-dev Google Group. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list. - -SBOL workshops should be held twice per year. These may be stand-alone workshops or in combination with another event, but must provide ample time for attending members to hold focused discussions on the development of SBOL. - -All members of the SBOL Development Group are encouraged (but not required) to: - -* Attend the SBOL Workshops and other meetings -* Participate in discussions on SBOL mailing lists -* Support the SBOL standard in any tools and systems they work on -* Provide constructive feedback for improving the standard - -## Ad-Hoc Subgroups -Certain activities of the SBOL community are expected to either generate noticeably higher volumes of communication (e.g., software development and support) or to address topics expected to be of interest only to certain special interest groups. When deemed appropriate, ad-hoc subgroups may be created for addressing such topics. - -Subgroups must communicate via open lists that may be readily accessed and joined by any member of the SBOL Development Group. Any communication regarding standards changes, however, should be migrated back to the SBOL Development Group mailing list. - -## SBOL editors -As a matter of pragmatism, many organizational decisions and actions are delegated to an elected group of SBOL Editors, so named because their primary responsibility is ensuring the effective curation of documents for the community. - -The responsibilities of the SBOL Editors are: - -* Equitably representing the community in voting, documents, and guidance of discussion. -* Curation and dissemination of the SBOL standards and related documents (including writing, editing, and coordinating changes). -* Maintaining an open and structured process by which members of the SBOL Development Group can modify and improve SBOL standards (including timely implementation of tracking, processing, responding to, and organizing voting on change proposals). -* Ensuring effective development and maintenance of official SBOL software libraries and associated documentation and tutorials. -* Coordinating scholarly publications and ensuring proper attribution of contributions. -* Running elections and other community votes. -* Organization (or delegation) of SBOL Workshops and other events. -* Maintaining community infrastructure, including: the SBOL web site, source code repositories, mailing lists - -The SBOL Editors shall hold weekly meetings to coordinate their execution of these responsibilities. These meetings should be open, and their minutes should be reported to the SBOL Development Group. - -The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. - -SBOL Editors are elected by a community vote, following the process below. Editors serve initially for a two-year term, and upon unanimous approval of the editors and chair, an editor's term can be extended for an additional third year. After completing their term as editor, a person may not run for editor again for at least one year. To maximize continuity, editors' terms should be de-synchronized. There are 5 editorial positions, currently held by: - -* Pedro Fontanarrosa, University of Utah -* James Scott-Brown, University of Oxford -* Prashant Vaidyananthan, Microsoft Research -* Gonzalo Vidal Peña, Pontificia Universidad Católica de Chile -* Tom Mitchell, Raytheon BBN Technologies - -Previous SBOL Editors include: Hasan Baig (University of Connecticut), Vishwesh Kulkarni (University of Warwick), Zach Palchik (Zymergen), Curtis Madsen (Sandia National Labs), Nicholas Roehner (BBN Technologies), Angel Goñi Moreno (Newcastle University), Umesh P (Kerala Technological University), Tramy Nguyen (University of Utah), James McLaughlin (Newcastle University), Robert Sidney Cox (Kobe University), Raik Grunberg (University of Montreal), Jacob Beal (BBN Technologies), Bryan Bartley (University of Washington), Kevin Clancy (ThermoFisher), Michal Galdzicki (University of Washington), Goksel Misirli (Newcastle University), Ernst Oberortner (Boston University), Matthew Pocock, (Newcastle University), Jacqueline Quinn (Google), Cesar Rodriguez (Autodesk), Mandy Wilson (Virginia Bioinformatics Institute). - -## SBOL Chair and Steering Committee -The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. - -The SBOL Chair is the head of the SBOL Steering Committee. The SBOL Chair is responsible for ensuring regular steering committee meetings are held, for effective moderation of these meetings, and for being an advertised public point of contact for outside organizations. - -The SBOL Chair is elected by a community vote, following the process below. Chairs serve for a four year term. In order to ensure a smooth working relationship between the SBOL Chair and SBOL Editors, the SBOL Editors can remove a chair by a no-confidence vote amongst the SBOL Editors at any time. - -The rest of the SBOL Steering Committee are appointed (and removed) by the SBOL Chair. The Steering Committee has no fixed size or fixed term, but should generally comprise the set of PI-level members who are strongly active, have a strong stake in SBOL, and are willing to assume community leadership responsibilities. - -The SBOL Steering Committee shall hold monthly meetings to coordinate around strategic issues for the community (e.g., funding, setting key priorities and goals). These meetings should be open, and their minutes should be reported to the SBOL Development Group. The SBOL Steering Committee should also convene an external advisory board to help maintain strategic links with other communities and to obtain useful advice in guiding the community. - -The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. - -The SBOL current chair: - -**Chris Myers (May, 2019-), University of Colorado, Boulder** - -Previous Chairs: - -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Kevin Clancy, Synthetic Genomics, Inc. -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Utah -* Ernst Oberortner, DOE Joint Genome Institute (JGI) -* Timothy Rudge, Pontificia Universidad Católica de Chile -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University - - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Panel is currently (listed alphabetically): - -* Prof. Matthew Chang, National University of Singapore -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Traci Haddock, iGEM Foundation -* Prof. Richard Kitney, Imperial College London -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University -* Prof. Chris Voigt, Massachusetts Institute of Technology - -## SBOL Industrial Consortium -The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. -As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium shall be free, open, and support the core values of the SBOL community. - -The SBOL Industrial Consortium will organize an Industrial Advisory Board to provide an industrial perspective on SBOL. The SBOL Chair shall hold quarterly meetings with the Industrial Advisory Board. These meetings (which may co-occur with Steering Committee Meetings) should be open and their minutes should be reported to the SBOL Development Group. - -Subject to these constraints, the SBOL Industrial Consortium is otherwise organized independently and operates under its own internal governance. Similarly, membership in the SBOL Industrial Consortium neither implies nor impairs membership in the SBOL Development Group. - -## Voting Procedures - -#### Elections Process: -Before any election, there is a nomination period of 5 working days. -All members of the SBOL Development Group are eligible for all offices (except those that are term-limited). -Any member can self-nominate or can nominate any other member. -Voting runs for 5 working days, starting at the end of the nomination period. All members of the SBOL Development Group are eligible to vote. -Candidates are elected by plurality. - -#### Voting process: -1. Any member of the SBOL Developers Group can submit an SBOL Enhancement Proposal (SEP) to the editors and/or to the community at large. See [SEP #1](https://github.com/SynBioDex/SEPs/issues/1) for a description of when and how to write and submit an SEP. - -2. SBOL editors are expected to move a given SEP draft to a vote once they agree that there has been sufficient debate. However, any member of the SBOL Developers Group can initiate the vote as long as one other member of the group seconds the motion. - -3. SBOL Editors post a voting form (see below), for a final discussion period of 2 working days. - -4. Voting runs for 5 working days, starting at the end of the discussion period. All members of the SBOL Development Group are eligible to vote. - -5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. - -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. - 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. - 2. The reasons for decisions must be recorded with the results of the vote. - 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. - - -#### Voting form must: - -1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” -3. Provide the following options for the vote: - * accept — vote to accept the SEP - * reject — vote to reject the SEP - * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). - -#### Ground-rules for moderating discussions in SBOL breakout sessions - -1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. -2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. -4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” -5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. -6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/.history/content/community-meetings/_index_20210325110750.md b/.history/content/community-meetings/_index_20210325110750.md deleted file mode 100644 index 3cb1b4522..000000000 --- a/.history/content/community-meetings/_index_20210325110750.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -title: Meetings - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL Developers community meets approximately every 6 months. The discussion at these workshops is often convivial, collegiate, and interesting. In May 2014 the SBOL Developers group elected to co-locate future SBOL workshops with similar workshops hosted by the ["Computational Modeling in Biolog Network (COMBINE)"](http://co.mbine.org/). This creates an atmosphere where synthetic biologists and systems biologists can work toward a common goal of integrating biological knowledge through inter-operable and non-overlapping data standards. Our “COMBINE”d efforts empower exciting innovations like [modeling whole cells](https://sites.google.com/site/vwwholecellsummerschool/). - -We welcome participants from industry to these discussions, as the SBOL standard exists to support commercial as well as scientific innovation in synthetic biology and biotechnology. - - -### SBOL Workshops and Conferences - -| Event | Date (YYYY/DD/MM) | Location | Materials | -|--------------------------------------------------------------------------------------|----------------------|--------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------| -| COMBINE 2020 | 2020/05-09/10 | UConn Health, Connecticut, USA | Slides | -| HARMONY 2020 | 2020/09-13/03 | EMBL-EBI, Cambridgeshire, UK | Slides | -| COMBINE 2019 & EU-STANDS4PM | 2019/15-19/07 | Studio Villa Bosch, Heidelberg, Germany | Slides | -| HARMONY 2019 | 2019/25-29/03 | Caltech, Pasadena, California, USA | | -| COMBINE 2018 | 2018/08-12/10 | Boston University in Boston, MA, USA | | -| HARMONY 2018 | 2018/18-22/06 | Oxford University, UK | Slides | -| COMBINE 2017 | 2017/09-13/10 | Università degli Studi di Milano Bicocca in Milan, Italy | Slides | -| HARMONY 2017 | 2017/26-30/06 | University of Washington in Seattle, WA, USA | Slides | -| COMBINE 2016 | 2016/19-24/09 | Newcastle University in Newcastle Upon Tyne, UK | Slides | -| SBOL 14 | 2016/14-16/03 | Raytheon BBN Technologies in Boston, MA, USA | Slides | -| COMBINE 2015 | 2015/12-16/10 | University of Utah in Salt Lake City, UT, USA | Slides | -| HARMONY 2015 | 2015/20/03 | Wittenberg, Germany, EU | | -| COMBINE 2014 | 2014/18-22/08 | University of Southern California in Los Angeles, CA, USA | Slides | -| SBOL 10 | 2014/07-09/01 | UC Berkeley, CA, USA | Slides | -| SBOL 9 | 2013/24-26/04 | Newcastle University in Newcastle, UK | Slides | -| SBOL 8 | 2012/07-08/11 | Boston University in Boston, MA, USA | Slides | -| SBOL 7 | 2012/05/06 | Marriot Courtyard in San Francisco, CA, USA | Slides | -| SBOL 6 | 2012/05-06/01 | Univeristy of Washington in Seattle, WA, USA | Slides | -| SBOL 5 | 2011/08/06 | The Omni Hotel in San Diego, CA, USA | | -| SBOL 4 | 2011/07/01 | The Inn at Virginia Tech in Blacksburg, VA, USA | | -| SBOL 3 | 2010/13/06 | Hilton Anaheim in Anaheim, CA, USA | | -| SBOL 2 | 2009/26/07 | Stanford University in Stanford, CA, USA | Slides | -| SBOL 1 | 2008/27/04 | University of Washington in WA, USA | Programme | diff --git a/.history/content/community-meetings/_index_20210825145651.md b/.history/content/community-meetings/_index_20210825145651.md deleted file mode 100644 index d89190190..000000000 --- a/.history/content/community-meetings/_index_20210825145651.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: Meetings - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL Developers community meets approximately every 6 months. The discussion at these workshops is often convivial, collegiate, and interesting. In May 2014 the SBOL Developers group elected to co-locate future SBOL workshops with similar workshops hosted by the ["Computational Modeling in Biolog Network (COMBINE)"](http://co.mbine.org/). This creates an atmosphere where synthetic biologists and systems biologists can work toward a common goal of integrating biological knowledge through inter-operable and non-overlapping data standards. Our “COMBINE”d efforts empower exciting innovations like [modeling whole cells](https://sites.google.com/site/vwwholecellsummerschool/). - -We welcome participants from industry to these discussions, as the SBOL standard exists to support commercial as well as scientific innovation in synthetic biology and biotechnology. - - -### SBOL Workshops and Conferences - -| Event | Date (YYYY/DD/MM) | Location | Materials | -|--------------------------------------------------------------------------------------|----------------------|--------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------| -| SEED 2021 | 2021/15-18/05 | Virtual | Slides | -| COMBINE 2020 | 2020/05-09/10 | UConn Health, Connecticut, USA | Slides | -| HARMONY 2020 | 2020/09-13/03 | EMBL-EBI, Cambridgeshire, UK | Slides | -| COMBINE 2019 & EU-STANDS4PM | 2019/15-19/07 | Studio Villa Bosch, Heidelberg, Germany | Slides | -| HARMONY 2019 | 2019/25-29/03 | Caltech, Pasadena, California, USA | | -| COMBINE 2018 | 2018/08-12/10 | Boston University in Boston, MA, USA | | -| HARMONY 2018 | 2018/18-22/06 | Oxford University, UK | Slides | -| COMBINE 2017 | 2017/09-13/10 | Università degli Studi di Milano Bicocca in Milan, Italy | Slides | -| HARMONY 2017 | 2017/26-30/06 | University of Washington in Seattle, WA, USA | Slides | -| COMBINE 2016 | 2016/19-24/09 | Newcastle University in Newcastle Upon Tyne, UK | Slides | -| SBOL 14 | 2016/14-16/03 | Raytheon BBN Technologies in Boston, MA, USA | Slides | -| COMBINE 2015 | 2015/12-16/10 | University of Utah in Salt Lake City, UT, USA | Slides | -| HARMONY 2015 | 2015/20/03 | Wittenberg, Germany, EU | | -| COMBINE 2014 | 2014/18-22/08 | University of Southern California in Los Angeles, CA, USA | Slides | -| SBOL 10 | 2014/07-09/01 | UC Berkeley, CA, USA | Slides | -| SBOL 9 | 2013/24-26/04 | Newcastle University in Newcastle, UK | Slides | -| SBOL 8 | 2012/07-08/11 | Boston University in Boston, MA, USA | Slides | -| SBOL 7 | 2012/05/06 | Marriot Courtyard in San Francisco, CA, USA | Slides | -| SBOL 6 | 2012/05-06/01 | Univeristy of Washington in Seattle, WA, USA | Slides | -| SBOL 5 | 2011/08/06 | The Omni Hotel in San Diego, CA, USA | | -| SBOL 4 | 2011/07/01 | The Inn at Virginia Tech in Blacksburg, VA, USA | | -| SBOL 3 | 2010/13/06 | Hilton Anaheim in Anaheim, CA, USA | | -| SBOL 2 | 2009/26/07 | Stanford University in Stanford, CA, USA | Slides | -| SBOL 1 | 2008/27/04 | University of Washington in WA, USA | Programme | diff --git a/.history/content/community/_index_20210124122229.md b/.history/content/community/_index_20210124122229.md deleted file mode 100644 index aac95397b..000000000 --- a/.history/content/community/_index_20210124122229.md +++ /dev/null @@ -1,205 +0,0 @@ ---- -title: The SBOL Community - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - -The SBOL community works actively on the SBOL data model and visual standard, participates in online discussions, and meets semi-annually. We represent over 170+ members from 17 different countries, 42 institutions, and 28 different industries. Many of our members are also actively involved in other standards communities, like the Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN). - - -To join our growing community, contact the SBOL Editors [here](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit). - -### Members - -| Name | Affiliation | Country | -|----------------------------|-----------------------------------------------------------|-----------------| -| Alex McFadden | Zymergen Inc | USA | -| Alexis Casas | Imperial College London | UK | -| Alice Boo | Imperial College London | UK | -| Ana Delgado | University of Oslo | Norway | -| Angel Goñi-Moreno | Newcastle University | UK | -| Anil Wipat | Newcastle University | UK | -| Anton Kulaga | Computation Biology of Aging Group | Romania | -| Augustin Luna | Dana-Farber Cancer Institute | USA | -| Benjamin Aleritsch | Technical University of Munich | Germany | -| Benjamin Chan | Boston University | USA | -| Bill Yang | Newcastle University | UK | -| Birjesh Kumar | ICGEB, Delhi | India | -| Brad Chapman | Ginkgo Bioworks | USA | -| Brigitte Dreger | BioRender Inc. | Toronto | -| Bryan Bartley | BBN Technologies | USA | -| Bryan Der | MIT | USA | -| Carlog Olguin | Autodesk | USA | -| Cesar Rodriguez | Florida State University | USA | -| Chih-Hsien Yang | National Yang Ming University | Taiwan | -| Chris Anderson | University of California, Berkeley | USA | -| Chris Myers | University of Colorado | USA | -| Chris Walker | Macquarie University | Australia | -| Christian Atallah | Newcastle University | UK | -| Christian Nyumbayire | Independent | Italy | -| Christian Olsen | Centers for Disease Control and Prevention | USA | -| Christopher Voigt | MIT | USA | -| Craig Struble | Inscripta Inc. | USA | -| Curtis Madsen | Sandia National Laboratories | USA | -| DA Ball | University of Tennessee | USA | -| Daniel Dixon | University of Bristol | UK | -| Daniel Sutantyo | Macquarie University | USA | -| Dany Entezari | University of Edinburgh | UAE | -| Darren Platt | Amyris | USA | -| David Lomelin | Synthetic Genomics | USA | -| David Ross | NIST | USA | -| David Zong | Rice University | USA | -| Douglas Densmore | Boston University | USA | -| Drew Endy | Stanford University & BIOFAB | USA | -| Eduardo Abeliuk | Teselagen | USA | -| Egils Stalidzans | University of Latvia | Latvia | -| Elizabeth Robinson | UT Austin | USA | -| Elizabeth Strychalsky | NIST | USA | -| Emek Demir | Memorial Sloan Kettering Cancer Center | USA | -| Eric van der Helm | SNIPRBIOME | Denmark | -| Eric Young | Worchester Polytechnic Institute | USA | -| Ernst Oberortner | Lawrence Berkeley National Labs | USA | -| Evan Appleton | Boston University | USA | -| Evren Sirin | Clark & Parsia | USA | -| Falk Schreiber | University of Konstanz | Germany | -| Falk Shreiber | University of Konstanz | Germany | -| Florencio Mazzoldi | Ginkgo Bioworks | USA | -| Gary Bader | University of Toronto | Canada | -| Geoff Baldwin | Imperial College London | USA | -| George McArthur | GenoCAD | USA | -| Göksel Mısırlı | Keele University | UK | -| Gonzalo Vidal Pena | University of Chile | Chile | -| Grimaldo Elias Urena M. | Technological University of Panama | Panama | -| Guillermo Yanez Feliu | Rudge Lab, PUC. | Chile | -| Guy Bart-Stan | Imperial College London | UK | -| Harold Fellermann | Newcastle University | UK | -| Hasan Baig | Independent | Pakistan | -| Hasan Baig | University of Connecticut | USA | -| Hector Plahar | Joint Bioenergy Institute (JBEI) | USA | -| Henry Holbrook | Benchling | USA | -| Herbert Sauro | University of Washington | USA | -| Hiroyuki Kuwahara | KAUST | Saudi Arabia | -| Huaiyu Mi | USC | USA | -| Igor Durovic | Google | USA | -| Isabel Pötzsch | University of Cambridge | UK | -| Jackie Quinn | Google | USA | -| Jake Beal | BBN Technologies | USA | -| James Diggans | Twist Bioscience | USA | -| James McLaughlin | EMBL-EBI | UK | -| James Scott Brown | Imperial College London | UK | -| James Skelton | Newcastle University | UK | -| Jan Madsen | DTU | Denmark | -| Jared Earl | Forcepoint | USA | -| Jason Mohabir | Columbia University | USA | -| Jasper Koehorst | Wageningen University | Netherlands | -| Jean Peccoud | Colorado State University | USA | -| Jeanet Mante | University of Colorado | USA | -| Jeffrey Barrick | UT Austin | USA | -| Jeffrey Elhai | Virginia Commonwealth University | USA | -| Jenhan Tao | University of California, San Diego | USA | -| Jennifer Hallinan | Macquarie University | Australia | -| John Gennari | University of Washington | USA | -| John Meng | Lawrence Berkeley National Labs | USA | -| John T. Sexton | Independent | USA | -| Jonathan Karr | Mount Sinai | USA | -| Joseph Hellerstein | University of Washington | USA | -| Joshua Rawlins | UW-Madison | USA | -| Juston Farlow | Serotiny | USA | -| Jyotsna Venkata | St. Joseph's Institute of Technology | India | -| Kelvin Clancy | BioCoder Consulting | USA | -| Kevin Clancy | BioCoder Consulting | USA | -| Kiri Choi | University of Washington | USA | -| Kirtan Dave | Sardar Patel University | India | -| Kyle Medley | University of Washington | USA | -| Laura Adam | Virginia Bioinformatics Institute | USA | -| Linda Kahl | Stanford University | USA | -| Linh Huynh | UC Davis | USA | -| Linhao Meng | Zhejiang University | China | -| Maciek Jacek Swat | CSIRO | Australia | -| Mandy Wilson | Virginia Tech | USA | -| Marc Juul | BIOFAB | USA | -| Marco Castelejin | VTT Technical Research Centre | Finland | -| Mario Marchiso | Tianjin University | China | -| Marta Vazquez-Vilar | CSIC (Consejo Superior de Investigaciones Científicas) | Spain | -| Matthew Crowther | Newcastle University | UK | -| Matthew Lux | Army Research Lab | USA | -| Matthew Pocock | Newcastle University | UK | -| Matthieu Bultelle | Imperial College London | UK | -| Maurice Ling | AdvanceSyn Private Limited | Singapore | -| Maxwell Bates | Autodesk | USA | -| Meher Samineni | REI | USA | -| Michael Zhang | Google | USA | -| Michal Galdzicki | Arzeda | USA | -| Michihiro Araki | Kobe University | Japan | -| Mike Bissell | Shipyard Toolchains | USA | -| Mike Fero | Teselagen | USA | -| Nathan Hillson | Joint Bioenergy Institute | USA | -| Nathan Wilkinson | Recursion Pharmaceuticals | USA | -| Neil Swainston | Manchester BioFactory Ltd. | UK | -| Neil Thompson | Massachusetts Institute of Technology | USA | -| Nicholas Roehner | BBN Technologies | USA | -| Nicolas Le Novere | EMBL-EBI | UK | -| Owen Gilfellon | Newcastle University | UK | -| Pablo Carbonell | Manchester Institute of Biotechnology | USA | -| Patrick Yizhi | University of Edinburgh | UK | -| Pedro Fontanarrosa | University of Utah | USA | -| Peter Dun | Stanford University | USA | -| Philip Bradley | Newcastle University | UK | -| Prashant Vaidyanathan | Microsoft Inc. | UK | -| Prem Prakash | BITS Pilani | India | -| Rahmi Lale | NTNU | Norway | -| Raik Gruenberg | KAUST | Saudi Arabia | -| Richard Kitney | Imperial College London | UK | -| Robert Sidney Cox | Robert Sydney Cox III Co. | USA | -| Robin Emig | Augment Bioworks | USA | -| S. Castillo Hair | Rice University | USA | -| Sarah Munro | NIST | USA | -| Sean Leonard | University of Texas at Austin | USA | -| Shamseen Rahman | Boston University | USA | -| Shashank | IIT Delhi | India | -| Shyam Bhakta | UC Berkeley | USA | -| SSBSS Summer School | SSBSS Summer School | Italy | -| Stefan Claesen | Visbion Ltd. | UK | -| Stuart Moodie | Eight Pillars Ltd. | Edinburgh | -| Sunwoo Kang | Stanford University | USA | -| Swapnil Bhatiya | Catalog Inc | USA | -| Thomas Gorochowski | Bio Compute Lab, Bristol University | UK | -| Tim Fiori | University of Australia | Australia | -| Todd Slaby | Lawrence Berkeley National Labs | USA | -| Tramy Nguyen | BBN Technologies | USA | -| Tyler Camp | University of Texas at Austin | USA | -| Ueno Masayoshi | Kitasato University | Japan | -| Umesh P | University of Kerala | India | -| Vinod Tek | Imperial College London | UK | -| Vishvesh Kulkarni | University of Warwick | UK | -| Vittorio Bartoli | University of Bristol | UK | -| Walid El-Sharoud | Mansoura University | Egypt | -| William Byrd | University of Alabama | USA | -| Xin Gao | KAUST | Saudi Arabia | -| Xuefeng Cui | University of Washington | USA | -| Yaman Sirin | BBN Technologies | USA | -| Yogev Debbi | Genome Compiler | USA | -| Ysis Tarter | Amyris | USA | -| Zach Palchick | Zymergen | USA | -| Zach Zundel | Facebook | USA | -| Zhen Zhang | Utah State University | USA | -| Zhiyang Ong | Texas A&M University | USA | -| Mudasir Shaikh | Habib University | Pakistan | -| Ritwik Agarwal | Iiit Hyderabad | India | -| Ming Hia | Imperial College | UK | -| Zhiyang Ong | Texas A&M University | USA | -| Ana Delgado | University of Oslo | Norway | -| William Poole | Caltech | USA | -| Stephanie Nicole Call | University of Massachusetts Amherst | USA | -| Gurvinder Dahiya | Independent | Norway | diff --git a/.history/content/community/_index_20210222150331.md b/.history/content/community/_index_20210222150331.md deleted file mode 100644 index 6482a2188..000000000 --- a/.history/content/community/_index_20210222150331.md +++ /dev/null @@ -1,206 +0,0 @@ ---- -title: The SBOL Community - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - -The SBOL community works actively on the SBOL data model and visual standard, participates in online discussions, and meets semi-annually. We represent over 170+ members from 17 different countries, 42 institutions, and 28 different industries. Many of our members are also actively involved in other standards communities, like the Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN). - - -To join our growing community, contact the SBOL Editors [here](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit). - -### Members - -| Name | Affiliation | Country | -|----------------------------|-----------------------------------------------------------|-----------------| -| Alex McFadden | Zymergen Inc | USA | -| Alexis Casas | Imperial College London | UK | -| Alice Boo | Imperial College London | UK | -| Ana Delgado | University of Oslo | Norway | -| Angel Goñi-Moreno | Newcastle University | UK | -| Anil Wipat | Newcastle University | UK | -| Anton Kulaga | Computation Biology of Aging Group | Romania | -| Augustin Luna | Dana-Farber Cancer Institute | USA | -| Benjamin Aleritsch | Technical University of Munich | Germany | -| Benjamin Chan | Boston University | USA | -| Bill Yang | Newcastle University | UK | -| Birjesh Kumar | ICGEB, Delhi | India | -| Brad Chapman | Ginkgo Bioworks | USA | -| Brigitte Dreger | BioRender Inc. | Toronto | -| Bryan Bartley | BBN Technologies | USA | -| Bryan Der | MIT | USA | -| Carlog Olguin | Autodesk | USA | -| Cesar Rodriguez | Florida State University | USA | -| Chih-Hsien Yang | National Yang Ming University | Taiwan | -| Chris Anderson | University of California, Berkeley | USA | -| Chris Myers | University of Colorado | USA | -| Chris Walker | Macquarie University | Australia | -| Christian Atallah | Newcastle University | UK | -| Christian Nyumbayire | Independent | Italy | -| Christian Olsen | Centers for Disease Control and Prevention | USA | -| Christopher Voigt | MIT | USA | -| Craig Struble | Inscripta Inc. | USA | -| Curtis Madsen | Sandia National Laboratories | USA | -| DA Ball | University of Tennessee | USA | -| Daniel Dixon | University of Bristol | UK | -| Daniel Sutantyo | Macquarie University | USA | -| Dany Entezari | University of Edinburgh | UAE | -| Darren Platt | Amyris | USA | -| David Lomelin | Synthetic Genomics | USA | -| David Ross | NIST | USA | -| David Zong | Rice University | USA | -| Douglas Densmore | Boston University | USA | -| Drew Endy | Stanford University & BIOFAB | USA | -| Eduardo Abeliuk | Teselagen | USA | -| Egils Stalidzans | University of Latvia | Latvia | -| Elizabeth Robinson | UT Austin | USA | -| Elizabeth Strychalsky | NIST | USA | -| Emek Demir | Memorial Sloan Kettering Cancer Center | USA | -| Eric van der Helm | SNIPRBIOME | Denmark | -| Eric Young | Worchester Polytechnic Institute | USA | -| Ernst Oberortner | Lawrence Berkeley National Labs | USA | -| Evan Appleton | Boston University | USA | -| Evren Sirin | Clark & Parsia | USA | -| Falk Schreiber | University of Konstanz | Germany | -| Falk Shreiber | University of Konstanz | Germany | -| Florencio Mazzoldi | Ginkgo Bioworks | USA | -| Gary Bader | University of Toronto | Canada | -| Geoff Baldwin | Imperial College London | USA | -| George McArthur | GenoCAD | USA | -| Göksel Mısırlı | Keele University | UK | -| Gonzalo Vidal Pena | University of Chile | Chile | -| Grimaldo Elias Urena M. | Technological University of Panama | Panama | -| Guillermo Yanez Feliu | Rudge Lab, PUC. | Chile | -| Guy Bart-Stan | Imperial College London | UK | -| Harold Fellermann | Newcastle University | UK | -| Hasan Baig | Independent | Pakistan | -| Hasan Baig | University of Connecticut | USA | -| Hector Plahar | Joint Bioenergy Institute (JBEI) | USA | -| Henry Holbrook | Benchling | USA | -| Herbert Sauro | University of Washington | USA | -| Hiroyuki Kuwahara | KAUST | Saudi Arabia | -| Huaiyu Mi | USC | USA | -| Igor Durovic | Google | USA | -| Isabel Pötzsch | University of Cambridge | UK | -| Jackie Quinn | Google | USA | -| Jake Beal | BBN Technologies | USA | -| James Diggans | Twist Bioscience | USA | -| James McLaughlin | EMBL-EBI | UK | -| James Scott Brown | Imperial College London | UK | -| James Skelton | Newcastle University | UK | -| Jan Madsen | DTU | Denmark | -| Jared Earl | Forcepoint | USA | -| Jason Mohabir | Columbia University | USA | -| Jasper Koehorst | Wageningen University | Netherlands | -| Jean Peccoud | Colorado State University | USA | -| Jeanet Mante | University of Colorado | USA | -| Jeffrey Barrick | UT Austin | USA | -| Jeffrey Elhai | Virginia Commonwealth University | USA | -| Jenhan Tao | University of California, San Diego | USA | -| Jennifer Hallinan | Macquarie University | Australia | -| John Gennari | University of Washington | USA | -| John Meng | Lawrence Berkeley National Labs | USA | -| John T. Sexton | Independent | USA | -| Jonathan Karr | Mount Sinai | USA | -| Joseph Hellerstein | University of Washington | USA | -| Joshua Rawlins | UW-Madison | USA | -| Juston Farlow | Serotiny | USA | -| Jyotsna Venkata | St. Joseph's Institute of Technology | India | -| Kelvin Clancy | BioCoder Consulting | USA | -| Kevin Clancy | BioCoder Consulting | USA | -| Kiri Choi | University of Washington | USA | -| Kirtan Dave | Sardar Patel University | India | -| Kyle Medley | University of Washington | USA | -| Laura Adam | Virginia Bioinformatics Institute | USA | -| Linda Kahl | Stanford University | USA | -| Linh Huynh | UC Davis | USA | -| Linhao Meng | Zhejiang University | China | -| Maciek Jacek Swat | CSIRO | Australia | -| Mandy Wilson | Virginia Tech | USA | -| Marc Juul | BIOFAB | USA | -| Marco Castelejin | VTT Technical Research Centre | Finland | -| Mario Marchiso | Tianjin University | China | -| Marta Vazquez-Vilar | CSIC (Consejo Superior de Investigaciones Científicas) | Spain | -| Matthew Crowther | Newcastle University | UK | -| Matthew Lux | Army Research Lab | USA | -| Matthew Pocock | Newcastle University | UK | -| Matthieu Bultelle | Imperial College London | UK | -| Maurice Ling | AdvanceSyn Private Limited | Singapore | -| Maxwell Bates | Autodesk | USA | -| Meher Samineni | REI | USA | -| Michael Zhang | Google | USA | -| Michal Galdzicki | Arzeda | USA | -| Michihiro Araki | Kobe University | Japan | -| Mike Bissell | Shipyard Toolchains | USA | -| Mike Fero | Teselagen | USA | -| Nathan Hillson | Joint Bioenergy Institute | USA | -| Nathan Wilkinson | Recursion Pharmaceuticals | USA | -| Neil Swainston | Manchester BioFactory Ltd. | UK | -| Neil Thompson | Massachusetts Institute of Technology | USA | -| Noah Sprent | Imperial College | UK | -| Nicholas Roehner | BBN Technologies | USA | -| Nicolas Le Novere | EMBL-EBI | UK | -| Owen Gilfellon | Newcastle University | UK | -| Pablo Carbonell | Manchester Institute of Biotechnology | USA | -| Patrick Yizhi | University of Edinburgh | UK | -| Pedro Fontanarrosa | University of Utah | USA | -| Peter Dun | Stanford University | USA | -| Philip Bradley | Newcastle University | UK | -| Prashant Vaidyanathan | Microsoft Inc. | UK | -| Prem Prakash | BITS Pilani | India | -| Rahmi Lale | NTNU | Norway | -| Raik Gruenberg | KAUST | Saudi Arabia | -| Richard Kitney | Imperial College London | UK | -| Robert Sidney Cox | Robert Sydney Cox III Co. | USA | -| Robin Emig | Augment Bioworks | USA | -| S. Castillo Hair | Rice University | USA | -| Sarah Munro | NIST | USA | -| Sean Leonard | University of Texas at Austin | USA | -| Shamseen Rahman | Boston University | USA | -| Shashank | IIT Delhi | India | -| Shyam Bhakta | UC Berkeley | USA | -| SSBSS Summer School | SSBSS Summer School | Italy | -| Stefan Claesen | Visbion Ltd. | UK | -| Stuart Moodie | Eight Pillars Ltd. | Edinburgh | -| Sunwoo Kang | Stanford University | USA | -| Swapnil Bhatiya | Catalog Inc | USA | -| Thomas Gorochowski | Bio Compute Lab, Bristol University | UK | -| Tim Fiori | University of Australia | Australia | -| Todd Slaby | Lawrence Berkeley National Labs | USA | -| Tramy Nguyen | BBN Technologies | USA | -| Tyler Camp | University of Texas at Austin | USA | -| Ueno Masayoshi | Kitasato University | Japan | -| Umesh P | University of Kerala | India | -| Vinod Tek | Imperial College London | UK | -| Vishvesh Kulkarni | University of Warwick | UK | -| Vittorio Bartoli | University of Bristol | UK | -| Walid El-Sharoud | Mansoura University | Egypt | -| William Byrd | University of Alabama | USA | -| Xin Gao | KAUST | Saudi Arabia | -| Xuefeng Cui | University of Washington | USA | -| Yaman Sirin | BBN Technologies | USA | -| Yogev Debbi | Genome Compiler | USA | -| Ysis Tarter | Amyris | USA | -| Zach Palchick | Zymergen | USA | -| Zach Zundel | Facebook | USA | -| Zhen Zhang | Utah State University | USA | -| Zhiyang Ong | Texas A&M University | USA | -| Mudasir Shaikh | Habib University | Pakistan | -| Ritwik Agarwal | Iiit Hyderabad | India | -| Ming Hia | Imperial College | UK | -| Zhiyang Ong | Texas A&M University | USA | -| Ana Delgado | University of Oslo | Norway | -| William Poole | Caltech | USA | -| Stephanie Nicole Call | University of Massachusetts Amherst | USA | -| Gurvinder Dahiya | Independent | Norway | diff --git a/.history/content/contact/_index_20210124122229.md b/.history/content/contact/_index_20210124122229.md deleted file mode 100644 index b64b8bd29..000000000 --- a/.history/content/contact/_index_20210124122229.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: Contact - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The [sbol-announce](mailto:sbol-announce@googlegroups.com), [sbol-users](mailto:sbol-users@googlegroups.com), [sbol-dev](mailto:sbol-dev@googlegroups.com), and [sbol-visual](mailto:sbol-visual@googlegroups.com) are mailing lists open to all members of the SBOL community to post discussions and ask questions about SBOL. These mailing lists are moderated by the SBOL Editors. If the discussions and comments become inappropriate, the SBOL editors reserve the right to disallow future posting to be made by the community until further notice. - - -| Group | Description | -| ------------------------| ---------------------- | -| **SBOL Editors** | The [SBOL Editors](mailto:sbol-editors@googlegroups.com) are available to help answer any questions that the community may have. | -| **SBOL Announce** | [sbol-announce](mailto:sbol-announce@googlegroups.com) is a mailing list created for the SBOL Editors inform the SBOL community about current news regarding SBOL, community member introduction, SEP voting, and editor elections. This mailing list is also a place where the SBOL community members can post their announcements that they would like to share amongst the community. | -| **SBOL Users** | [sbol-users](mailto:sbol-users@googlegroups.com) is a mailing list created for those who are using SBOL in their software tool and have questions about how they can incorporate features of the SBOL data model and/or sbol-visual glyphs within their tool. | -| **SBOL Developers** | [sbol-dev](mailto:sbol-dev@googlegroups.com) is a mailing list created for those who want to implement the SBOL data model library. All discussions related to proposing a new feature to the SBOL data model and SBOL Enhancement Proposals (SEPs) are taken place in this mailing list. | -| **SBOL Visual** | [sbol-visual](mailto:sbol-visual@googlegroups.com) is a mailing list created for those who want to discuss and propose glyphs to represent engineered biological organisms through diagrams. | -| **SBOL Website Issues** | For website issues, please report them to our [SBOL website GitHub repository](https://github.com/SynBioDex/SBOL_website/issues) by submitting a GitHub issue. | - - - -Please fill in the following form if you would like to **join the SBOL community** or **subscribe** to the sbol-dev, sbol-visual, sbol-users, or sbol-announce mailing list: - - -{{< gdocs src="https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit?usp=sharing" >}} - - -If you are unable to view the form, try this [link](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU). Alternatively, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com) along with your name, institution/affiliation, country, your interest in SBOL, and which email list(s) you would like to subscribe to. diff --git a/.history/content/contact/_index_20210125111509.md b/.history/content/contact/_index_20210125111509.md deleted file mode 100644 index d0c6d7081..000000000 --- a/.history/content/contact/_index_20210125111509.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: Contact - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The [sbol-announce](mailto:sbol-announce@googlegroups.com), [sbol-users](mailto:sbol-users@googlegroups.com), [sbol-dev](mailto:sbol-dev@googlegroups.com), and [sbol-visual](mailto:sbol-visual@googlegroups.com) are mailing lists open to all members of the SBOL community to post discussions and ask questions about SBOL. These mailing lists are moderated by the SBOL Editors. If the discussions and comments become inappropriate, the SBOL editors reserve the right to disallow future posting to be made by the community until further notice. - - -| Group | Description | -| ------------------------| ---------------------- | -| **SBOL Editors** | The [SBOL Editors](mailto:sbol-editors@googlegroups.com) are available to help answer any questions that the community may have. | -| **SBOL Announce** | [sbol-announce](mailto:sbol-announce@googlegroups.com) is a mailing list created for the SBOL Editors inform the SBOL community about current news regarding SBOL, community member introduction, SEP voting, and editor elections. This mailing list is also a place where the SBOL community members can post their announcements that they would like to share amongst the community. | -| **SBOL Users** | [sbol-users](mailto:sbol-users@googlegroups.com) is a mailing list created for those who are using SBOL in their software tool and have questions about how they can incorporate features of the SBOL data model and/or sbol-visual glyphs within their tool. | -| **SBOL Developers** | [sbol-dev](mailto:sbol-dev@googlegroups.com) is a mailing list created for those who want to implement the SBOL data model library. All discussions related to proposing a new feature to the SBOL data model and SBOL Enhancement Proposals (SEPs) are taken place in this mailing list. | -| **SBOL Visual** | [sbol-visual](mailto:sbol-visual@googlegroups.com) is a mailing list created for those who want to discuss and propose glyphs to represent engineered biological organisms through diagrams. | -| **SBOL Website Issues** | For website issues, please report them to our [SBOL website GitHub repository](https://github.com/SynBioDex/SBOL_website/issues) by submitting a GitHub issue. | - - - -Please fill in the following form if you would like to **join the SBOL community** or **subscribe** to the sbol-dev, sbol-visual, sbol-users, or sbol-announce mailing list: - - -{{< gdocs src="https://docs.google.com/forms/d/e/1FAIpQLScp8lomURs-y-8BlptY0fFgLSFIl0cKvcMkOBc_JVlEgW22Sw/viewform?embedded=true" >}} - - - - -If you are unable to view the form, try this [link](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU). Alternatively, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com) along with your name, institution/affiliation, country, your interest in SBOL, and which email list(s) you would like to subscribe to. diff --git a/.history/content/contact/_index_20210125111537.md b/.history/content/contact/_index_20210125111537.md deleted file mode 100644 index 5dc21d762..000000000 --- a/.history/content/contact/_index_20210125111537.md +++ /dev/null @@ -1,36 +0,0 @@ ---- -title: Contact - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The [sbol-announce](mailto:sbol-announce@googlegroups.com), [sbol-users](mailto:sbol-users@googlegroups.com), [sbol-dev](mailto:sbol-dev@googlegroups.com), and [sbol-visual](mailto:sbol-visual@googlegroups.com) are mailing lists open to all members of the SBOL community to post discussions and ask questions about SBOL. These mailing lists are moderated by the SBOL Editors. If the discussions and comments become inappropriate, the SBOL editors reserve the right to disallow future posting to be made by the community until further notice. - - -| Group | Description | -| ------------------------| ---------------------- | -| **SBOL Editors** | The [SBOL Editors](mailto:sbol-editors@googlegroups.com) are available to help answer any questions that the community may have. | -| **SBOL Announce** | [sbol-announce](mailto:sbol-announce@googlegroups.com) is a mailing list created for the SBOL Editors inform the SBOL community about current news regarding SBOL, community member introduction, SEP voting, and editor elections. This mailing list is also a place where the SBOL community members can post their announcements that they would like to share amongst the community. | -| **SBOL Users** | [sbol-users](mailto:sbol-users@googlegroups.com) is a mailing list created for those who are using SBOL in their software tool and have questions about how they can incorporate features of the SBOL data model and/or sbol-visual glyphs within their tool. | -| **SBOL Developers** | [sbol-dev](mailto:sbol-dev@googlegroups.com) is a mailing list created for those who want to implement the SBOL data model library. All discussions related to proposing a new feature to the SBOL data model and SBOL Enhancement Proposals (SEPs) are taken place in this mailing list. | -| **SBOL Visual** | [sbol-visual](mailto:sbol-visual@googlegroups.com) is a mailing list created for those who want to discuss and propose glyphs to represent engineered biological organisms through diagrams. | -| **SBOL Website Issues** | For website issues, please report them to our [SBOL website GitHub repository](https://github.com/SynBioDex/SBOL_website/issues) by submitting a GitHub issue. | - - - -Please fill in the following form if you would like to **join the SBOL community** or **subscribe** to the sbol-dev, sbol-visual, sbol-users, or sbol-announce mailing list: - - -{{< gdocs src="https://docs.google.com/forms/d/e/1FAIpQLScp8lomURs-y-8BlptY0fFgLSFIl0cKvcMkOBc_JVlEgW22Sw/viewform?embedded=true" >}} - -If you are unable to view the form, try this [link](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU). Alternatively, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com) along with your name, institution/affiliation, country, your interest in SBOL, and which email list(s) you would like to subscribe to. diff --git a/.history/content/faq/_index_20211014101920.md b/.history/content/faq/_index_20211014101920.md deleted file mode 100644 index fc27db336..000000000 --- a/.history/content/faq/_index_20211014101920.md +++ /dev/null @@ -1,226 +0,0 @@ ---- -title: Frequently Asked Questions - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -Didn’t find an answer to your question? Post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. - - -## SBOL - -
- What is Synthetic Biology? - Synthetic biology is a new frontier in biological research where scientists and engineers design and create living systems to carry out useful tasks. In the last half century, the fundamental biochemical pieces and processes that comprise the phenomena of life have been isolated and studied by scientists in the laboratory. This reductionist approach to molecular biology has yielded enormous insight into the basic molecular units that govern life, such as genes encoded on DNA. Today, a new approach, synthetic biology, is possible in which basic units of biochemistry are re-assembled into new living systems, using platform technologies such as DNA synthesis, genome engineering, simulation tools, and computer-aided-design. In the future, important technologies like solar energy, biofuels, and medicines may be synthesized out of “wetware.” -
-
- What is the role of a standard language in synthetic biology? - Standards decrease friction in markets by reducing the cost of translating data and designs. So commercial entities can concentrate on transacting the goods and services in which they create the most value. -
- - -
- What is SBOL? - The design process is fundamental to synthetic biology. The SBOL standard empowers and enables a design-oriented, forward-engineering approach for synthetic biology in the following ways: - -- Facilitates storage of genetic designs in repositories -- Helps synthetic biologists and genetic engineers electronically exchange designs with each other and with biofabrication centers -- Supports development of Genetic Design Automation (GDA) software tools for synthetic biologists -- Represents hierarchically assembled genetic compositions -- Represents abstract genetic compositions without an explicit nucleotide sequence -- Allows expression of genetic designs in publications and thus aids scientific reproducibility -- Captures elements of a design that move beyond DNA Sequences to include RNA, proteins, small molecules and molecular interactions -- SBOL is extensible to allow other kinds of data to be attached to the core data model. This includes, for example, experimental data, host information and mathematical models -- Introductory slides on SBOL can be found {{% staticref "docs/WhatIsSBOL.pdf" "newtab" %}}here{{% /staticref %}}. -
- -
- Is SBOL free? - Yes. SBOL is not patented, has no royalties, and does not cost anything to use. -
- -
- Is SBOL open? - SBOL is open source and licensed under the {{% staticref "http://creativecommons.org/licenses/by/4.0/" "newtab" %}}Creative Commons Attribution 4.0 International License{{% /staticref %}}. -
- -
- How will SBOL help me? - Using the {{% staticref "/datamodel-about/" "newtab" %}}SBOL data model{{% /staticref %}} will let you download sequence designs from published experiments. You can retrieve SBOL designs from repositories like {{% staticref "http://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}}, and {{% staticref "https://acs-registry.jbei.org/" "newtab" %}}JBEI-ICE{{% /staticref %}}. Take a look at our applications page to see the {{% staticref "/applications/" "newtab" %}}software tools{{% /staticref %}} that currently support SBOL. If you want to support SBOL data in your tool, take a look at the available programming languages that are available to use in your tool. - -You can also express your design using {{% staticref "/visual-about/" "newtab" %}}SBOL Visual{{% /staticref %}}. If you want to use SBOL visual in your tool, you can download the available SBOL graphical notations {{% staticref "/visual-about/" "newtab" %}}here{{% /staticref %}}. - -
- -
- What can I do with SBOL? - You can describe the components of a design and the interactions between components like circuit diagrams in the file using {{% staticref "/datamodel-about/" "newtab" %}}SBOL data{{% /staticref %}}. And you can draw them to prepare publications using {{% staticref "/visual-about/" "newtab" %}}SBOL Visual{{% /staticref %}}. You can submit genetic designs to include all sequence -information for your paper in one file. You can also attach mathematical models to genetic designs SBOL will let you move your designs and work history between different tools. -
- -
- Where can I ask questions about SBOL? - - You can always post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. - - Alternatevily, you can post your question using the [SBOL tag](https://bioinformatics.stackexchange.com/questions/tagged/sbol) in the [BioInformatics Stack Exchange](https://bioinformatics.stackexchange.com/). This way, everyone can see your question and learn from the answers you obtain. -
- -
- What kinds of companies should use SBOL? - SynBio software companies, DNA synthesis companies, DNA design companies, really any company that makes or uses genetic materials. -
- -
- I’m a small company. Why should I use the SBOL standard? - Use of the SBOL standard promotes ease of data access across applications and devices. Which means faster development time with fewer resources required, so you can get to market quickly. -
- -
- I’m a large company. Why should I use SBOL? - There are no royalties to pay, and you won’t be sued for using it. Contributes to efficient patent searching. Patented devices can be represented in SBOL, so you can more easily search for comparison to your proposed designs. Use of open standards is also a key element of corporate social responsibility. -
- -
- Why not just store all my sequence data in Word and Excel? - Designs in these tools become ambiguous to other people and are not easily read by, and swapped between software applications. -
- -
- Can I use the SBOL logo in my own work/tools? - Yes, the SBOL Logo is free to use under the Creative Commons license. - - You can get the SBOL logo {{% staticref "media/Logos/SBOLlogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLlogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL logo (without text) {{% staticref "media/Logos/SBOL-logo-NoText.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOL-Logo-NoText.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL logo favicon {{% staticref "media/Logos/SBOL_Logo_Simple.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOL_Logo_Simple.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Visual logo {{% staticref "media/Logos/SBOLVisualLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLVisualLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Industrial Consortium logo {{% staticref "media/Logos/SBOLIndustrialLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLIndustrialLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - All of these logos, and more, can be downloaded from the [SBOL Community Media](https://github.com/SynBioDex/Community-Media). - - We’d be very flattered if you wanted to use it, but if you like us that much, please consider donating or sponsoring development of SBOL. We’d love to have you. Note, however, that use of the SBOL logo does not convey any kind of endorsement or certification by sbolstandard.org. -
- -
- How is the SBOL standard funded? - SBOL was funded by grants through the National Science Foundation through Collaborative awards #1355909 and #1356401 and EPSRC grant -#EP/J02175X/1. Other sponsorship, support, or endorsements have been provided by the federal agencies, federal research centers, -commercial enterprises, and academic institutions. Please contact the SBOL Editors for donation consideration. -
- -
- SBOL vs. GenBank - With the emergence of large-scale DNA sequencing technology in the last few decades, there has also emerged a need to manage and share vast amounts of sequence data. For researchers in the biological sciences, the public GenBank database, data standard, and file format has become a familiar friend. However, there are several reasons why the GenBank standard is insufficient for satisfying the needs of synthetic biologists. While the GenBank standard is used to primarily describe sequences that correspond to an existing DNA sample, the SBOL standard promotes forward-engineering of novel sequences. In other words, SBOL makes it easy to assemble novel sequences from DNA components using computer-aided design and genetic design automation. Moreover, SBOL is able to capture elements of intended design about proteins and small molecules for example, as well as the interactions between them. - - Genbank is a great file format for sequences and unstructured annotations. What can you do with SBOL that you can’t with Genbank? Genbank isn’t meant for designs. It will not represent interactions between components, let you specify undefined components, is not modular and won’t describe designs using proteins and small molecules. -
- -
- Which tools will allow me to build SBOL? - We have summarize a list of SBOL data and SBOL visual tools that were reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Data - -
- Where can I get detailed information on SBOL Data? - SBOL is described in detail in the current {{% staticref "/datamodel-about/" "newtab" %}}SBOL specification{{% /staticref %}}. -
- -
- What is the difference between SBOL 1.1 and 2.0? - SBOL 1.1 provides users with the ability to specify the structure of their designs. SBOL 2.0 improves upon the expressibility by adding the ability to specify function. More details of the differences can be found by reading the specifications for SBOL 1.1 and SBOL 2.0. -
- -
- Are there repositories that store SBOL data? - Yes, there are several repositories. For instance, the {{% staticref "https://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}} and {{% staticref "https://public-registry.jbei.org/" "newtab" %}}JBEI ICE{{% /staticref %}}. You can have a look at the current repositories that have been reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Visual - -
- What is SBOL visual? - SBOL visual is a uniform way to draw diagrams of synthetic biology designs. Currently, these designs are depicted at the genetic level. -
- -
- How do I draw SBOL visual designs? - There are a couple of SBOL visual software tools that you can use to draw SBOL visual glyphs such as {{% staticref "http://visbol.org/" "newtab" %}}VisBOL{{% /staticref %}}, {{% staticref "https://github.com/SynBioDex/SBOLDesigner/releases" "newtab" %}}SBOLDesigner{{% /staticref %}}, and {{% staticref "http://pigeon.synbiotools.org/" "newtab" %}}PigeonCAD{{% /staticref %}}. You can view a full list of SBOL visual tools that we have recorded {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Community - -
- How can I contribute to the community? - More information can be found {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. -
- -
- When does the SBOL community meet? - The SBOL community meets approximately every 6 months. A list of previous and upcoming meetings can be found {{% staticref "/community-meetings/" "newtab" %}}here{{% /staticref %}}. -
- -
- Is there a mailing list for the SBOL community? -Yes! There are multiple mailing lists depending on how you'd like to interact with the community and your interests in SBOL. You can find details {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. - - -
- -## Citing SBOL - -
- What paper should I cite for SBOL data? - - - -
- -
- What paper should I cite for SBOL Visual? - - - -
- -
- What papers should I cite for SBOL libraries and utilities? - - -
diff --git a/.history/content/faq/_index_20211014103933.md b/.history/content/faq/_index_20211014103933.md deleted file mode 100644 index f6ee64add..000000000 --- a/.history/content/faq/_index_20211014103933.md +++ /dev/null @@ -1,229 +0,0 @@ ---- -title: Frequently Asked Questions - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -Didn't find an answer to your question? Post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. - - -## SBOL - -
- What is Synthetic Biology? - Synthetic biology is a new frontier in biological research where scientists and engineers design and create living systems to carry out useful tasks. In the last half century, the fundamental biochemical pieces and processes that comprise the phenomena of life have been isolated and studied by scientists in the laboratory. This reductionist approach to molecular biology has yielded enormous insight into the basic molecular units that govern life, such as genes encoded on DNA. Today, a new approach, synthetic biology, is possible in which basic units of biochemistry are re-assembled into new living systems, using platform technologies such as DNA synthesis, genome engineering, simulation tools, and computer-aided-design. In the future, important technologies like solar energy, biofuels, and medicines may be synthesized out of “wetware.” -
-
- What is the role of a standard language in synthetic biology? - Standards decrease friction in markets by reducing the cost of translating data and designs. So commercial entities can concentrate on transacting the goods and services in which they create the most value. -
- - -
- What is SBOL? - The design process is fundamental to synthetic biology. The SBOL standard empowers and enables a design-oriented, forward-engineering approach for synthetic biology in the following ways: - -- Facilitates storage of genetic designs in repositories -- Helps synthetic biologists and genetic engineers electronically exchange designs with each other and with biofabrication centers -- Supports development of Genetic Design Automation (GDA) software tools for synthetic biologists -- Represents hierarchically assembled genetic compositions -- Represents abstract genetic compositions without an explicit nucleotide sequence -- Allows expression of genetic designs in publications and thus aids scientific reproducibility -- Captures elements of a design that move beyond DNA Sequences to include RNA, proteins, small molecules and molecular interactions -- SBOL is extensible to allow other kinds of data to be attached to the core data model. This includes, for example, experimental data, host information and mathematical models -- Introductory slides on SBOL can be found {{% staticref "docs/WhatIsSBOL.pdf" "newtab" %}}here{{% /staticref %}}. -
- -
- Is SBOL free? - Yes. SBOL is not patented, has no royalties, and does not cost anything to use. -
- -
- Is SBOL open? - SBOL is open source and licensed under the {{% staticref "http://creativecommons.org/licenses/by/4.0/" "newtab" %}}Creative Commons Attribution 4.0 International License{{% /staticref %}}. -
- -
- How will SBOL help me? - Using the {{% staticref "/datamodel-about/" "newtab" %}}SBOL data model{{% /staticref %}} will let you download sequence designs from published experiments. You can retrieve SBOL designs from repositories like {{% staticref "http://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}}, and {{% staticref "https://acs-registry.jbei.org/" "newtab" %}}JBEI-ICE{{% /staticref %}}. Take a look at our applications page to see the {{% staticref "/applications/" "newtab" %}}software tools{{% /staticref %}} that currently support SBOL. If you want to support SBOL data in your tool, take a look at the available programming languages that are available to use in your tool. - -You can also express your design using {{% staticref "/visual-about/" "newtab" %}}SBOL Visual{{% /staticref %}}. If you want to use SBOL visual in your tool, you can download the available SBOL graphical notations {{% staticref "/visual-about/" "newtab" %}}here{{% /staticref %}}. - -
- -
- What can I do with SBOL? - You can describe the components of a design and the interactions between components like circuit diagrams in the file using {{% staticref "/datamodel-about/" "newtab" %}}SBOL data{{% /staticref %}}. And you can draw them to prepare publications using {{% staticref "/visual-about/" "newtab" %}}SBOL Visual{{% /staticref %}}. You can submit genetic designs to include all sequence -information for your paper in one file. You can also attach mathematical models to genetic designs SBOL will let you move your designs and work history between different tools. -
- -
- Where can I ask questions about SBOL? - - You can always post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. - - Alternatevily, you can post your question using the [SBOL tag](https://bioinformatics.stackexchange.com/questions/tagged/sbol) in the [BioInformatics Stack Exchange](https://bioinformatics.stackexchange.com/). This way, everyone can see your question and learn from the answers you obtain. - - Currently, there is a proposal to create a Q&A [Synthetic Biology stack exchange](https://area51.stackexchange.com/proposals/125068/synthetic-biology) for researchers, students, teachers, engineers, biohackers, and any others working with or learning about Synthetic Biology. This could potentially be a good home for SBOL Q&A as well. Please support this endeavour and help us create a Synthetic Biology StackExchange! - -
- -
- What kinds of companies should use SBOL? - SynBio software companies, DNA synthesis companies, DNA design companies, really any company that makes or uses genetic materials. -
- -
- I'm a small company. Why should I use the SBOL standard? - Use of the SBOL standard promotes ease of data access across applications and devices. Which means faster development time with fewer resources required, so you can get to market quickly. -
- -
- I'm a large company. Why should I use SBOL? - There are no royalties to pay, and you won't be sued for using it. Contributes to efficient patent searching. Patented devices can be represented in SBOL, so you can more easily search for comparison to your proposed designs. Use of open standards is also a key element of corporate social responsibility. -
- -
- Why not just store all my sequence data in Word and Excel? - Designs in these tools become ambiguous to other people and are not easily read by, and swapped between software applications. -
- -
- Can I use the SBOL logo in my own work/tools? - Yes, the SBOL Logo is free to use under the Creative Commons license. - - You can get the SBOL logo {{% staticref "media/Logos/SBOLlogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLlogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL logo (without text) {{% staticref "media/Logos/SBOL-logo-NoText.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOL-Logo-NoText.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL logo favicon {{% staticref "media/Logos/SBOL_Logo_Simple.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOL_Logo_Simple.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Visual logo {{% staticref "media/Logos/SBOLVisualLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLVisualLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Industrial Consortium logo {{% staticref "media/Logos/SBOLIndustrialLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLIndustrialLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - All of these logos, and more, can be downloaded from the [SBOL Community Media](https://github.com/SynBioDex/Community-Media). - - We'd be very flattered if you wanted to use it, but if you like us that much, please consider donating or sponsoring development of SBOL. We'd love to have you. Note, however, that use of the SBOL logo does not convey any kind of endorsement or certification by sbolstandard.org. -
- -
- How is the SBOL standard funded? - SBOL was funded by grants through the National Science Foundation through Collaborative awards #1355909 and #1356401 and EPSRC grant -#EP/J02175X/1. Other sponsorship, support, or endorsements have been provided by the federal agencies, federal research centers, -commercial enterprises, and academic institutions. Please contact the SBOL Editors for donation consideration. -
- -
- SBOL vs. GenBank - With the emergence of large-scale DNA sequencing technology in the last few decades, there has also emerged a need to manage and share vast amounts of sequence data. For researchers in the biological sciences, the public GenBank database, data standard, and file format has become a familiar friend. However, there are several reasons why the GenBank standard is insufficient for satisfying the needs of synthetic biologists. While the GenBank standard is used to primarily describe sequences that correspond to an existing DNA sample, the SBOL standard promotes forward-engineering of novel sequences. In other words, SBOL makes it easy to assemble novel sequences from DNA components using computer-aided design and genetic design automation. Moreover, SBOL is able to capture elements of intended design about proteins and small molecules for example, as well as the interactions between them. - - Genbank is a great file format for sequences and unstructured annotations. What can you do with SBOL that you can't with Genbank? Genbank isn't meant for designs. It will not represent interactions between components, let you specify undefined components, is not modular and won't describe designs using proteins and small molecules. -
- -
- Which tools will allow me to build SBOL? - We have summarize a list of SBOL data and SBOL visual tools that were reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Data - -
- Where can I get detailed information on SBOL Data? - SBOL is described in detail in the current {{% staticref "/datamodel-about/" "newtab" %}}SBOL specification{{% /staticref %}}. -
- -
- What is the difference between SBOL 1.1 and 2.0? - SBOL 1.1 provides users with the ability to specify the structure of their designs. SBOL 2.0 improves upon the expressibility by adding the ability to specify function. More details of the differences can be found by reading the specifications for SBOL 1.1 and SBOL 2.0. -
- -
- Are there repositories that store SBOL data? - Yes, there are several repositories. For instance, the {{% staticref "https://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}} and {{% staticref "https://public-registry.jbei.org/" "newtab" %}}JBEI ICE{{% /staticref %}}. You can have a look at the current repositories that have been reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Visual - -
- What is SBOL visual? - SBOL visual is a uniform way to draw diagrams of synthetic biology designs. Currently, these designs are depicted at the genetic level. -
- -
- How do I draw SBOL visual designs? - There are a couple of SBOL visual software tools that you can use to draw SBOL visual glyphs such as {{% staticref "http://visbol.org/" "newtab" %}}VisBOL{{% /staticref %}}, {{% staticref "https://github.com/SynBioDex/SBOLDesigner/releases" "newtab" %}}SBOLDesigner{{% /staticref %}}, and {{% staticref "http://pigeon.synbiotools.org/" "newtab" %}}PigeonCAD{{% /staticref %}}. You can view a full list of SBOL visual tools that we have recorded {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Community - -
- How can I contribute to the community? - More information can be found {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. -
- -
- When does the SBOL community meet? - The SBOL community meets approximately every 6 months. A list of previous and upcoming meetings can be found {{% staticref "/community-meetings/" "newtab" %}}here{{% /staticref %}}. -
- -
- Is there a mailing list for the SBOL community? -Yes! There are multiple mailing lists depending on how you'd like to interact with the community and your interests in SBOL. You can find details {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. - - -
- -## Citing SBOL - -
- What paper should I cite for SBOL data? - - - -
- -
- What paper should I cite for SBOL Visual? - - - -
- -
- What papers should I cite for SBOL libraries and utilities? - - -
diff --git a/.history/content/faq/_index_20211014104114.md b/.history/content/faq/_index_20211014104114.md deleted file mode 100644 index 5a806882b..000000000 --- a/.history/content/faq/_index_20211014104114.md +++ /dev/null @@ -1,226 +0,0 @@ ---- -title: Frequently Asked Questions - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -Didn't find an answer to your question? Post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. - - -## SBOL - -
- What is Synthetic Biology? - Synthetic biology is a new frontier in biological research where scientists and engineers design and create living systems to carry out useful tasks. In the last half century, the fundamental biochemical pieces and processes that comprise the phenomena of life have been isolated and studied by scientists in the laboratory. This reductionist approach to molecular biology has yielded enormous insight into the basic molecular units that govern life, such as genes encoded on DNA. Today, a new approach, synthetic biology, is possible in which basic units of biochemistry are re-assembled into new living systems, using platform technologies such as DNA synthesis, genome engineering, simulation tools, and computer-aided-design. In the future, important technologies like solar energy, biofuels, and medicines may be synthesized out of "wetware". -
-
- What is the role of a standard language in synthetic biology? - Standards decrease friction in markets by reducing the cost of translating data and designs. So commercial entities can concentrate on transacting the goods and services in which they create the most value. -
- - -
- What is SBOL? - The design process is fundamental to synthetic biology. The SBOL standard empowers and enables a design-oriented, forward-engineering approach for synthetic biology in the following ways: - -- Facilitates storage of genetic designs in repositories -- Helps synthetic biologists and genetic engineers electronically exchange designs with each other and with biofabrication centers -- Supports development of Genetic Design Automation (GDA) software tools for synthetic biologists -- Represents hierarchically assembled genetic compositions -- Represents abstract genetic compositions without an explicit nucleotide sequence -- Allows expression of genetic designs in publications and thus aids scientific reproducibility -- Captures elements of a design that move beyond DNA Sequences to include RNA, proteins, small molecules and molecular interactions -- SBOL is extensible to allow other kinds of data to be attached to the core data model. This includes, for example, experimental data, host information and mathematical models -- Introductory slides on SBOL can be found {{% staticref "docs/WhatIsSBOL.pdf" "newtab" %}}here{{% /staticref %}}. -
- -
- Is SBOL free? - Yes. SBOL is not patented, has no royalties, and does not cost anything to use. -
- -
- Is SBOL open? - SBOL is open source and licensed under the {{% staticref "http://creativecommons.org/licenses/by/4.0/" "newtab" %}}Creative Commons Attribution 4.0 International License{{% /staticref %}}. -
- -
- How will SBOL help me? - Using the {{% staticref "/datamodel-about/" "newtab" %}}SBOL data model{{% /staticref %}} will let you download sequence designs from published experiments. You can retrieve SBOL designs from repositories like {{% staticref "http://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}}, and {{% staticref "https://acs-registry.jbei.org/" "newtab" %}}JBEI-ICE{{% /staticref %}}. Take a look at our applications page to see the {{% staticref "/applications/" "newtab" %}}software tools{{% /staticref %}} that currently support SBOL. If you want to support SBOL data in your tool, take a look at the available programming languages that are available to use in your tool. - -You can also express your design using {{% staticref "/visual-about/" "newtab" %}}SBOL Visual{{% /staticref %}}. If you want to use SBOL visual in your tool, you can download the available SBOL graphical notations {{% staticref "/visual-about/" "newtab" %}}here{{% /staticref %}}. - -
- -
- What can I do with SBOL? - You can describe the components of a design and the interactions between components like circuit diagrams in the file using {{% staticref "/datamodel-about/" "newtab" %}}SBOL data{{% /staticref %}}. And you can draw them to prepare publications using {{% staticref "/visual-about/" "newtab" %}}SBOL Visual{{% /staticref %}}. You can submit genetic designs to include all sequence -information for your paper in one file. You can also attach mathematical models to genetic designs SBOL will let you move your designs and work history between different tools. -
- -
- Where can I ask questions about SBOL? - - You can always post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. - - Alternatevily, you can post your question using the [SBOL tag](https://bioinformatics.stackexchange.com/questions/tagged/sbol) in the [BioInformatics Stack Exchange](https://bioinformatics.stackexchange.com/). This way, everyone can see your question and learn from the answers you obtain. -
- -
- What kinds of companies should use SBOL? - SynBio software companies, DNA synthesis companies, DNA design companies, really any company that makes or uses genetic materials. -
- -
- I'm a small company. Why should I use the SBOL standard? - Use of the SBOL standard promotes ease of data access across applications and devices. Which means faster development time with fewer resources required, so you can get to market quickly. -
- -
- I'm a large company. Why should I use SBOL? - There are no royalties to pay, and you won't be sued for using it. Contributes to efficient patent searching. Patented devices can be represented in SBOL, so you can more easily search for comparison to your proposed designs. Use of open standards is also a key element of corporate social responsibility. -
- -
- Why not just store all my sequence data in Word and Excel? - Designs in these tools become ambiguous to other people and are not easily read by, and swapped between software applications. -
- -
- Can I use the SBOL logo in my own work/tools? - Yes, the SBOL Logo is free to use under the Creative Commons license. - - You can get the SBOL logo {{% staticref "media/Logos/SBOLlogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLlogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL logo (without text) {{% staticref "media/Logos/SBOL-logo-NoText.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOL-Logo-NoText.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL logo favicon {{% staticref "media/Logos/SBOL_Logo_Simple.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOL_Logo_Simple.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Visual logo {{% staticref "media/Logos/SBOLVisualLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLVisualLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Industrial Consortium logo {{% staticref "media/Logos/SBOLIndustrialLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "media/Logos/SBOLIndustrialLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - All of these logos, and more, can be downloaded from the [SBOL Community Media](https://github.com/SynBioDex/Community-Media). - - We'd be very flattered if you wanted to use it, but if you like us that much, please consider donating or sponsoring development of SBOL. We'd love to have you. Note, however, that use of the SBOL logo does not convey any kind of endorsement or certification by sbolstandard.org. -
- -
- How is the SBOL standard funded? - SBOL was funded by grants through the National Science Foundation through Collaborative awards #1355909 and #1356401 and EPSRC grant -#EP/J02175X/1. Other sponsorship, support, or endorsements have been provided by the federal agencies, federal research centers, -commercial enterprises, and academic institutions. Please contact the SBOL Editors for donation consideration. -
- -
- SBOL vs. GenBank - With the emergence of large-scale DNA sequencing technology in the last few decades, there has also emerged a need to manage and share vast amounts of sequence data. For researchers in the biological sciences, the public GenBank database, data standard, and file format has become a familiar friend. However, there are several reasons why the GenBank standard is insufficient for satisfying the needs of synthetic biologists. While the GenBank standard is used to primarily describe sequences that correspond to an existing DNA sample, the SBOL standard promotes forward-engineering of novel sequences. In other words, SBOL makes it easy to assemble novel sequences from DNA components using computer-aided design and genetic design automation. Moreover, SBOL is able to capture elements of intended design about proteins and small molecules for example, as well as the interactions between them. - - Genbank is a great file format for sequences and unstructured annotations. What can you do with SBOL that you can't with Genbank? Genbank isn't meant for designs. It will not represent interactions between components, let you specify undefined components, is not modular and won't describe designs using proteins and small molecules. -
- -
- Which tools will allow me to build SBOL? - We have summarize a list of SBOL data and SBOL visual tools that were reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Data - -
- Where can I get detailed information on SBOL Data? - SBOL is described in detail in the current {{% staticref "/datamodel-about/" "newtab" %}}SBOL specification{{% /staticref %}}. -
- -
- What is the difference between SBOL 1.1 and 2.0? - SBOL 1.1 provides users with the ability to specify the structure of their designs. SBOL 2.0 improves upon the expressibility by adding the ability to specify function. More details of the differences can be found by reading the specifications for SBOL 1.1 and SBOL 2.0. -
- -
- Are there repositories that store SBOL data? - Yes, there are several repositories. For instance, the {{% staticref "https://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}} and {{% staticref "https://public-registry.jbei.org/" "newtab" %}}JBEI ICE{{% /staticref %}}. You can have a look at the current repositories that have been reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Visual - -
- What is SBOL visual? - SBOL visual is a uniform way to draw diagrams of synthetic biology designs. Currently, these designs are depicted at the genetic level. -
- -
- How do I draw SBOL visual designs? - There are a couple of SBOL visual software tools that you can use to draw SBOL visual glyphs such as {{% staticref "http://visbol.org/" "newtab" %}}VisBOL{{% /staticref %}}, {{% staticref "https://github.com/SynBioDex/SBOLDesigner/releases" "newtab" %}}SBOLDesigner{{% /staticref %}}, and {{% staticref "http://pigeon.synbiotools.org/" "newtab" %}}PigeonCAD{{% /staticref %}}. You can view a full list of SBOL visual tools that we have recorded {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Community - -
- How can I contribute to the community? - More information can be found {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. -
- -
- When does the SBOL community meet? - The SBOL community meets approximately every 6 months. A list of previous and upcoming meetings can be found {{% staticref "/community-meetings/" "newtab" %}}here{{% /staticref %}}. -
- -
- Is there a mailing list for the SBOL community? -Yes! There are multiple mailing lists depending on how you'd like to interact with the community and your interests in SBOL. You can find details {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. - - -
- -## Citing SBOL - -
- What paper should I cite for SBOL data? - - - -
- -
- What paper should I cite for SBOL Visual? - - - -
- -
- What papers should I cite for SBOL libraries and utilities? - - -
diff --git a/.history/content/home/specifications_20211027092728.md b/.history/content/home/specifications_20211027092728.md deleted file mode 100644 index fc7306142..000000000 --- a/.history/content/home/specifications_20211027092728.md +++ /dev/null @@ -1,75 +0,0 @@ -+++ -# A Projects section created with the Portfolio widget. -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = true # Activate this widget? true/false -weight = 40 # Order that this section will appear. - -title = "Latest SBOL Specifications" -subtitle = "" - -[content] - # Page type to display. E.g. project. - page_type = "about" - - # Filter toolbar (optional). - # Add or remove as many filters (`[[content.filter_button]]` instances) as you like. - # To show all items, set `tag` to "*". - # To filter by a specific tag, set `tag` to an existing tag name. - # To remove toolbar, delete/comment all instances of `[[content.filter_button]]` below. - - # Default filter index (e.g. 0 corresponds to the first `[[filter_button]]` instance below). - filter_default = 0 - -[design] - - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "2" - - # Toggle between the various page layout types. - # 1 = List - # 2 = Compact - # 3 = Card - # 5 = Showcase - view = 5 - - # For Showcase view, flip alternate rows? - flip_alt_rows = false - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "navy" - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "background.jpg" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - - # Text color (true=light or false=dark). - # text_color_light = true - -[advanced] - # Custom CSS. - css_style = "" - - # CSS class. - css_class = "" - -# Commenting this section out. This can be used if we want a shorter description. -# The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. - -+++ - -SBOL has a come a long way! As our community has grown, so has our specification and data model! Here are the quick links to the latest specifications: -* SBOL - [Version 3.0.0](/docs/SBOL3.0specification.pdf) -* SBOL Visual - [Version 3.0.0](/docs/SBOL-Visual-3.0.pdf) - -{{< figure library="true" src="sbol3_evolution.svg" title="" lightbox="false" >}} diff --git a/.history/content/home/specifications_20211027094035.md b/.history/content/home/specifications_20211027094035.md deleted file mode 100644 index 2d573b988..000000000 --- a/.history/content/home/specifications_20211027094035.md +++ /dev/null @@ -1,75 +0,0 @@ -+++ -# A Projects section created with the Portfolio widget. -widget = "blank" # See https://sourcethemes.com/academic/docs/page-builder/ -headless = true # This file represents a page section. -active = true # Activate this widget? true/false -weight = 40 # Order that this section will appear. - -title = "Latest SBOL Specifications" -subtitle = "" - -[content] - # Page type to display. E.g. project. - page_type = "about" - - # Filter toolbar (optional). - # Add or remove as many filters (`[[content.filter_button]]` instances) as you like. - # To show all items, set `tag` to "*". - # To filter by a specific tag, set `tag` to an existing tag name. - # To remove toolbar, delete/comment all instances of `[[content.filter_button]]` below. - - # Default filter index (e.g. 0 corresponds to the first `[[filter_button]]` instance below). - filter_default = 0 - -[design] - - # Choose how many columns the section has. Valid values: 1 or 2. - columns = "2" - - # Toggle between the various page layout types. - # 1 = List - # 2 = Compact - # 3 = Card - # 5 = Showcase - view = 5 - - # For Showcase view, flip alternate rows? - flip_alt_rows = false - -[design.background] - # Apply a background color, gradient, or image. - # Uncomment (by removing `#`) an option to apply it. - # Choose a light or dark text color by setting `text_color_light`. - # Any HTML color name or Hex value is valid. - - # Background color. - # color = "navy" - - # Background gradient. - # gradient_start = "DeepSkyBlue" - # gradient_end = "SkyBlue" - - # Background image. - # image = "background.jpg" # Name of image in `static/img/`. - # image_darken = 0.6 # Darken the image? Range 0-1 where 0 is transparent and 1 is opaque. - - # Text color (true=light or false=dark). - # text_color_light = true - -[advanced] - # Custom CSS. - css_style = "" - - # CSS class. - css_class = "" - -# Commenting this section out. This can be used if we want a shorter description. -# The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. - -+++ - -SBOL has a come a long way! As our community has grown, so has our specification and data model! Here are the quick links to the latest specifications: -* SBOL - [Version 3.0.0](/docs/SBOL3.0.0.pdf) -* SBOL Visual - [Version 3.0.0](/docs/SBOL-Visual-3.0.pdf) - -{{< figure library="true" src="sbol3_evolution.svg" title="" lightbox="false" >}} diff --git a/.history/content/publication/sbol-canvas-visual-editor-terry-2021/index_20210712134511.md b/.history/content/publication/sbol-canvas-visual-editor-terry-2021/index_20210712134511.md deleted file mode 100644 index d4400f557..000000000 --- a/.history/content/publication/sbol-canvas-visual-editor-terry-2021/index_20210712134511.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -# Documentation: https://wowchemy.com/docs/managing-content/ - -title: 'SBOLCanvas: A Visual Editor for Genetic Designs' -subtitle: '' -summary: '' -authors: -- Logan Terry -- Jared Earl -- Sam Thayer -- Samuel Bridge -- Chris J. Myers -tags: [] -categories: [] -date: '2021-06-01' -lastmod: 2021-07-12T13:45:12-03:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-07-12T16:44:22.592324Z' -publication_types: -- 2 -abstract: SBOLCanvas is a web-based application that can create and edit genetic constructs - using the SBOL data and visual standards. SBOLCanvas allows a user to create a genetic - design visually and structurally from start to finish. It also allows users to incorporate - existing SBOL data from a SynBioHub repository. By the nature of being a web-based - application, SBOLCanvas is readily accessible and easy to use. A live version of - the latest release can be found at https://sbolcanvas.org. -publication: '*ACS Synthetic Biology*' -doi: 10.1021/acssynbio.1c00096 ---- diff --git a/.history/content/publication/sbol-canvas-visual-editor-terry-2021/index_20210712134746.md b/.history/content/publication/sbol-canvas-visual-editor-terry-2021/index_20210712134746.md deleted file mode 100644 index 522bbc990..000000000 --- a/.history/content/publication/sbol-canvas-visual-editor-terry-2021/index_20210712134746.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -# Documentation: https://wowchemy.com/docs/managing-content/ - -title: 'SBOLCanvas: A Visual Editor for Genetic Designs' -subtitle: '' -summary: '' -authors: -- Logan Terry -- Jared Earl -- Sam Thayer -- Samuel Bridge -- Chris J. Myers -tags: [] -categories: [] -date: '2021-06-01' -lastmod: 2021-07-12T13:45:12-03:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-07-12T16:44:22.592324Z' -publication_types: -- 2 -abstract: SBOLCanvas is a web-based application that can create and edit genetic constructs - using the SBOL data and visual standards. SBOLCanvas allows a user to create a genetic - design visually and structurally from start to finish. It also allows users to incorporate - existing SBOL data from a SynBioHub repository. By the nature of being a web-based - application, SBOLCanvas is readily accessible and easy to use. A live version of - the latest release can be found at https://sbolcanvas.org. -publication: '*ACS Synthetic Biology*' -doi: 10.1021/acssynbio.1c00096 ---- diff --git a/.history/content/publication/synthetic-biology-knowledge-mante-2021/index_20210901105710.md b/.history/content/publication/synthetic-biology-knowledge-mante-2021/index_20210901105710.md deleted file mode 100644 index b0c99a19b..000000000 --- a/.history/content/publication/synthetic-biology-knowledge-mante-2021/index_20210901105710.md +++ /dev/null @@ -1,63 +0,0 @@ ---- -# Documentation: https://wowchemy.com/docs/managing-content/ - -title: Synthetic Biology Knowledge System -subtitle: '' -summary: '' -authors: -- Jeanet Mante -- Yikai Hao -- Jacob Jett -- Udayan Joshi -- Kevin Keating -- Xiang Lu -- Gaurav Nakum -- Nicholas E. Rodriguez -- Jiawei Tang -- Logan Terry -- Xuanyu Wu -- Eric Yu -- J. Stephen Downie -- Bridget T. McInnes -- Mai H. Nguyen -- Brandon Sepulvado -- Eric M. Young -- Chris J. Myers -tags: [] -categories: [] -date: '2021-08-01' -lastmod: 2021-09-01T10:57:11-03:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-09-01T13:56:48.798412Z' -publication_types: -- 2 -abstract: The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub - repository that includes text and data information that has been mined from papers - published in ACS Synthetic Biology. This paper describes the SBKS curation framework - that is being developed to construct the knowledge stored in this repository. The - text mining pipeline performs automatic annotation of the articles using natural - language processing techniques to identify salient content such as key terms, relationships - between terms, and main topics. The data mining pipeline performs automatic annotation - of the sequences extracted from the supplemental documents with the genetic parts - used in them. Together these two pipelines link genetic parts to papers describing - the context in which they are used. Ultimately, SBKS will reduce the time necessary - for synthetic biologists to find the information necessary to complete their designs. -publication: '*ACS Synthetic Biology*' -doi: 10.1021/acssynbio.1c00188 ---- diff --git a/.history/content/publication/synthetic-biology-knowledge-mante-2021/index_20210901105904.md b/.history/content/publication/synthetic-biology-knowledge-mante-2021/index_20210901105904.md deleted file mode 100644 index 21149cfe0..000000000 --- a/.history/content/publication/synthetic-biology-knowledge-mante-2021/index_20210901105904.md +++ /dev/null @@ -1,63 +0,0 @@ ---- -# Documentation: https://wowchemy.com/docs/managing-content/ - -title: Synthetic Biology Knowledge System -subtitle: '' -summary: '' -authors: -- Jeanet Mante -- Yikai Hao -- Jacob Jett -- Udayan Joshi -- Kevin Keating -- Xiang Lu -- Gaurav Nakum -- Nicholas E. Rodriguez -- Jiawei Tang -- Logan Terry -- Xuanyu Wu -- Eric Yu -- J. Stephen Downie -- Bridget T. McInnes -- Mai H. Nguyen -- Brandon Sepulvado -- Eric M. Young -- Chris J. Myers -tags: [] -categories: [] -date: '2021-08-01' -lastmod: 2021-09-01T10:57:11-03:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-09-01T13:56:48.798412Z' -publication_types: -- 2 -abstract: The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub - repository that includes text and data information that has been mined from papers - published in ACS Synthetic Biology. This paper describes the SBKS curation framework - that is being developed to construct the knowledge stored in this repository. The - text mining pipeline performs automatic annotation of the articles using natural - language processing techniques to identify salient content such as key terms, relationships - between terms, and main topics. The data mining pipeline performs automatic annotation - of the sequences extracted from the supplemental documents with the genetic parts - used in them. Together these two pipelines link genetic parts to papers describing - the context in which they are used. Ultimately, SBKS will reduce the time necessary - for synthetic biologists to find the information necessary to complete their designs. -publication: '*ACS Synthetic Biology*' -doi: 10.1021/acssynbio.1c00188 ---- diff --git a/.history/content/publication/synthetic-biology-open-baig-2021/cite_20211027095937.bib b/.history/content/publication/synthetic-biology-open-baig-2021/cite_20211027095937.bib deleted file mode 100644 index e557c2ffe..000000000 --- a/.history/content/publication/synthetic-biology-open-baig-2021/cite_20211027095937.bib +++ /dev/null @@ -1,16 +0,0 @@ -@article{SyntheticBiologyOpen_baig_2021, - abstract = {People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level ``interactions with interactions,'' such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new ``unspecified interaction'' glyph is added for visualizing interactions whose nature is unknown, the ``insulator'' glyph is deprecated in favor of a new ``inert DNA spacer'' glyph, and the polypeptide region glyph is recommended for showing 2A sequences.}, - annotation = {00000}, - author = {Baig, Hasan and Fontanarrosa, Pedro and Kulkarni, Vishwesh and McLaughlin, James and Vaidyanathan, Prashant and Bartley, Bryan and Bhakta, Shyam and Bhatia, Swapnil and Bissell, Mike and Clancy, Kevin and Cox, Robert Sidney and Moreno, Angel Goñi and Gorochowski, Thomas and Grunberg, Raik and Lee, Jihwan and Luna, Augustin and Madsen, Curtis and Misirli, Goksel and Nguyen, Tramy and Novere, Nicolas Le and Palchick, Zachary and Pocock, Matthew and Roehner, Nicholas and Sauro, Herbert and Scott-Brown, James and Sexton, John T. and Stan, Guy-Bart and Tabor, Jeffrey J. and Terry, Logan and Vilar, Marta Vazquez and Voigt, Christopher A. and Wipat, Anil and Zong, David and Zundel, Zach and Beal, Jacob and Myers, Chris}, - chapter = {Journal of Integrative Bioinformatics}, - doi = {10.1515/jib-2020-0045}, - file = {C\:\\Users\\elros\\Dropbox\\SYNTHETIC BIOLOGY\\Synthetic Biology Papers\\Synthetic biology open language visual (SBOL Visual) version 2_Baig et al_2021.pdf}, - issn = {1613-4516}, - journal = {Journal of Integrative Bioinformatics}, - langid = {english}, - month = {June}, - publisher = {De Gruyter}, - title = {Synthetic Biology Open Language Visual (SBOL Visual) Version 2.3}, - year = {2021} -} - diff --git a/.history/content/publication/synthetic-biology-open-baig-2021/cite_20211027100513.bib b/.history/content/publication/synthetic-biology-open-baig-2021/cite_20211027100513.bib deleted file mode 100644 index d2e6b7883..000000000 --- a/.history/content/publication/synthetic-biology-open-baig-2021/cite_20211027100513.bib +++ /dev/null @@ -1,16 +0,0 @@ -@article{SyntheticBiologyOpen_baig_2021, - abstract = {People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.3 of SBOL Visual, which builds on the prior SBOL Visual 2.2 in several ways. First, the specification now includes higher-level ``interactions with interactions,'' such as an inducer molecule stimulating a repression interaction. Second, binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes. Finally, a new ``unspecified interaction'' glyph is added for visualizing interactions whose nature is unknown, the ``insulator'' glyph is deprecated in favor of a new ``inert DNA spacer'' glyph, and the polypeptide region glyph is recommended for showing 2A sequences.}, - annotation = {00000}, - author = {Baig, Hasan and Fontanarrosa, Pedro and Kulkarni, Vishwesh and McLaughlin, James and Vaidyanathan, Prashant and Bartley, Bryan and Bhakta, Shyam and Bhatia, Swapnil and Bissell, Mike and Clancy, Kevin and Cox, Robert Sidney and Moreno, Angel Goñi and Gorochowski, Thomas and Grunberg, Raik and Lee, Jihwan and Luna, Augustin and Madsen, Curtis and Misirli, Goksel and Nguyen, Tramy and Novere, Nicolas Le and Palchick, Zachary and Pocock, Matthew and Roehner, Nicholas and Sauro, Herbert and Scott-Brown, James and Sexton, John T. and Stan, Guy-Bart and Tabor, Jeffrey J. and Terry, Logan and Vilar, Marta Vazquez and Voigt, Christopher A. and Wipat, Anil and Zong, David and Zundel, Zach and Beal, Jacob and Myers, Chris}, - chapter = {Journal of Integrative Bioinformatics}, - doi = {10.1515/jib-2020-0045}, - file = {C\:\\Users\\elros\\Dropbox\\SYNTHETIC BIOLOGY\\Synthetic Biology Papers\\Synthetic biology open language visual (SBOL Visual) version 2_Baig et al_2021.pdf}, - issn = {1613-4516}, - journal = {Journal of Integrative Bioinformatics}, - langid = {english}, - month = {June}, - publisher = {De Gruyter}, - title = {Synthetic Biology Open Language Visual (SBOL Visual) Version 2.3}, - year = {2019} -} - diff --git a/.history/content/publication/vis-bol-2-improving-web-based-hatch-2021/index_20210901105716.md b/.history/content/publication/vis-bol-2-improving-web-based-hatch-2021/index_20210901105716.md deleted file mode 100644 index e6250ec77..000000000 --- a/.history/content/publication/vis-bol-2-improving-web-based-hatch-2021/index_20210901105716.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -# Documentation: https://wowchemy.com/docs/managing-content/ - -title: VisBOL2—Improving Web-Based Visualization for Synthetic Biology Designs -subtitle: '' -summary: '' -authors: -- Benjamin Hatch -- Linhao Meng -- Jeanet Mante -- James A. McLaughlin -- James Scott-Brown -- Chris J. Myers -tags: [] -categories: [] -date: '2021-08-01' -lastmod: 2021-09-01T10:57:17-03:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-09-01T13:57:11.980617Z' -publication_types: -- 2 -abstract: VisBOL is a web-based visualization tool used to depict genetic circuit - designs. This tool depicts simple DNA circuits adequately, but it has become increasingly - outdated as new versions of SBOL Visual were released. This paper introduces VisBOL2, - a heavily redesigned version of VisBOL that makes a number of improvements to the - original VisBOL, including proper functional interaction rendering, dynamic viewing, - a more maintainable code base, and modularity that facilitates compatibility with - other software tools. This modularity is demonstrated by incorporating VisBOL2 into - a sequence visualization plugin for SynBioHub. -publication: '*ACS Synthetic Biology*' -doi: 10.1021/acssynbio.1c00147 ---- diff --git a/.history/content/publication/vis-bol-2-improving-web-based-hatch-2021/index_20210901105855.md b/.history/content/publication/vis-bol-2-improving-web-based-hatch-2021/index_20210901105855.md deleted file mode 100644 index d17a26a0c..000000000 --- a/.history/content/publication/vis-bol-2-improving-web-based-hatch-2021/index_20210901105855.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -# Documentation: https://wowchemy.com/docs/managing-content/ - -title: VisBOL2—Improving Web-Based Visualization for Synthetic Biology Designs -subtitle: '' -summary: '' -authors: -- Benjamin Hatch -- Linhao Meng -- Jeanet Mante -- James A. McLaughlin -- James Scott-Brown -- Chris J. Myers -tags: [] -categories: [] -date: '2021-08-01' -lastmod: 2021-09-01T10:57:17-03:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-09-01T13:57:11.980617Z' -publication_types: -- 2 -abstract: VisBOL is a web-based visualization tool used to depict genetic circuit - designs. This tool depicts simple DNA circuits adequately, but it has become increasingly - outdated as new versions of SBOL Visual were released. This paper introduces VisBOL2, - a heavily redesigned version of VisBOL that makes a number of improvements to the - original VisBOL, including proper functional interaction rendering, dynamic viewing, - a more maintainable code base, and modularity that facilitates compatibility with - other software tools. This modularity is demonstrated by incorporating VisBOL2 into - a sequence visualization plugin for SynBioHub. -publication: '*ACS Synthetic Biology*' -doi: 10.1021/acssynbio.1c00147 ---- diff --git a/.history/content/sbol-visual-ontology/_index_20211014094249.md b/.history/content/sbol-visual-ontology/_index_20211014094249.md deleted file mode 100644 index 9b3431e27..000000000 --- a/.history/content/sbol-visual-ontology/_index_20211014094249.md +++ /dev/null @@ -1,75 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -* Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -* [http://vows.sbolstandard.org/metadata/CDSGlyph](https://vows.sbolstandard.org/metadata/CDSGlyph) - -### Programmatic access to SBOL-VOWS - -Python and Java examples and related documentation can be found in the following GitHub repository: - -[https://github.com/dissys/sbol-visual-client](https://github.com/dissys/sbol-visual-client) - -The web service returns data using the RDF/JSON format. Hence, any RDF or JSON library can be used to access information regarding the mapping, query, and metadata interfaces. Please note that examples are provided using the RDFLib and Jena libraries for Python and Java programming languages respectively. \ No newline at end of file diff --git a/.history/content/sbol-visual-ontology/_index_20211014095708.md b/.history/content/sbol-visual-ontology/_index_20211014095708.md deleted file mode 100644 index b108da5d5..000000000 --- a/.history/content/sbol-visual-ontology/_index_20211014095708.md +++ /dev/null @@ -1,75 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology (Please note that your browser may not allow direct downloads. If it does not, please copy and paste the following link on a new tab: http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf). - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -* Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -* [http://vows.sbolstandard.org/metadata/CDSGlyph](https://vows.sbolstandard.org/metadata/CDSGlyph) - -### Programmatic access to SBOL-VOWS - -Python and Java examples and related documentation can be found in the following GitHub repository: - -[https://github.com/dissys/sbol-visual-client](https://github.com/dissys/sbol-visual-client) - -The web service returns data using the RDF/JSON format. Hence, any RDF or JSON library can be used to access information regarding the mapping, query, and metadata interfaces. Please note that examples are provided using the RDFLib and Jena libraries for Python and Java programming languages respectively. \ No newline at end of file diff --git a/.history/content/sbol-visual-ontology/_index_20211014112232.md b/.history/content/sbol-visual-ontology/_index_20211014112232.md deleted file mode 100644 index 27bf9d7c4..000000000 --- a/.history/content/sbol-visual-ontology/_index_20211014112232.md +++ /dev/null @@ -1,75 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology (**please note** that your browser may not allow direct downloads. If it does not, please copy and paste the following link on a new tab: http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf ). - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -* Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -* [http://vows.sbolstandard.org/metadata/CDSGlyph](https://vows.sbolstandard.org/metadata/CDSGlyph) - -### Programmatic access to SBOL-VOWS - -Python and Java examples and related documentation can be found in the following GitHub repository: - -[https://github.com/dissys/sbol-visual-client](https://github.com/dissys/sbol-visual-client) - -The web service returns data using the RDF/JSON format. Hence, any RDF or JSON library can be used to access information regarding the mapping, query, and metadata interfaces. Please note that examples are provided using the RDFLib and Jena libraries for Python and Java programming languages respectively. \ No newline at end of file diff --git a/.history/content/visual-about/_index_20210209104909.md b/.history/content/visual-about/_index_20210209104909.md deleted file mode 100644 index 16cc15f0f..000000000 --- a/.history/content/visual-about/_index_20210209104909.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - - - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209105350.md b/.history/content/visual-about/_index_20210209105350.md deleted file mode 100644 index 622990729..000000000 --- a/.history/content/visual-about/_index_20210209105350.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - - - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209105508.md b/.history/content/visual-about/_index_20210209105508.md deleted file mode 100644 index 48c98f7e6..000000000 --- a/.history/content/visual-about/_index_20210209105508.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="\Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - - - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209105511.md b/.history/content/visual-about/_index_20210209105511.md deleted file mode 100644 index ff81d431b..000000000 --- a/.history/content/visual-about/_index_20210209105511.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - - - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209105521.md b/.history/content/visual-about/_index_20210209105521.md deleted file mode 100644 index ff81d431b..000000000 --- a/.history/content/visual-about/_index_20210209105521.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - - - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209105532.md b/.history/content/visual-about/_index_20210209105532.md deleted file mode 100644 index ff81d431b..000000000 --- a/.history/content/visual-about/_index_20210209105532.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - - - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209105749.md b/.history/content/visual-about/_index_20210209105749.md deleted file mode 100644 index 45e2c30e1..000000000 --- a/.history/content/visual-about/_index_20210209105749.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos\SBOLlogo.png" width="500" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209105820.md b/.history/content/visual-about/_index_20210209105820.md deleted file mode 100644 index 07f1dfea4..000000000 --- a/.history/content/visual-about/_index_20210209105820.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos\SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209110317.md b/.history/content/visual-about/_index_20210209110317.md deleted file mode 100644 index 5a51cee52..000000000 --- a/.history/content/visual-about/_index_20210209110317.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure width="600px" library="true" src="SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209110325.md b/.history/content/visual-about/_index_20210209110325.md deleted file mode 100644 index 5a51cee52..000000000 --- a/.history/content/visual-about/_index_20210209110325.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure width="600px" library="true" src="SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209110408.md b/.history/content/visual-about/_index_20210209110408.md deleted file mode 100644 index fa0c4ec75..000000000 --- a/.history/content/visual-about/_index_20210209110408.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure width="600px" library="true" src="Logos/SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209110411.md b/.history/content/visual-about/_index_20210209110411.md deleted file mode 100644 index 5c8aac32c..000000000 --- a/.history/content/visual-about/_index_20210209110411.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure width="600px" library="true" src="Logos\SBOL_2_demo_workflow_chris.png" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209110624.md b/.history/content/visual-about/_index_20210209110624.md deleted file mode 100644 index 87a9009b9..000000000 --- a/.history/content/visual-about/_index_20210209110624.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure width="600px" library="true" src="Logos/SBOLlogo.png" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209110726.md b/.history/content/visual-about/_index_20210209110726.md deleted file mode 100644 index 36e324b86..000000000 --- a/.history/content/visual-about/_index_20210209110726.md +++ /dev/null @@ -1,54 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure width="600px" library="true" src="Logos/SBOLVisualLogo.svg" title="" lightbox="true" >}} - -
- -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-about/_index_20210209110737.md b/.history/content/visual-about/_index_20210209110737.md deleted file mode 100644 index e0c19909d..000000000 --- a/.history/content/visual-about/_index_20210209110737.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure width="600px" library="true" src="Logos/SBOLVisualLogo.svg" title="" lightbox="true" >}} - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/content/visual-examples/_index_20210209104909.md b/.history/content/visual-examples/_index_20210209104909.md deleted file mode 100644 index b879c0cad..000000000 --- a/.history/content/visual-examples/_index_20210209104909.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli-sbol-owl_2019" view="3" >}} - -## 2015 (Visual Examples) - -{{< cite page="/publication/composable-modular-models-misirli-2015" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - - - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - - diff --git a/.history/content/visual-examples/_index_20210209111133.md b/.history/content/visual-examples/_index_20210209111133.md deleted file mode 100644 index eb867aa05..000000000 --- a/.history/content/visual-examples/_index_20210209111133.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli-sbol-owl_2019" view="3" >}} - -## 2015 (Visual Examples) - -{{< cite page="/publication/composable-modular-models-misirli-2015" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - -{{< figure library="true" src="SBOLVisualExamples/example1-1.jpg" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} - - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - - diff --git a/.history/content/visual-examples/_index_20210209111141.md b/.history/content/visual-examples/_index_20210209111141.md deleted file mode 100644 index 3604ced50..000000000 --- a/.history/content/visual-examples/_index_20210209111141.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli-sbol-owl_2019" view="3" >}} - -## 2015 (Visual Examples) - -{{< cite page="/publication/composable-modular-models-misirli-2015" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - -{{< figure library="true" src="SBOLVisualExamples/example1-1.jpg" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - - diff --git a/.history/content/visual-examples/_index_20210209111158.md b/.history/content/visual-examples/_index_20210209111158.md deleted file mode 100644 index 007edf0e0..000000000 --- a/.history/content/visual-examples/_index_20210209111158.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli-sbol-owl_2019" view="3" >}} - -## 2015 (Visual Examples) - -{{< cite page="/publication/composable-modular-models-misirli-2015" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - -{{< figure library="true" src="SBOLVisualExamples/example1-1.jpg" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - -{{< figure library="true" src="SBOLVisualExamples/example2.jpg" title="Example 2: Phosphorylation of an inactive transcription factor" lightbox="true" width="670" >}} diff --git a/.history/content/visual-examples/_index_20210209112813.md b/.history/content/visual-examples/_index_20210209112813.md deleted file mode 100644 index 007edf0e0..000000000 --- a/.history/content/visual-examples/_index_20210209112813.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli-sbol-owl_2019" view="3" >}} - -## 2015 (Visual Examples) - -{{< cite page="/publication/composable-modular-models-misirli-2015" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - -{{< figure library="true" src="SBOLVisualExamples/example1-1.jpg" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - -{{< figure library="true" src="SBOLVisualExamples/example2.jpg" title="Example 2: Phosphorylation of an inactive transcription factor" lightbox="true" width="670" >}} diff --git a/.history/content/visual-glyphs/_index_20210209104909.md b/.history/content/visual-glyphs/_index_20210209104909.md deleted file mode 100644 index ac3b3923a..000000000 --- a/.history/content/visual-glyphs/_index_20210209104909.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - - - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - - diff --git a/.history/content/visual-glyphs/_index_20210209110900.md b/.history/content/visual-glyphs/_index_20210209110900.md deleted file mode 100644 index 9b6585445..000000000 --- a/.history/content/visual-glyphs/_index_20210209110900.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - - - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - - diff --git a/.history/content/visual-glyphs/_index_20210209111216.md b/.history/content/visual-glyphs/_index_20210209111216.md deleted file mode 100644 index 38c6d1589..000000000 --- a/.history/content/visual-glyphs/_index_20210209111216.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - - diff --git a/.history/content/visual-glyphs/_index_20210209111221.md b/.history/content/visual-glyphs/_index_20210209111221.md deleted file mode 100644 index d4ae3b32a..000000000 --- a/.history/content/visual-glyphs/_index_20210209111221.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - - - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - - diff --git a/.history/content/visual-glyphs/_index_20210209111244.md b/.history/content/visual-glyphs/_index_20210209111244.md deleted file mode 100644 index fb00038a7..000000000 --- a/.history/content/visual-glyphs/_index_20210209111244.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - - diff --git a/.history/content/visual-glyphs/_index_20210209111256.md b/.history/content/visual-glyphs/_index_20210209111256.md deleted file mode 100644 index 782ed6f39..000000000 --- a/.history/content/visual-glyphs/_index_20210209111256.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/content/visual-glyphs/_index_20210209112733.md b/.history/content/visual-glyphs/_index_20210209112733.md deleted file mode 100644 index 782ed6f39..000000000 --- a/.history/content/visual-glyphs/_index_20210209112733.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/content/visual-specification/_index_20210531072059.md b/.history/content/visual-specification/_index_20210531072059.md deleted file mode 100644 index 714a9c58f..000000000 --- a/.history/content/visual-specification/_index_20210531072059.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: SBOL Visual Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Visual Specification](https://github.com/SynBioDex/SBOL-visual/issues) - -___ - -[Glyphs]({{< relref "visual-glyphs" >}}) - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model.

A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed. Until a decision is made about how to represent constraints, the specification is mute on both constraints and dashed undirected lines, which means that it is acceptable to use them, if desired, as an annotation indicating identity.

In addition, collection of glyphs has been modified as follows:
  • The deprecated Insulator glyph and “shmoo” Macromolecule alternative glyph have been removed.
  • Deprecated BioPAX alternatives to SBO terms for molecular species glyphs have been removed.
The changes for this release were approved as SEP V024.

|{{% staticref "docs/SBOL-Visual-3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | | - - - -| **2.x.x Release** | | | -|---|---|---| -| **2.3.0**
SBOL Visual 2.3 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.3 enhances the prior SBOL Visual 2.2 standard as follows:
  • Adds higher-level "interactions with interactions", such as an inducer molecule stimulating a repression interaction
  • Binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes
  • Recommends using polypeptide region glyph to show 2A sequences
  • Adds new "unspecified interaction" glyph for visualizing interactions whose nature is unknown
  • Deprecates "insulator" glyph in favor of new "inert DNA spacer" glyph
|{{% staticref "docs/SBOL-Visual-2.3.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
SBOL Visual 2.2 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.2 enhances the prior SBOL Visual 2.1 standard as follows:
  • Grounding for molecular species glyphs is changed from BioPAX to SBO (BioPAX terms are retained as deprecated alternatives).
  • New glyphs are added for introns and polypeptide regions (e.g., protein domains).
  • The macromolecule glyph often confused with yeast is deprecated, and a new glyph for proteins added
  • Small polygons are recommended as alternative glyphs for simple chemicals.
| {{% staticref "docs/SBOL-Visual-2.2.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.1.0**
SBOL Visual 2.1 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions). SBOL Visual 2.1 enhances the prior SBOL Visual 2.0 standard with the addition of methods for showing modular structure and mappings between elements of a system, and new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons. Additionally, interactions arrows were modified such that they can split or join, with the glyph at the split or join indicating either superposition or a chemical process. | {{% staticref "docs/SBOL-Visual-2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
A diagram language and collection of symbols that can be used to graphically depict a genetic design and its functional interactions. SBOL Visual 2.0 builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs | {{% staticref "docs/SBOLVisual_Specification_2_0_0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20170074.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.0.0**
A set of symbols that can be used to graphically depict functional information encoded by nucleic acid sequences. Each symbol in the set has three components: a shape, a display name, and a definition. | {{% staticref "docs/BBFRFC93.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002310) | diff --git a/.history/content/visual-specification/_index_20211014094216.md b/.history/content/visual-specification/_index_20211014094216.md deleted file mode 100644 index 2288655df..000000000 --- a/.history/content/visual-specification/_index_20211014094216.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: SBOL Visual Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Visual Specification](https://github.com/SynBioDex/SBOL-visual/issues) - -___ - -[Glyphs]({{< relref "visual-glyphs" >}}) - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model.

A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed. Until a decision is made about how to represent constraints, the specification is mute on both constraints and dashed undirected lines, which means that it is acceptable to use them, if desired, as an annotation indicating identity.

In addition, collection of glyphs has been modified as follows:
  • The deprecated Insulator glyph and “shmoo” Macromolecule alternative glyph have been removed.
  • Deprecated BioPAX alternatives to SBO terms for molecular species glyphs have been removed.
The changes for this release were approved as SEP V024.

|{{% staticref "docs/SBOL-Visual-3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | | - - - -| **2.x.x Release** | | | -|---|---|---| -| **2.3.0**
SBOL Visual 2.3 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.3 enhances the prior SBOL Visual 2.2 standard as follows:
  • Adds higher-level "interactions with interactions", such as an inducer molecule stimulating a repression interaction
  • Binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes
  • Recommends using polypeptide region glyph to show 2A sequences
  • Adds new "unspecified interaction" glyph for visualizing interactions whose nature is unknown
  • Deprecates "insulator" glyph in favor of new "inert DNA spacer" glyph
|{{% staticref "docs/SBOL-Visual-2.3.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/document/doi/10.1515/jib-2019-0025/html) | -| **2.2.0**
SBOL Visual 2.2 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.2 enhances the prior SBOL Visual 2.1 standard as follows:
  • Grounding for molecular species glyphs is changed from BioPAX to SBO (BioPAX terms are retained as deprecated alternatives).
  • New glyphs are added for introns and polypeptide regions (e.g., protein domains).
  • The macromolecule glyph often confused with yeast is deprecated, and a new glyph for proteins added
  • Small polygons are recommended as alternative glyphs for simple chemicals.
| {{% staticref "docs/SBOL-Visual-2.2.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/document/doi/10.1515/jib-2020-0014/html) | -| **2.1.0**
SBOL Visual 2.1 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions). SBOL Visual 2.1 enhances the prior SBOL Visual 2.0 standard with the addition of methods for showing modular structure and mappings between elements of a system, and new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons. Additionally, interactions arrows were modified such that they can split or join, with the glyph at the split or join indicating either superposition or a chemical process. | {{% staticref "docs/SBOL-Visual-2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/document/doi/10.1515/jib-2018-0101/html) | -| **2.0.0**
A diagram language and collection of symbols that can be used to graphically depict a genetic design and its functional interactions. SBOL Visual 2.0 builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs | {{% staticref "docs/SBOLVisual_Specification_2_0_0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20170074.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.0.0**
A set of symbols that can be used to graphically depict functional information encoded by nucleic acid sequences. Each symbol in the set has three components: a shape, a display name, and a definition. | {{% staticref "docs/BBFRFC93.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002310) | diff --git a/.history/content/visual-specification/_index_20211027095154.md b/.history/content/visual-specification/_index_20211027095154.md deleted file mode 100644 index 87f936ed5..000000000 --- a/.history/content/visual-specification/_index_20211027095154.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: SBOL Visual Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Visual Specification](https://github.com/SynBioDex/SBOL-visual/issues) - -___ - -[Glyphs]({{< relref "visual-glyphs" >}}) - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
The major difference between SBOL Visual 3 and SBOL Visual 2 is that diagrams and glyphs are defined with respect to the SBOL 3 data model rather than the SBOL 2 data model.

A byproduct of this change is that the use of dashed undirected lines for subsystem mappings has been removed. Until a decision is made about how to represent constraints, the specification is mute on both constraints and dashed undirected lines, which means that it is acceptable to use them, if desired, as an annotation indicating identity.

In addition, collection of glyphs has been modified as follows:
  • The deprecated Insulator glyph and “shmoo” Macromolecule alternative glyph have been removed.
  • Deprecated BioPAX alternatives to SBO terms for molecular species glyphs have been removed.
The changes for this release were approved as SEP V024.

|{{% staticref "docs/SBOL-Visual-3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/document/doi/10.1515/jib-2021-0013/html) | - - - -| **2.x.x Release** | | | -|---|---|---| -| **2.3.0**
SBOL Visual 2.3 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.3 enhances the prior SBOL Visual 2.2 standard as follows:
  • Adds higher-level "interactions with interactions", such as an inducer molecule stimulating a repression interaction
  • Binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes
  • Recommends using polypeptide region glyph to show 2A sequences
  • Adds new "unspecified interaction" glyph for visualizing interactions whose nature is unknown
  • Deprecates "insulator" glyph in favor of new "inert DNA spacer" glyph
|{{% staticref "docs/SBOL-Visual-2.3.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](http://www.degruyter.com/document/doi/10.1515/jib-2020-0045/html) | -| **2.2.0**
SBOL Visual 2.2 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.2 enhances the prior SBOL Visual 2.1 standard as follows:
  • Grounding for molecular species glyphs is changed from BioPAX to SBO (BioPAX terms are retained as deprecated alternatives).
  • New glyphs are added for introns and polypeptide regions (e.g., protein domains).
  • The macromolecule glyph often confused with yeast is deprecated, and a new glyph for proteins added
  • Small polygons are recommended as alternative glyphs for simple chemicals.
| {{% staticref "docs/SBOL-Visual-2.2.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/document/doi/10.1515/jib-2020-0014/html) | -| **2.1.0**
SBOL Visual 2.1 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions). SBOL Visual 2.1 enhances the prior SBOL Visual 2.0 standard with the addition of methods for showing modular structure and mappings between elements of a system, and new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons. Additionally, interactions arrows were modified such that they can split or join, with the glyph at the split or join indicating either superposition or a chemical process. | {{% staticref "docs/SBOL-Visual-2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/document/doi/10.1515/jib-2018-0101/html) | -| **2.0.0**
A diagram language and collection of symbols that can be used to graphically depict a genetic design and its functional interactions. SBOL Visual 2.0 builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs | {{% staticref "docs/SBOLVisual_Specification_2_0_0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20170074.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.0.0**
A set of symbols that can be used to graphically depict functional information encoded by nucleic acid sequences. Each symbol in the set has three components: a shape, a display name, and a definition. | {{% staticref "docs/BBFRFC93.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002310) | diff --git a/.history/hugo_themes/config/_default/menus_20200921104705.toml b/.history/hugo_themes/config/_default/menus_20200921104705.toml deleted file mode 100644 index 3ad2dd4e9..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921104705.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel-about" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "#dom-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "#dom-about" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "#dom-about" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "#dom-about" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "#dom-about" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "#dom-about" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921104731.toml b/.history/hugo_themes/config/_default/menus_20200921104731.toml deleted file mode 100644 index 77208af22..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921104731.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel-about" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "#dom-about" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "#dom-about" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "#dom-about" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "#dom-about" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "#dom-about" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921104803.toml b/.history/hugo_themes/config/_default/menus_20200921104803.toml deleted file mode 100644 index 240fa8f09..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921104803.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel-about" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id2" - -[[main]] - name = "Specification" - url = "#dom-about" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "#dom-about" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "#dom-about" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "#dom-about" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "#dom-about" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921104842.toml b/.history/hugo_themes/config/_default/menus_20200921104842.toml deleted file mode 100644 index 34599366e..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921104842.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel-about" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel" - weight = 5 - parent = "dom-id2" - -[[main]] - name = "Specification" - url = "#dom-about" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "#dom-about" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "#dom-about" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "#dom-about" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "#dom-about" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921104936.toml b/.history/hugo_themes/config/_default/menus_20200921104936.toml deleted file mode 100644 index eb4b39d7b..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921104936.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel-about" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "#dom-about" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "#dom-about" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "#dom-about" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "#dom-about" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "#dom-about" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921105012.toml b/.history/hugo_themes/config/_default/menus_20200921105012.toml deleted file mode 100644 index fb3ccff33..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921105012.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "#dom-about" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "#dom-about" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "#dom-about" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "#dom-about" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "#dom-about" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921105412.toml b/.history/hugo_themes/config/_default/menus_20200921105412.toml deleted file mode 100644 index 8de6eeae2..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921105412.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "#dom-about" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "#dom-about" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "#dom-about" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921105614.toml b/.history/hugo_themes/config/_default/menus_20200921105614.toml deleted file mode 100644 index a6926a616..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921105614.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "/DataMdel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "/DataModel-Converter" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921105839.toml b/.history/hugo_themes/config/_default/menus_20200921105839.toml deleted file mode 100644 index a6926a616..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921105839.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "/DataMdel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "/DataModel-Converter" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921105848.toml b/.history/hugo_themes/config/_default/menus_20200921105848.toml deleted file mode 100644 index a6926a616..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921105848.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "/DataMdel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "/DataModel-Converter" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921105858.toml b/.history/hugo_themes/config/_default/menus_20200921105858.toml deleted file mode 100644 index a6926a616..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921105858.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "/DataMdel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "/DataModel-Converter" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921110122.toml b/.history/hugo_themes/config/_default/menus_20200921110122.toml deleted file mode 100644 index 07053cc63..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921110122.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "Ontology" - url = "/DataMdel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "/DataModel-Converter" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921111308.toml b/.history/hugo_themes/config/_default/menus_20200921111308.toml deleted file mode 100644 index a6510e2d9..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921111308.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "SBOL Ontology" - url = "/DataMdel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "/DataModel-Converter" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921111359.toml b/.history/hugo_themes/config/_default/menus_20200921111359.toml deleted file mode 100644 index 2f4c6f2b4..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921111359.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "SBOL Ontology" - url = "/DataModel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "/DataModel-Converter" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921155520.toml b/.history/hugo_themes/config/_default/menus_20200921155520.toml deleted file mode 100644 index 3890417a2..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921155520.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "SBOL Ontology" - url = "/DataModel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "https://converter.sbolstandard.org/" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "#dom-about" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20200921155640.toml b/.history/hugo_themes/config/_default/menus_20200921155640.toml deleted file mode 100644 index 5861b076c..000000000 --- a/.history/hugo_themes/config/_default/menus_20200921155640.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "Libraries" - url = "/DataModel-Libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "SBOL Ontology" - url = "/DataModel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "Converter" - url = "https://converter.sbolstandard.org/" - weight = 25 - parent = "dom-id" - -[[main]] - name = "Validator" - url = "https://validator.sbolstandard.org/" - weight = 30 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/menus_20201009091046.toml b/.history/hugo_themes/config/_default/menus_20201009091046.toml deleted file mode 100644 index 97a64a11a..000000000 --- a/.history/hugo_themes/config/_default/menus_20201009091046.toml +++ /dev/null @@ -1,156 +0,0 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - -[[main]] - name = "Home" - url = "#about" - weight = 10 - -[[main]] - name = "Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" - -[[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "SBOL Specification" - url = "/DataModel-Specification" - weight = 10 - parent = "dom-id" - -[[main]] - name = "SBOL Libraries" - url = "/libraries" - weight = 15 - parent = "dom-id" - -[[main]] - name = "SBOL Ontology" - url = "/DataModel-Ontology" - weight = 20 - parent = "dom-id" - -[[main]] - name = "SBOL Converter" - url = "https://converter.sbolstandard.org/" - weight = 25 - parent = "dom-id" - -[[main]] - name = "SBOL Validator" - url = "https://validator.sbolstandard.org/" - weight = 30 - parent = "dom-id" - -[[main]] - name = "SBOL Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Ontology" - url = "/visual-ontology" - weight = 20 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Examples" - url = "/visual-examples" - weight = 25 - parent = "visual-id" - -[[main]] - name = "Applications" - url = "/applications" - weight = 30 - -[[main]] - name = "Publications" - url = "#featured" - weight = 40 - -[[main]] - name = "Community" - url = "/community" - weight = 50 - identifier = "community-id" - -[[main]] - name = "About" - url = "/community" - weight = 5 - parent = "community-id" - -[[main]] - name = "Meetings" - url = "/community-meetings" - weight = 10 - parent = "community-id" - -[[main]] - name = "Outreach" - url = "/community-outreach" - weight = 15 - parent = "community-id" - -[[main]] - name = "Governance" - url = "/community-governance" - weight = 20 - parent = "community-id" - -[[main]] - name = "SBOL Industrial Consortium" - url = "/sbol-industrial" - weight = 25 - parent = "community-id" - -[[main]] - name = "Contact" - url = "/contact" - weight = 55 - -[[main]] - name = "FAQ" - url = "/faq" - weight = 60 - -# Link to a PDF of your resume/CV from the menu. -# To enable, copy your resume/CV to `static/files/cv.pdf` and uncomment the lines below. -# [[main]] -# name = "CV" -# url = "files/cv.pdf" -# weight = 70 diff --git a/.history/hugo_themes/config/_default/params_20200708105246.toml b/.history/hugo_themes/config/_default/params_20200708105246.toml deleted file mode 100644 index 1d9650bab..000000000 --- a/.history/hugo_themes/config/_default/params_20200708105246.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "L" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "circle" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/hugo_themes/config/_default/params_20201012162821.toml b/.history/hugo_themes/config/_default/params_20201012162821.toml deleted file mode 100644 index 703b5ab65..000000000 --- a/.history/hugo_themes/config/_default/params_20201012162821.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "circle" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/hugo_themes/config/_default/params_20201202164519.toml b/.history/hugo_themes/config/_default/params_20201202164519.toml deleted file mode 100644 index cb3ed9b6c..000000000 --- a/.history/hugo_themes/config/_default/params_20201202164519.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "square" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/hugo_themes/config/_default/params_20201202164530.toml b/.history/hugo_themes/config/_default/params_20201202164530.toml deleted file mode 100644 index 703b5ab65..000000000 --- a/.history/hugo_themes/config/_default/params_20201202164530.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "circle" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/hugo_themes/config/_default/params_20201202164541.toml b/.history/hugo_themes/config/_default/params_20201202164541.toml deleted file mode 100644 index cb3ed9b6c..000000000 --- a/.history/hugo_themes/config/_default/params_20201202164541.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "square" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/hugo_themes/config/_default/params_20201202165541.toml b/.history/hugo_themes/config/_default/params_20201202165541.toml deleted file mode 100644 index 703b5ab65..000000000 --- a/.history/hugo_themes/config/_default/params_20201202165541.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "circle" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/hugo_themes/config/_default/params_20201202172604.toml b/.history/hugo_themes/config/_default/params_20201202172604.toml deleted file mode 100644 index cb3ed9b6c..000000000 --- a/.history/hugo_themes/config/_default/params_20201202172604.toml +++ /dev/null @@ -1,292 +0,0 @@ -# SITE SETUP -# Guide: https://sourcethemes.com/academic/docs/get-started/ -# Documentation: https://sourcethemes.com/academic/docs/ -# -# This file is formatted using TOML syntax - learn more at https://learnxinyminutes.com/docs/toml/ -# Each configuration section is defined by a name in square brackets (e.g. `[search]`). - -############################ -## Theme -############################ - -# Choose a theme. -# Latest themes (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in themes in `themes/academic/data/themes/` -# Browse user installed themes in `data/themes/` -theme = "sbol" - -# Enable users to switch between day and night mode? -day_night = true - -# Override the theme's font set (optional). -# Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ -# Browse built-in font sets in `themes/academic/data/fonts/` -# Browse user installed font sets in `data/fonts/` -font = "" - -# Choose a font size. -# Sizes: XS (extra small), S (small), M (medium), L (large - DEFAULT), XL (extra large) -font_size = "M" - -############################ -## Basic Info -############################ - -# Website type -# Improve how search engines understand your site. -# For personal sites, choose "Person". -# For organizations and projects, choose from https://schema.org/Organization#subtypes -# E.g. Person, Organization, LocalBusiness, Project, EducationalOrganization -site_type = "Organization" - -# Local business type (optional) -# If you entered "LocalBusiness" above, choose the type of business from https://schema.org/LocalBusiness#subtypes -local_business_type = "" - -# Organization name (optional) -# Enter an organization or project name. Defaults to the site title from `config.toml`. -org_name = "Synthetic Biology Open Language" - -# Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" - -############################ -## Site Features -############################ - -# Enable source code highlighting? true/false -# Documentation: https://sourcethemes.com/academic/docs/writing-markdown-latex/#highlighting-options -highlight = true -highlight_languages = ["r"] # Add support for highlighting additional languages -# highlight_style = "github" # For supported styles, see https://cdnjs.com/libraries/highlight.js/ - -# Enable LaTeX math rendering? true/false -# If false, you can enable math on a per page basis as needed. -math = false - -# Enable diagram rendering? true/false -# If false, you can enable diagrams on a per page basis as needed. -diagram = false - -# Privacy pack -# Show a cookie consent message to visitors -# Anonymize IP in Google Analytics (if enabled) -privacy_pack = false - -# Enable visitors to edit pages? -# `repo` defines the repository URL. `editable` defines which page types can be edited. -edit_page = {repo_url = "https://github.com/gcushen/hugo-academic", content_dir = "", repo_branch = "master", editable = {docs = true, page = false, post = false}} - -# Show related content at the bottom of pages? -show_related = {docs = true, page = false, post = true, project = true, publication = true, talk = true} - -############################ -## Contact details -## -## These details power the Contact widget (if enabled). -## Additionally, for organizations, these details may be used to enrich search engine results. -############################ - -# Enter contact details (optional). To hide a field, clear it to "". -email = "test@example.org" -phone = "888 888 88 88" - -# Address -# For country_code, use the 2-letter ISO code (see https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 ) -address = {street = "450 Serra Mall", city = "Stanford", region = "CA", postcode = "94305", country = "United States", country_code = "US"} - -# Geographic coordinates -# To get your coordinates, right-click on Google Maps and choose "What's here?". The coords will show up at the bottom. -coordinates = {latitude = "37.4275", longitude = "-122.1697"} - -# Directions for visitors to locate you. -directions = "Enter Building 1 and take the stairs to Office 200 on Floor 2" - -# Office hours -# A list of your office hours. To remove, set to an empty list `[]`. -office_hours = ["Monday 10:00 to 13:00", "Wednesday 09:00 to 10:00"] - -# Enter an optional link for booking appointments (e.g. calendly.com). -appointment_url = "https://calendly.com" - -# Contact links -# Set to `[]` to disable, or comment out unwanted lines with a hash `#`. -contact_links = [ - {icon = "twitter", icon_pack = "fab", name = "DM Me", link = "https://twitter.com/Twitter"}, - {icon = "skype", icon_pack = "fab", name = "Skype Me", link = "skype:echo123?call"}, - {icon = "keybase", icon_pack = "fab", name = "Chat on Keybase", link = "https://keybase.io/"}, - {icon = "comments", icon_pack = "fas", name = "Discuss on Forum", link = "https://discourse.gohugo.io"}, - # {icon = "telegram", icon_pack = "fab", name = "Telegram Me", link = "https://telegram.me/@Telegram"}, - ] - -############################ -## Social -############################ - -# Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" - -# Twitter username (without @). Used when a visitor shares your site on Twitter. -twitter = "" - -############################ -## Regional Settings -############################ - -# Date and time format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) -# Examples: "Mon, Jan 2, 2006" or "2006-01-02" -date_format = "Jan 2, 2006" -# Examples: "3:04 pm" or "15:04" -time_format = "3:04 PM" - -# Address format (choose from the [address_formats] list below or add you own to the list). -address_format = "en-us" - -############################ -## Advanced -############################ - -# Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} - -# Show estimated reading time for posts? (true/false) -reading_time = true - -# Display next/previous section pager? (true/false) -section_pager = false -docs_section_pager = true # Display pager in Docs layout (e.g. tutorials)? - -# Enable in-built social sharing buttons? (true/false) -sharing = true - -# Show a copyright license from creativecommons.org in the site footer? -# Page specific copyright licenses are also possible by adding this option to a page's front matter. -copyright_license = {enable = false, allow_derivatives = false, share_alike = true, allow_commercial = false, notice = "This work is licensed under {license}"} - -# Highlight the site author (superuser) in author lists? (true/false) -highlight_superuser = false - -# Link authors to their profile page? (true/false) -link_authors = true - -# Abstract length (characters) in the Compact and Portfolio Card list views. Also, see `summaryLength` in `config.toml`. -abstract_length = 135 - -# Load JS plugins -# E.g. To load `/assets/js/custom.js`, set `plugins_js = ["custom"]`. -plugins_js = [] - -# Avatars. -# An avatar is an image that appears next to a user's name. -# An avatar can be uploaded as an image named `avatar` to each user's profile or fetched from Gravatar.com. -[avatar] - # Get user avatars from Gravatar.com? (true/false) - gravatar = false - - # Choose a shape for avatar images. Options: circle, square. - shape = "square" - -# Available address formats. -[address_formats] - en-us = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ' ', '']} - en-gb = {order = ['street', 'city', 'region', 'postcode'], delimiters = [', ', ', ', ', ', '']} - de = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - fr-fr = {order = ['street', 'postcode', 'city'], delimiters = ['
', ' ', '']} - zh = {order = ['postcode', 'region', 'city', 'street'], delimiters = [' ', ' ', ' ', '']} - -# Configuration of publication pages. -[publications] - # Date format (refer to https://sourcethemes.com/academic/docs/customization/#date-format ) - # Examples: "Mon, Jan 2, 2006" or "2006-01-02" - date_format = "January 2006" - - # Citation style ("apa" or "mla") - citation_style = "apa" - -# Configuration of project pages. -[projects] - # Views for associated content. - # 1: List - # 2: Compact - # 3: Card - # 4: Citation (publications only) - post_view = 2 - publication_view = 2 - talk_view = 2 - -############################ -## Comments -############################ -[comments] - # Comment provider: - # 0: Disabled - # 1: Disqus (https://disqus.com) - # 2: Commento (https://commento.io) - engine = 0 - - # Which page types are commentable? - commentable = {page = false, post = false, docs = false, project = false, publication = false, talk = false} - - # Configuration of Disqus. - [comments.disqus] - shortname = "" # Paste the shortname from your Disqus dashboard. - show_count = true # Show comment count in page header? (true/false) - - # Configuration of Commento. - [comments.commento] - # If self-hosting Commento, enter its URL here (e.g. "https://commento.?.com"), otherwise leave empty. - url = "" - -############################ -## Search -############################ -[search] - # Search provider: - # 0: No search engine - # 1: Academic (built-in) - # 2: Algolia (https://www.algolia.com) - engine = 1 - - # Configuration of Algolia search engine. - # Paste the values from your Algolia dashboard. - [search.algolia] - app_id = "" - api_key = "" - index_name = "" - show_logo = false - -############################ -## Maps -############################ -[map] - # To show your address on a map in the Contact widget, enter your latitude and longitude (above) - # and choose a map provider below. - # - # To use Google Maps, set `engine` to 1 and enter your API key that can be obtained here: - # https://developers.google.com/maps/documentation/javascript/get-api-key - # To use OpenStreetMap tiles, set `engine` to 2. - # To use OpenStreetMap on a high traffic site, set `engine` to 3 and enter your API key that can be obtained here: - # https://www.mapbox.com/studio/account/tokens - # - # Map provider: - # 0: No map - # 1: Google Maps - # 2: OpenStreetMap (Mapnik) - # 3: OpenStreetMap (Mapbox) - engine = 2 - api_key = "" - zoom = 15 - -############################ -## Marketing -############################ -[marketing] - google_analytics = "" - google_tag_manager = "" - -############################ -## Content Management System -############################ -[cms] - # See https://sourcethemes.com/academic/docs/install/#install-with-web-browser - netlify_cms = true diff --git a/.history/hugo_themes/content/DataModel-Converter/_index_20200921105324.md b/.history/hugo_themes/content/DataModel-Converter/_index_20200921105324.md deleted file mode 100644 index 8a48d2664..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/_index_20200921105324.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Converter/_index_20200921105718.md b/.history/hugo_themes/content/DataModel-Converter/_index_20200921105718.md deleted file mode 100644 index b4c80c5d1..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/_index_20200921105718.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Converter - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Converter/_index_20200921114458.md b/.history/hugo_themes/content/DataModel-Converter/_index_20200921114458.md deleted file mode 100644 index cbdc6a73d..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/_index_20200921114458.md +++ /dev/null @@ -1,54 +0,0 @@ -external_link: "http://external-project.com" - ---- -title: SBOL Converter - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Converter/_index_20200921114519.md b/.history/hugo_themes/content/DataModel-Converter/_index_20200921114519.md deleted file mode 100644 index cbdc6a73d..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/_index_20200921114519.md +++ /dev/null @@ -1,54 +0,0 @@ -external_link: "http://external-project.com" - ---- -title: SBOL Converter - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Converter/_index_20200921115419.md b/.history/hugo_themes/content/DataModel-Converter/_index_20200921115419.md deleted file mode 100644 index 92a18116e..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/_index_20200921115419.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: SBOL Converter - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Sbol Converter \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114852.md b/.history/hugo_themes/content/DataModel-Converter/converter_20200921114852.md deleted file mode 100644 index 3d21cdac8..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114852.md +++ /dev/null @@ -1,5 +0,0 @@ -+++ - -external_link: "http://external-project.com" - -+++ \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114904.md b/.history/hugo_themes/content/DataModel-Converter/converter_20200921114904.md deleted file mode 100644 index 33603bc0a..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114904.md +++ /dev/null @@ -1,3 +0,0 @@ -+++ - -external_link: "http://external-project.com" diff --git a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114943.md b/.history/hugo_themes/content/DataModel-Converter/converter_20200921114943.md deleted file mode 100644 index 0f4bf3711..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114943.md +++ /dev/null @@ -1,3 +0,0 @@ -+++ - -external_link: "https://converter.sbolstandard.org/" diff --git a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114952.md b/.history/hugo_themes/content/DataModel-Converter/converter_20200921114952.md deleted file mode 100644 index 0f4bf3711..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/converter_20200921114952.md +++ /dev/null @@ -1,3 +0,0 @@ -+++ - -external_link: "https://converter.sbolstandard.org/" diff --git a/.history/hugo_themes/content/DataModel-Converter/converter_20200921115000.md b/.history/hugo_themes/content/DataModel-Converter/converter_20200921115000.md deleted file mode 100644 index 7218709b7..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/converter_20200921115000.md +++ /dev/null @@ -1,5 +0,0 @@ -+++ - -external_link: "https://converter.sbolstandard.org/" - -+++ diff --git a/.history/hugo_themes/content/DataModel-Converter/index_20200921114520.md b/.history/hugo_themes/content/DataModel-Converter/index_20200921114520.md deleted file mode 100644 index cbdc6a73d..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/index_20200921114520.md +++ /dev/null @@ -1,54 +0,0 @@ -external_link: "http://external-project.com" - ---- -title: SBOL Converter - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Converter/index_20200921114524.md b/.history/hugo_themes/content/DataModel-Converter/index_20200921114524.md deleted file mode 100644 index cbdc6a73d..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/index_20200921114524.md +++ /dev/null @@ -1,54 +0,0 @@ -external_link: "http://external-project.com" - ---- -title: SBOL Converter - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Converter/index_20200921114625.md b/.history/hugo_themes/content/DataModel-Converter/index_20200921114625.md deleted file mode 100644 index cbdc6a73d..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/index_20200921114625.md +++ /dev/null @@ -1,54 +0,0 @@ -external_link: "http://external-project.com" - ---- -title: SBOL Converter - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Converter/index_20200921114730.md b/.history/hugo_themes/content/DataModel-Converter/index_20200921114730.md deleted file mode 100644 index 3d21cdac8..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/index_20200921114730.md +++ /dev/null @@ -1,5 +0,0 @@ -+++ - -external_link: "http://external-project.com" - -+++ \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Converter/index_20200921114851.md b/.history/hugo_themes/content/DataModel-Converter/index_20200921114851.md deleted file mode 100644 index 3d21cdac8..000000000 --- a/.history/hugo_themes/content/DataModel-Converter/index_20200921114851.md +++ /dev/null @@ -1,5 +0,0 @@ -+++ - -external_link: "http://external-project.com" - -+++ \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20200921105326.md b/.history/hugo_themes/content/DataModel-Examples/_index_20200921105326.md deleted file mode 100644 index 8a48d2664..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20200921105326.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20200921105629.md b/.history/hugo_themes/content/DataModel-Examples/_index_20200921105629.md deleted file mode 100644 index 7498961c6..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20200921105629.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20200921155851.md b/.history/hugo_themes/content/DataModel-Examples/_index_20200921155851.md deleted file mode 100644 index 5c0594407..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20200921155851.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20200921155917.md b/.history/hugo_themes/content/DataModel-Examples/_index_20200921155917.md deleted file mode 100644 index 9db08a068..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20200921155917.md +++ /dev/null @@ -1,21 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -### SBOL 2.0 Examples - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005202211.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005202211.md deleted file mode 100644 index ed8033ca6..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005202211.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005203936.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005203936.md deleted file mode 100644 index 9c2e17a8a..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005203936.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="2" >}} - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204003.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204003.md deleted file mode 100644 index 9a2879333..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204003.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204136.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204136.md deleted file mode 100644 index 96c77eba8..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204136.md +++ /dev/null @@ -1,28 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204229.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204229.md deleted file mode 100644 index 368bf2c4c..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204229.md +++ /dev/null @@ -1,30 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204307.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204307.md deleted file mode 100644 index 7d42a2067..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204307.md +++ /dev/null @@ -1,32 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204407.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204407.md deleted file mode 100644 index 9ab99fbb6..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204407.md +++ /dev/null @@ -1,34 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204434.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204434.md deleted file mode 100644 index c715b23a0..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204434.md +++ /dev/null @@ -1,36 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - - -### SBOL 1.1 Examples \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204545.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204545.md deleted file mode 100644 index be639c53b..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204545.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located here. This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204816.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005204816.md deleted file mode 100644 index 1edaac93f..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005204816.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205200.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005205200.md deleted file mode 100644 index beac6eaba..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205200.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL File{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205333.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005205333.md deleted file mode 100644 index d656aea14..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205333.md +++ /dev/null @@ -1,43 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL File{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205636.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005205636.md deleted file mode 100644 index 1fa56160f..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205636.md +++ /dev/null @@ -1,46 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL file example{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch example{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{% staticref "zip/GeneticToggleSwitch.zip" "newtab" %}}Genetic Toggle Switch example{{% /staticref %}}\ -{{% staticref "zip/four-input AND gate Example.zip" "newtab" %}}Four-input AND gate example{{% /staticref %}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205845.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005205845.md deleted file mode 100644 index e1f27964c..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205845.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL file example{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch example{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{% staticref "zip/GeneticToggleSwitch.zip" "newtab" %}}Genetic Toggle Switch example{{% /staticref %}}\ -{{% staticref "zip/four-input AND gate Example.zip" "newtab" %}}Four-input AND gate example{{% /staticref %}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{% staticref "zip/SBOL Specs Exampless.zip" "newtab" %}}SBOL 2.0 Specification examples{{% /staticref %}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205919.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005205919.md deleted file mode 100644 index a4982f595..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005205919.md +++ /dev/null @@ -1,48 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL file example{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch example{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{% staticref "zip/GeneticToggleSwitch.zip" "newtab" %}}Genetic Toggle Switch example{{% /staticref %}}\ -{{% staticref "zip/four-input AND gate Example.zip" "newtab" %}}Four-input AND gate example{{% /staticref %}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{% staticref "zip/SBOL Specs Examples.zip" "newtab" %}}SBOL 2.0 Specification examples{{% /staticref %}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210055.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005210055.md deleted file mode 100644 index 6020378d8..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210055.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL file example{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch example{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{% staticref "zip/GeneticToggleSwitch.zip" "newtab" %}}Genetic Toggle Switch example{{% /staticref %}}\ -{{% staticref "zip/four-input AND gate Example.zip" "newtab" %}}Four-input AND gate example{{% /staticref %}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{% staticref "zip/SBOL Specs Examples.zip" "newtab" %}}SBOL 2.0 Specification examples{{% /staticref %}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{% staticref "zip/sbsi_002.zip" "newtab" %}}GeneticToggleSwitch Systems Biology Model Example{{% /staticref %}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210239.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005210239.md deleted file mode 100644 index d4dc346e4..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210239.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL file example{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch example{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{% staticref "zip/GeneticToggleSwitch.zip" "newtab" %}}Genetic Toggle Switch example{{% /staticref %}}\ -{{% staticref "zip/four-input AND gate Example.zip" "newtab" %}}Four-input AND gate example{{% /staticref %}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{% staticref "zip/SBOL Specs Examples.zip" "newtab" %}}SBOL 2.0 Specification examples{{% /staticref %}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{% staticref "zip/sbsi_002.zip" "newtab" %}}GeneticToggleSwitch Systems Biology Model example{{% /staticref %}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -{{% staticref "zip/sb400135t_si_001.zip" "newtab" %}Directed Acyclic Genetic Circuit examples{{% /staticref %}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210319.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005210319.md deleted file mode 100644 index dbd5d4c27..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210319.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL file example{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch example{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{% staticref "zip/GeneticToggleSwitch.zip" "newtab" %}}Genetic Toggle Switch example{{% /staticref %}}\ -{{% staticref "zip/four-input AND gate Example.zip" "newtab" %}}Four-input AND gate example{{% /staticref %}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{% staticref "zip/SBOL Specs Examples.zip" "newtab" %}}SBOL 2.0 Specification examples{{% /staticref %}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{% staticref "zip/sbsi_002.zip" "newtab" %}}GeneticToggleSwitch Systems Biology Model example{{% /staticref %}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -{{% staticref "zip/sb400135t_si_001.zip" "newtab" %}}Directed Acyclic Genetic Circuit examples{{% /staticref %}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210958.md b/.history/hugo_themes/content/DataModel-Examples/_index_20201005210958.md deleted file mode 100644 index 0153ec580..000000000 --- a/.history/hugo_themes/content/DataModel-Examples/_index_20201005210958.md +++ /dev/null @@ -1,56 +0,0 @@ ---- -title: SBOL Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### 2019 (Data Model Examples) - -{{< cite page="/publication/roehner-specifying-2019" view="3" >}} - -### SBOL 2.0 Examples - -{{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}} - -{{% staticref "zip/RepressionModel.zip" "newtab" %}}CRISPR Repression Model SBOL file example{{% /staticref %}} - -{{< cite page="/publication/mclaughlin-visbol-2016" view="1" >}} - -{{% staticref "zip/Toggle_Switch.zip" "newtab" %}}VisBol Toggle Switch example{{% /staticref %}} - -{{< cite page="/publication/nguyen-converter-2016" view="1" >}} - -{{% staticref "zip/GeneticToggleSwitch.zip" "newtab" %}}Genetic Toggle Switch example{{% /staticref %}}\ -{{% staticref "zip/four-input AND gate Example.zip" "newtab" %}}Four-input AND gate example{{% /staticref %}} - -{{< cite page="/publication/bartley-bbf-2015" view="1" >}} - -{{% staticref "zip/SBOL Specs Examples.zip" "newtab" %}}SBOL 2.0 Specification examples{{% /staticref %}} - -{{< cite page="/publication/roehner-generating-2015" view="1" >}} - -{{% staticref "zip/sbsi_002.zip" "newtab" %}}GeneticToggleSwitch Systems Biology Model example{{% /staticref %}} - -{{< cite page="/publication/roehner-directed-2014" view="1" >}} - -{{% staticref "zip/sb400135t_si_001.zip" "newtab" %}}Directed Acyclic Genetic Circuit examples{{% /staticref %}} - -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. - -### SBOL 1.1 Examples - -{{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}} - -{{% staticref "zip/nbt_pIKE_pTAK_cassettes.zip" "newtab" %}}NBT Examples: pIKE and pTAK_cassettes{{% /staticref %}}\ -{{% staticref "zip/nbt_pIKE_pTAK_partial_cassettes.zip" "newtab" %}}NBT Example: pIKE and pTAK partial cassettes{{% /staticref %}}\ -{{% staticref "zip/nbt_pIKE_pTAK_toggle_switches.zip" "newtab" %}}NBT Example: pIKE and pTAK toggle switches{{% /staticref %}} diff --git a/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105329.md b/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105329.md deleted file mode 100644 index 8a48d2664..000000000 --- a/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105329.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105649.md b/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105649.md deleted file mode 100644 index 3013f2512..000000000 --- a/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105649.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Libraries - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Ontology/_index_20201202162653.md b/.history/hugo_themes/content/DataModel-Ontology/_index_20201202162653.md deleted file mode 100644 index e49fbc42d..000000000 --- a/.history/hugo_themes/content/DataModel-Ontology/_index_20201202162653.md +++ /dev/null @@ -1,58 +0,0 @@ ---- -title: SBOL Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL-OWL ontology provides a set of controlled terms that are used to describe genetic circuit designs using SBOL. Terms are included for the followings. - -* Descriptions of SBOL entities (e.g. [“ComponentDefinition“](https://dissys.github.io/sbol-owl/sbol-owl.html#ComponentDefinition)) that are exchanged electronically. Constraints and validation rules that are enforced on SBOL entities are also captured as part of the ontology. -* SBOL entities (e.g. [“TopLevel“](https://dissys.github.io/sbol-owl/sbol-owl.html#TopLevel)) that are not serialised but are used to group different SBOL entities. SBOL-OWL exposes these entities to semantic reasoning tools via parent-child relationships. -* Terms (e.g. [“inline“](https://dissys.github.io/sbol-owl/sbol-owl.html#inline)) that are used to restrict values of SBOL entities. -* Properties (e.g. [“sequence“](https://dissys.github.io/sbol-owl/sbol-owl.html#sequence)) linking SBOL entities to accepted values. -* Metadata terms (e.g. [“Promoter“](https://dissys.github.io/sbol-owl/sbol-owl.html#Promoter)) for commonly used descriptions of design entities. Such terms may require the use of several SBOL entities and properties. - -### Browse - -[Browse the SBOL-OWL terms via an HTML page.](https://dissys.github.io/sbol-owl/sbol-owl.html) - -### Download - -SBOL-OWL is available in different formats. - -* {{% staticref "docs/sbol.owl" "newtab" %}}OWL file{{% /staticref %}} -* {{% staticref "docs/sbol.rdf" "newtab" %}}RDF file{{% /staticref %}} -* {{% staticref "docs/sbol.omn" "newtab" %}}OMN file (Manchester Syntax){{% /staticref %}} - -### Semantic reasoning - -SBOL-OWL can be combined with any SBOL document to query genetic circuit designs using semantic queries. The semanticSBOL Java library has been developed to facilitate this process. The resulting files can then be submitted to existing reasoners for semantic inferencing. The library also includes methods to check the consistency of SBOL files, to execute semantic queries, and to list inconsistencies programmatically. - -[Click here](https://github.com/dissys/sbol-owl) to access the documentation and examples to use the library programmatically. - -The semanticSBOL library can be used from the command line to merge SBOL files with the SBOL-OWL ontology. - -Usage: sbolowl_file sboldesign_file merged_file - -* `sbolowl_file: The RDF version of the SBOL-OWL ontology` -* `sboldesign_file: An SBOL file including genetic circuit designs` -* `merged_file: The output file name` - -Example: - -`java -cp semanticSBOL-1.0-SNAPSHOT-jar-with-dependencies.jar dissys.keele.ac.uk.RDFMerger sbol.rdf mapsto.rdf mapsto_sbolowl_consistent.rdf` - -### Download semanticSBOL - -{{% staticref "zip/semanticSBOL-1.0-SNAPSHOT-jar-with-dependencies.jar" "newtab" %}}Click here{{% /staticref %}} to download the standalone sbol-sem Java library as a single file including all the dependencies.\ -{{% staticref "zip/semanticSBOL-1.0-SNAPSHOT.jar" "newtab" %}}Click here{{% /staticref %}} to download the sbol-sem Java library only. Dependencies are not included. \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Specification/_index_20201123170456.md b/.history/hugo_themes/content/DataModel-Specification/_index_20201123170456.md deleted file mode 100644 index 4ade051e6..000000000 --- a/.history/hugo_themes/content/DataModel-Specification/_index_20201123170456.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -title: SBOL Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - -### SBOL Data Model Specification - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Specification/_index_20201123170921.md b/.history/hugo_themes/content/DataModel-Specification/_index_20201123170921.md deleted file mode 100644 index 836576e2b..000000000 --- a/.history/hugo_themes/content/DataModel-Specification/_index_20201123170921.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - -### SBOL Data Model Specification - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Specification/_index_20201123170954.md b/.history/hugo_themes/content/DataModel-Specification/_index_20201123170954.md deleted file mode 100644 index adec5fe38..000000000 --- a/.history/hugo_themes/content/DataModel-Specification/_index_20201123170954.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - -### SBOL Data Model Specification - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/BBFRFC93.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Specification/_index_20201123171707.md b/.history/hugo_themes/content/DataModel-Specification/_index_20201123171707.md deleted file mode 100644 index 47856e07d..000000000 --- a/.history/hugo_themes/content/DataModel-Specification/_index_20201123171707.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - -### SBOL Data Model Specification - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Specification/_index_20201123172017.md b/.history/hugo_themes/content/DataModel-Specification/_index_20201123172017.md deleted file mode 100644 index 8ce14860f..000000000 --- a/.history/hugo_themes/content/DataModel-Specification/_index_20201123172017.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - - -### SBOL Data Model Specification - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Specification/_index_20201215202328.md b/.history/hugo_themes/content/DataModel-Specification/_index_20201215202328.md deleted file mode 100644 index 1a8c2204e..000000000 --- a/.history/hugo_themes/content/DataModel-Specification/_index_20201215202328.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -title: SBOL Data Model Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - -___ - - -| **3.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **3.0.0**
Condenses and simplifies previous versions of SBOL, separates sequence features from part/sub-part relationships, renames ComponentDefinition/Component to Component/SubComponent, merges Component and Module classes, ensuring consistency between data model and ontology terms, extends the means to define and reference SubComponents, refines requirements on object URIs, enables graph-based serialization, moves Systems Biology Ontology (SBO) for Component types, makes all sequence associations explicit, makes interfaces explicit, generalizes SequenceConstraints into a general structural Constraint class, and expands the set of allowed constraints.| {{% staticref "docs/SBOL3.0specification.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/ahead-of-print/article-10.1515-jib-2020-0017/article-10.1515-jib-2020-0017.xml) | - -| **2.x.x Release** | [Library Implementation]({{< relref "libraries" >}}) | | -|---|---|---| -| **2.3.0**
Includes means of succinctly representing sequence modifications, an extension to support organization and attachment of experimental data, and an extension for describing numerical parameters of design elements. The new version also includes specifying types of synthetic biology activities, unambiguous locations for sequences with multiple encodings, and refinement of a number of validation rules. | {{% staticref "docs/SBOL2.3.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/16/2/article-20190025.xml) | -| **2.2.1**
Clarification on ontology terms on roles for proteins and small molecules, refining a number of validation rules, and illustrating a design for combinatorial derivations using Prov-O. | {{% staticref "docs/SBOL-data-model-2.2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
Introduces new classes for representing combinatorial genetic designs, physical implementations of genetic designs, and attachments to external files. It also adds best practices for using existing classes to encode provenance for the Design-Build-Test-Learn cycle. | {{% staticref "docs/BBF-RFC114-SBOL2.2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20180001.xml) | -| **2.1.0**
A backwards-compatible release extending the data model and updating ontology terms and best practices. | {{% staticref "docs/BBF-RFC112-SBOL2.1.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/13/3/article-p30.xml) | -| **2.0.1**
An updated version of SBOL 2.0 data model to refine validation rules. | {{% staticref "docs/SBOLv2.0.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
An extension of version 1.1 data model to allow flexibility and extendibility of the following: Represent non-DNA structural components of a biological design; Describe the behavioral aspects of a biological design; Associate structure and function to a design; Support rich annotation of biological designs. | {{% staticref "docs/BBF-RFC108-SBOL2.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/12/2/article-p902.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.1.0**
Version 1.1.0 of the SBOL core data model is limited to the description of discrete segments of DNA, called DNA components. To remove ambiguity when specifying the design of synthetic DNA, the information about DNA components is structured. DNA components described using the SBOL core data model may have an associated DNA sequence, or may be left as abstract descriptions. This flexibility allows for the description of DNA component designs which have not yet been realized, as well as those which are specific implementations of that design. | {{% staticref "docs/BBFRFC87.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | -| **1.0.0**
Define the vocabulary that contain a set of preferred terms and the core data model composed of a common computational representation, to enable the electronic exchange of information describing DNA components used in synthetic biology. | {{% staticref "docs/SBOLv1.0.0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.nature.com/articles/nbt.2891) | \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-Validator/_index_20200921105336.md b/.history/hugo_themes/content/DataModel-Validator/_index_20200921105336.md deleted file mode 100644 index 8a48d2664..000000000 --- a/.history/hugo_themes/content/DataModel-Validator/_index_20200921105336.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Validator/_index_20200921105400.md b/.history/hugo_themes/content/DataModel-Validator/_index_20200921105400.md deleted file mode 100644 index 8a48d2664..000000000 --- a/.history/hugo_themes/content/DataModel-Validator/_index_20200921105400.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Validator/_index_20200921105709.md b/.history/hugo_themes/content/DataModel-Validator/_index_20200921105709.md deleted file mode 100644 index c8d3220e1..000000000 --- a/.history/hugo_themes/content/DataModel-Validator/_index_20200921105709.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Validator - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-Validator/_index_20200921115449.md b/.history/hugo_themes/content/DataModel-Validator/_index_20200921115449.md deleted file mode 100644 index efd5f8c9e..000000000 --- a/.history/hugo_themes/content/DataModel-Validator/_index_20200921115449.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: SBOL Validator - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Sbol Validator \ No newline at end of file diff --git a/.history/hugo_themes/content/DataModel-about/_index_20201203125647.md b/.history/hugo_themes/content/DataModel-about/_index_20201203125647.md deleted file mode 100644 index 948ef3f37..000000000 --- a/.history/hugo_themes/content/DataModel-about/_index_20201203125647.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-about/_index_20201215202607.md b/.history/hugo_themes/content/DataModel-about/_index_20201215202607.md deleted file mode 100644 index ab29cd22b..000000000 --- a/.history/hugo_themes/content/DataModel-about/_index_20201215202607.md +++ /dev/null @@ -1,50 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLlogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -The SBOL data standard is a data exchange representation for synthetic biology designs. Its goal is to improve the efficiency of data exchange and reproducibility of synthetic biology research. SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard further describes the rules and best practices on how to use this data model and populate it with relevant design details. SBOL uses existing Semantic Web practices and resources, such as Uniform Resource Identifiers (URIs) and ontologies, to unambiguously identify and define genetic design elements. The definition of the data model and associated format, the rules on the addition of data within the format and the representation of this in electronic data files are intended to make the SBOL standard a useful means of promoting global data exchange between laboratories and between software programs. - -### Usage - -SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. -This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). - -### Download SBOL Data Library - -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-about/index_20200921105809.md b/.history/hugo_themes/content/DataModel-about/index_20200921105809.md deleted file mode 100644 index 8a48d2664..000000000 --- a/.history/hugo_themes/content/DataModel-about/index_20200921105809.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-about/index_20200921105916.md b/.history/hugo_themes/content/DataModel-about/index_20200921105916.md deleted file mode 100644 index 8a48d2664..000000000 --- a/.history/hugo_themes/content/DataModel-about/index_20200921105916.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and (SEED 2018 SBOL presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx]. - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-about/index_20200921110246.md b/.history/hugo_themes/content/DataModel-about/index_20200921110246.md deleted file mode 100644 index 296dad382..000000000 --- a/.history/hugo_themes/content/DataModel-about/index_20200921110246.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through (IWBDA 2019 SBOL Workshop presentation)[https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf] and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-about/index_20200921110317.md b/.history/hugo_themes/content/DataModel-about/index_20200921110317.md deleted file mode 100644 index a09d91155..000000000 --- a/.history/hugo_themes/content/DataModel-about/index_20200921110317.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/DataModel-about/index_20200921110334.md b/.history/hugo_themes/content/DataModel-about/index_20200921110334.md deleted file mode 100644 index a09d91155..000000000 --- a/.history/hugo_themes/content/DataModel-about/index_20200921110334.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Data - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. - -The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology. For a quick introduction to SBOL, please browse through [IWBDA 2019 SBOL Workshop presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/IWBDA2019.pdf) and [SEED 2018 SBOL presentation](https://github.com/SynBioDex/Community-Media/blob/master/2018/SEED/Workshop-Introduction.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/Visual/_index_20200819115351.md b/.history/hugo_themes/content/Visual/_index_20200819115351.md deleted file mode 100644 index c2e31856c..000000000 --- a/.history/hugo_themes/content/Visual/_index_20200819115351.md +++ /dev/null @@ -1,206 +0,0 @@ ---- -title: The SBOL Community - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL GitHub repository can be accessed here. - -The SBOL community works actively on the SBOL data model and visual standard, participates in online discussions, and meets semi-annually. We represent over 170+ members from 17 different countries, 42 institutions, and 28 different industries. Many of our members are also actively involved in other standards communities, like the Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN). - - -To join our growing community, contact the SBOL Editors at sbol-editors@googlegroups.com. - -### Members - -| Name | Affiliation | Country | -|----------------------------|-----------------------------------------------------------|-----------------| -| Alex McFadden | Zymergen Inc | USA | -| Alexis Casas | Imperial College London | UK | -| Alice Boo | Imperial College London | UK | -| Ana Delgado | University of Oslo | Norway | -| Angel Moreno | Newcastle University | UK | -| Anil Wipat | Newcastle University | UK | -| Anton Kulaga | Computation Biology of Aging Group | Romania | -| Augustin Luna | Dana-Farber Cancer Institute | USA | -| Benjamin Aleritsch | Technical University of Munich | Germany | -| Benjamin Chan | Boston University | USA | -| Bill Yang | Newcastle University | UK | -| Birjesh Kumar | ICGEB, Delhi | India | -| Brad Chapman | Ginkgo Bioworks | USA | -| Brigitte Dreger | BioRender Inc. | Toronto | -| Bryan Bartley | BBN Technologies | USA | -| Bryan Der | MIT | USA | -| Carlog Olguin | Autodesk | USA | -| Cesar Rodriguez | Florida State University | USA | -| Chih-Hsien Yang | National Yang Ming University | Taiwan | -| Chris Anderson | University of California, Berkeley | USA | -| Chris Myers | University of Utah | USA | -| Chris Walker | Macquarie University | Australia | -| Christian Atallah | Newcastle University | UK | -| Christian Nyumbayire | Independent | Italy | -| Christian Olsen | Centers for Disease Control and Prevention | USA | -| Christopher Voigt | MIT | USA | -| Craig Struble | Inscripta Inc. | USA | -| Curtis Madsen | Sandia National Laboratories | USA | -| DA Ball | University of Tennessee | USA | -| Daniel Dixon | University of Bristol | UK | -| Daniel Sutantyo | Macquarie University | USA | -| Dany Entezari | University of Edinburgh | UAE | -| Darren Platt | Amyris | USA | -| David Lomelin | Synthetic Genomics | USA | -| David Ross | NIST | USA | -| David Zong | Rice University | USA | -| Douglas Densmore | Boston University | USA | -| Drew Endy | Stanford University & BIOFAB | USA | -| Eduardo Abeliuk | Teselagen | USA | -| Egils Stalidzans | University of Latvia | Latvia | -| Elizabeth Robinson | UT Austin | USA | -| Elizabeth Strychalsky | NIST | USA | -| Emek Demir | Memorial Sloan Kettering Cancer Center | USA | -| Eric van der Helm | SNIPRBIOME | Denmark | -| Eric Young | Worchester Polytechnic Institute | USA | -| Ernst Oberortner | Lawrence Berkeley National Labs | USA | -| Evan Appleton | Boston University | USA | -| Evren Sirin | Clark & Parsia | USA | -| Falk Schreiber | University of Konstanz | Germany | -| Falk Shreiber | University of Konstanz | Germany | -| Florencio Mazzoldi | Ginkgo Bioworks | USA | -| Gary Bader | University of Toronto | Canada | -| Geoff Baldwin | Imperial College London | USA | -| George McArthur | GenoCAD | USA | -| Goksel Misirli | Keele University | UK | -| Gonzalo Vidal Pena | University of Chile | Chile | -| Grimaldo Elias Urena M. | Technological University of Panama | Panama | -| Guillermo Yanez Feliu | Rudge Lab, PUC. | Chile | -| Guy Bart-Stan | Imperial College London | UK | -| Harold Fellermann | Newcastle University | UK | -| Hasan Baig | Independent | Pakistan | -| Hasan Baig | University of Connecticut | USA | -| Hector Plahar | Joint Bioenergy Institute (JBEI) | USA | -| Henry Holbrook | Benchling | USA | -| Herbert Sauro | University of Washington | USA | -| Hiroyuki Kuwahara | KAUST | Saudi Arabia | -| Huaiyu Mi | USC | USA | -| Igor Durovic | University of Utah | USA | -| Isabel Pötzsch | University of Cambridge | UK | -| Jackie Quinn | Google | USA | -| Jake Beal | BBN Technologies | USA | -| James Diggans | Twist Bioscience | USA | -| James Mglaughlin | Newcastle University | UK | -| James Scott Brown | Imperial College London | UK | -| James Skelton | NEwcastle University | UK | -| Jan Madsen | DTU | Denmark | -| Jared Earl | University of Utah | USA | -| Jason Mohabir | Columbia University | USA | -| Jasper Koehorst | Wageningen University | Netherlands | -| Jean Peccoud | Colorado State University | USA | -| Jeanet Mante | University of Utah | USA | -| Jeffrey Barrick | UT Austin | USA | -| Jeffrey Elhai | Virginia Commonwealth University | USA | -| Jenhan Tao | University of California, San Diego | USA | -| Jennifer Hallinan | Macquarie University | Australia | -| John Gennari | University of Washington | USA | -| John Meng | Lawrence Berkeley National Labs | USA | -| John T. Sexton | Independent | USA | -| Jonathan Karr | Mount Sinai | USA | -| Joseph Hellerstein | University of Washington | USA | -| Joshua Rawlins | UW-Madison | USA | -| Juston Farlow | Serotiny | USA | -| Jyotsna Venkata | St. Joseph's Institute of Technology | India | -| Kelvin Clancy | BioCoder Consulting | USA | -| Kevin Clancy | BioCoder Consulting | USA | -| Kiri Choi | University of Washington | USA | -| Kirtan Dave | Sardar Patel University | India | -| Kyle Medley | University of Washington | USA | -| Laura Adam | Virginia Bioinformatics Institute | USA | -| Linda Kahl | Stanford University | USA | -| Linh Huynh | UC Davis | USA | -| Linhao Meng | Zhejiang University | China | -| Maciek Jacek Swat | CSIRO | Australia | -| Mandy Wilson | Virginia Tech | USA | -| Marc Juul | BIOFAB | USA | -| Marco Castelejin | VTT Technical Research Centre | Finland | -| Mario Marchiso | Tianjin University | China | -| Marta Vazquez-Vilar | CSIC (Consejo Superior de Investigaciones Científicas) | Spain | -| Matthew Crowther | Newcastle University | UK | -| Matthew Lux | Army Research Lab | USA | -| Matthew Pocock | Newcastle University | UK | -| Matthieu Bultelle | Imperial College London | UK | -| Maurice Ling | AdvanceSyn Private Limited | Singapore | -| Maxwell Bates | Autodesk | USA | -| Meher Samineni | REI | USA | -| Michael Zhang | Google | USA | -| Michal Galdzicki | Arzeda | USA | -| Michihiro Araki | Kobe University | Japan | -| Mike Bissell | Shipyard Toolchains | USA | -| Mike Fero | Teselagen | USA | -| Nathan Hillson | Joint Bioenergy Institute | USA | -| Nathan Wilkenson | University of Utah | USA | -| Neil Swainston | Manchester BioFactory Ltd. | UK | -| Neil Thompson | Massachusetts Institute of Technology | USA | -| Nicholas Roehner | BBN Technologies | USA | -| Nicolas Le Novere | EMBL-EBI | UK | -| Owen Gilfellon | Newcastle University | UK | -| Pablo Carbonell | Manchester Institute of Biotechnology | USA | -| Patrick Yizhi | University of Edinburgh | UK | -| Pedro Fontanarrosa | University of Utah | USA | -| Peter Dun | Stanford University | USA | -| Philip Bradley | Newcastle University | UK | -| Prashant Vaidyanathan | Microsoft Inc. | UK | -| Prem Prakash | BITS Pilani | India | -| Rahmi Lale | NTNU | Norway | -| Raik Gruenberg | KAUST | Saudi Arabia | -| Richard Kitney | Imperial College London | UK | -| Robert Cox | Kobe University | Japan | -| Robert Sidney Cox | Robert Sydney Cox III Co. | USA | -| Robin Emig | Augment Bioworks | USA | -| S. Castillo Hair | Rice University | USA | -| Sarah Munro | NIST | USA | -| Sean Leonard | University of Texas at Austin | USA | -| Shamseen Rahman | Boston University | USA | -| Shashank | IIT Delhi | India | -| Shyam Bhakta | UC Berkeley | USA | -| SSBSS Summer School | SSBSS Summer School | Italy | -| Stefan Claesen | Visbion Ltd. | UK | -| Stuart Moodie | Eight Pillars Ltd. | Edinburgh | -| Sunwoo Kang | Stanford University | USA | -| Swapnil Bhatiya | Catalog Inc | USA | -| Thomas Gorochowski | Bio Compute Lab | UK | -| Tim Fiori | University of Australia | Australia | -| Todd Slaby | Lawrence Berkeley National Labs | USA | -| Tramy Nguyen | University of Utah | USA | -| Tyler Camp | University of Texas at Austin | USA | -| Ueno Masayoshi | Kitasato University | Japan | -| Umesh P | University of Kerala | India | -| Vinod Tek | Imperial College London | UK | -| Vishvesh Kulkarni | University of Warwick | UK | -| Vittorio Bartoli | University of Bristol | UK | -| Walid El-Sharoud | Mansoura University | Egypt | -| William Byrd | University of Alabama | USA | -| Xin Gao | KAUST | Saudi Arabia | -| Xuefeng Cui | University of Washington | USA | -| Yaman Sirin | BBN Technologies | USA | -| Yogev Debbi | Genome Compiler | USA | -| Ysis Tarter | Amyris | USA | -| Zach Palchick | Zymergen | USA | -| Zach Zundel | University of Utah | USA | -| Zhen Zhang | University of Utah | USA | -| Zhiyang Ong | Texas A&M University | USA | -| Mudasir Shaikh | Habib University | Pakistan | -| Ritwik Agarwal | Iiit Hyderabad | India | -| Ming Hia | Imperial College | UK | -| Zhiyang Ong | Texas A&M University | USA | -| Ana Delgado | University of Oslo | Norway | -| William Poole | Caltech | USA | -| Stephanie Nicole Call | University of Massachusetts Amherst | USA | diff --git a/.history/hugo_themes/content/Visual/_index_20200819115544.md b/.history/hugo_themes/content/Visual/_index_20200819115544.md deleted file mode 100644 index fcac4c9ef..000000000 --- a/.history/hugo_themes/content/Visual/_index_20200819115544.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -title: SBOL Visual - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -#### Purpose -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the IWBDA 2019 SBOL Visual presentation. \ No newline at end of file diff --git a/.history/hugo_themes/content/Visual/_index_20200819115651.md b/.history/hugo_themes/content/Visual/_index_20200819115651.md deleted file mode 100644 index fcac4c9ef..000000000 --- a/.history/hugo_themes/content/Visual/_index_20200819115651.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -title: SBOL Visual - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -#### Purpose -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the IWBDA 2019 SBOL Visual presentation. \ No newline at end of file diff --git a/.history/hugo_themes/content/Visual/_index_20200819164025.md b/.history/hugo_themes/content/Visual/_index_20200819164025.md deleted file mode 100644 index 8acd84660..000000000 --- a/.history/hugo_themes/content/Visual/_index_20200819164025.md +++ /dev/null @@ -1,19 +0,0 @@ ---- -title: SBOL Visual - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). diff --git a/.history/hugo_themes/content/Visual/_index_20200819164146.md b/.history/hugo_themes/content/Visual/_index_20200819164146.md deleted file mode 100644 index 94de26a70..000000000 --- a/.history/hugo_themes/content/Visual/_index_20200819164146.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: SBOL Visual - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. diff --git a/.history/hugo_themes/content/community-governance/_index_20200819113224.md b/.history/hugo_themes/content/community-governance/_index_20200819113224.md deleted file mode 100644 index c2904f451..000000000 --- a/.history/hugo_themes/content/community-governance/_index_20200819113224.md +++ /dev/null @@ -1,180 +0,0 @@ ---- -title: Governance - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: - -SBOL should be free and open standard, developed by an open and inclusive processes. -SBOL is a community that believes in fostering, cultivating and preserving a culture of diversity and inclusion. -Leaders of the SBOL community are expected to actively foster a safe environment where all participants feel comfortable making their voices heard. -Leadership from new and diverse voices should be actively developed, including by participation in working groups and by public speaking at workshops. - -## SBOL Organization -The SBOL community has the following organization: - -* SBOL Development Group: general body comprising all members of the SBOL community, and ultimate authority -* Ad-Hoc Subgroups: portions of the general development group focused on particular aspects of SBOL development. -* SBOL Editors: operational executives for the community -* SBOL Chair and Steering Committee: strategic planning and guidance for the community -* SBOL Industrial Consortium: a pre-competitive organization of companies (or similar) investing in the SBOL community - -## SBOL Development Group -Membership in the SBOL Development Group is open to all interested parties. Individuals interested in joining the group should contact [the editors](mailto:sbol-editors@googlegroups.com). - -The SBOL Development Group as a whole is the ultimate authority and source of legitimacy for SBOL standards decisions. All elections, standards changes, and governance changes are voted on by the SBOL Development Group according to the procedures below. - -The primary means of communication for the SBOL Development Group is via the sbol-dev Google Group. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list. - -SBOL workshops should be held twice per year. These may be stand-alone workshops or in combination with another event, but must provide ample time for attending members to hold focused discussions on the development of SBOL. - -All members of the SBOL Development Group are encouraged (but not required) to: - -* Attend the SBOL Workshops and other meetings -* Participate in discussions on SBOL mailing lists -* Support the SBOL standard in any tools and systems they work on -* Provide constructive feedback for improving the standard - -## Ad-Hoc Subgroups -Certain activities of the SBOL community are expected to either generate noticeably higher volumes of communication (e.g., software development and support) or to address topics expected to be of interest only to certain special interest groups. When deemed appropriate, ad-hoc subgroups may be created for addressing such topics. - -Subgroups must communicate via open lists that may be readily accessed and joined by any member of the SBOL Development Group. Any communication regarding standards changes, however, should be migrated back to the SBOL Development Group mailing list. - -## SBOL editors -As a matter of pragmatism, many organizational decisions and actions are delegated to an elected group of SBOL Editors, so named because their primary responsibility is ensuring the effective curation of documents for the community. - -The responsibilities of the SBOL Editors are: - -* Equitably representing the community in voting, documents, and guidance of discussion. -* Curation and dissemination of the SBOL standards and related documents (including writing, editing, and coordinating changes). -* Maintaining an open and structured process by which members of the SBOL Development Group can modify and improve SBOL standards (including timely implementation of tracking, processing, responding to, and organizing voting on change proposals). -* Ensuring effective development and maintenance of official SBOL software libraries and associated documentation and tutorials. -* Coordinating scholarly publications and ensuring proper attribution of contributions. -* Running elections and other community votes. -* Organization (or delegation) of SBOL Workshops and other events. -* Maintaining community infrastructure, including: the SBOL web site, source code repositories, mailing lists - -The SBOL Editors shall hold weekly meetings to coordinate their execution of these responsibilities. These meetings should be open, and their minutes should be reported to the SBOL Development Group. - -The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. - -SBOL Editors are elected by a community vote, following the process below. Editors serve for a two year term and cannot serve terms consecutively. To maximize continuity, editors’ terms should be desynchronized. There are 5 editorial positions, currently held by: - -* James McLaughlin, Newcastle University -* Pedro Fontanarrosa, University of Utah -* Vishwesh Kulkarni, University of Warwick -* Prashant Vaidyananthan, Microsoft Research -* Hasan Baig, University of Connecticut - -Previous SBOL Editors include: Zach Palchik (Zymergen), Curtis Madsen (Sandia National Labs), Nicholas Roehner (BBN Technologies), Angel Goñi Moreno (Newcastle University), Umesh P (Kerala Technological University), Tramy Nguyen (University of Utah), James McLaughlin (Newcastle University), Robert Sidney Cox (Kobe University), Raik Grunberg (University of Montreal), Jacob Beal (BBN Technologies), Bryan Bartley (University of Washington), Kevin Clancy (ThermoFisher), Michal Galdzicki (University of Washington),
 Goksel -Misirli (Newcastle University), Ernst Oberortner (Boston University),
 Matthew Pocock, (Newcastle University), Jacqueline Quinn (Google), Cesar Rodriguez (Autodesk),
Mandy Wilson (Virginia Bioinformatics Institute). - -## SBOL Chair and Steering Committee -The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. - -The SBOL Chair is the head of the SBOL Steering Committee. The SBOL Chair is responsible for ensuring regular steering committee meetings are held, for effective moderation of these meetings, and for being an advertised public point of contact for outside organizations. - -The SBOL Chair is elected by a community vote, following the process below. Chairs serve for a four year term. In order to ensure a smooth working relationship between the SBOL Chair and SBOL Editors, the SBOL Editors can remove a chair by a no-confidence vote amongst the SBOL Editors at any time. - -The rest of the SBOL Steering Committee are appointed (and removed) by the SBOL Chair. The Steering Committee has no fixed size or fixed term, but should generally comprise the set of PI-level members who are strongly active, have a strong stake in SBOL, and are willing to assume community leadership responsibilities. - -The SBOL Steering Committee shall hold monthly meetings to coordinate around strategic issues for the community (e.g., funding, setting key priorities and goals). These meetings should be open, and their minutes should be reported to the SBOL Development Group. The SBOL Steering Committee should also convene an external advisory board to help maintain strategic links with other communities and to obtain useful advice in guiding the community. - -The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. - -The SBOL current chair: - -**Chris Myers (May, 2019-), University of Utah** - -Previous Chairs: - -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Kevin Clancy, Synthetic Genomics, Inc. -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Utah -* Ernst Oberortner, DOE Joint Genome Institute (JGI) -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Panel is currently (listed alphabetically): - -* Prof. Matthew Chang, National University of Singapore -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Traci Haddock, iGEM Foundation -* Prof. Richard Kitney, Imperial College London -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University -* Prof. Chris Voigt, Massachusetts Institute of Technology - -## SBOL Industrial Consortium -The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. -As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium shall be free, open, and support the core values of the SBOL community. - -The SBOL Industrial Consortium will organize an Industrial Advisory Board to provide an industrial perspective on SBOL. The SBOL Chair shall hold quarterly meetings with the Industrial Advisory Board. These meetings (which may co-occur with Steering Committee Meetings) should be open and their minutes should be reported to the SBOL Development Group. - -Subject to these constraints, the SBOL Industrial Consortium is otherwise organized independently and operates under its own internal governance. Similarly, membership in the SBOL Industrial Consortium neither implies nor impairs membership in the SBOL Development Group. - -## Voting Procedures - -#### Elections Process: -Before any election, there is a nomination period of 5 working days. -All members of the SBOL Development Group are eligible for all offices (except those that are term-limited). -Any member can self-nominate or can nominate any other member. -Voting runs for 5 working days, starting at the end of the nomination period. All members of the SBOL Development Group are eligible to vote. -Candidates are elected by plurality. - -#### Voting process: -1. Any member of the SBOL Developers Group can submit an SBOL Enhancement Proposal (SEP) to the editors and/or to the community at large. See [SEP #1](https://github.com/SynBioDex/SEPs/issues/1) for a description of when and how to write and submit an SEP. - -2. SBOL editors are expected to move a given SEP draft to a vote once they agree that there has been sufficient debate. However, any member of the SBOL Developers Group can initiate the vote as long as one other member of the group seconds the motion. - -3. SBOL Editors post a voting form (see below), for a final discussion period of 2 working days. - -4. Voting runs for 5 working days, starting at the end of the discussion period. All members of the SBOL Development Group are eligible to vote. - -5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. - -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. - 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. - 2. The reasons for decisions must be recorded with the results of the vote. - 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. - - -#### Voting form must: - -1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” -3. Provide the following options for the vote: - * accept — vote to accept the SEP - * reject — vote to reject the SEP - * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). - -#### Ground-rules for moderating discussions in SBOL breakout sessions - -1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. -2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. -4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” -5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. -6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/.history/hugo_themes/content/community-governance/_index_20201009090324.md b/.history/hugo_themes/content/community-governance/_index_20201009090324.md deleted file mode 100644 index 03505ba47..000000000 --- a/.history/hugo_themes/content/community-governance/_index_20201009090324.md +++ /dev/null @@ -1,180 +0,0 @@ ---- -title: Governance - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: - -* SBOL should be free and open standard, developed by an open and inclusive processes. -* SBOL is a community that believes in fostering, cultivating and preserving a culture of diversity and inclusion. -* Leaders of the SBOL community are expected to actively foster a safe environment where all participants feel comfortable making their voices heard. -* Leadership from new and diverse voices should be actively developed, including by participation in working groups and by public speaking at workshops. - -## SBOL Organization -The SBOL community has the following organization: - -* SBOL Development Group: general body comprising all members of the SBOL community, and ultimate authority -* Ad-Hoc Subgroups: portions of the general development group focused on particular aspects of SBOL development. -* SBOL Editors: operational executives for the community -* SBOL Chair and Steering Committee: strategic planning and guidance for the community -* SBOL Industrial Consortium: a pre-competitive organization of companies (or similar) investing in the SBOL community - -## SBOL Development Group -Membership in the SBOL Development Group is open to all interested parties. Individuals interested in joining the group should contact [the editors](mailto:sbol-editors@googlegroups.com). - -The SBOL Development Group as a whole is the ultimate authority and source of legitimacy for SBOL standards decisions. All elections, standards changes, and governance changes are voted on by the SBOL Development Group according to the procedures below. - -The primary means of communication for the SBOL Development Group is via the sbol-dev Google Group. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list. - -SBOL workshops should be held twice per year. These may be stand-alone workshops or in combination with another event, but must provide ample time for attending members to hold focused discussions on the development of SBOL. - -All members of the SBOL Development Group are encouraged (but not required) to: - -* Attend the SBOL Workshops and other meetings -* Participate in discussions on SBOL mailing lists -* Support the SBOL standard in any tools and systems they work on -* Provide constructive feedback for improving the standard - -## Ad-Hoc Subgroups -Certain activities of the SBOL community are expected to either generate noticeably higher volumes of communication (e.g., software development and support) or to address topics expected to be of interest only to certain special interest groups. When deemed appropriate, ad-hoc subgroups may be created for addressing such topics. - -Subgroups must communicate via open lists that may be readily accessed and joined by any member of the SBOL Development Group. Any communication regarding standards changes, however, should be migrated back to the SBOL Development Group mailing list. - -## SBOL editors -As a matter of pragmatism, many organizational decisions and actions are delegated to an elected group of SBOL Editors, so named because their primary responsibility is ensuring the effective curation of documents for the community. - -The responsibilities of the SBOL Editors are: - -* Equitably representing the community in voting, documents, and guidance of discussion. -* Curation and dissemination of the SBOL standards and related documents (including writing, editing, and coordinating changes). -* Maintaining an open and structured process by which members of the SBOL Development Group can modify and improve SBOL standards (including timely implementation of tracking, processing, responding to, and organizing voting on change proposals). -* Ensuring effective development and maintenance of official SBOL software libraries and associated documentation and tutorials. -* Coordinating scholarly publications and ensuring proper attribution of contributions. -* Running elections and other community votes. -* Organization (or delegation) of SBOL Workshops and other events. -* Maintaining community infrastructure, including: the SBOL web site, source code repositories, mailing lists - -The SBOL Editors shall hold weekly meetings to coordinate their execution of these responsibilities. These meetings should be open, and their minutes should be reported to the SBOL Development Group. - -The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. - -SBOL Editors are elected by a community vote, following the process below. Editors serve for a two year term and cannot serve terms consecutively. To maximize continuity, editors’ terms should be desynchronized. There are 5 editorial positions, currently held by: - -* James McLaughlin, Newcastle University -* Pedro Fontanarrosa, University of Utah -* Vishwesh Kulkarni, University of Warwick -* Prashant Vaidyananthan, Microsoft Research -* Hasan Baig, University of Connecticut - -Previous SBOL Editors include: Zach Palchik (Zymergen), Curtis Madsen (Sandia National Labs), Nicholas Roehner (BBN Technologies), Angel Goñi Moreno (Newcastle University), Umesh P (Kerala Technological University), Tramy Nguyen (University of Utah), James McLaughlin (Newcastle University), Robert Sidney Cox (Kobe University), Raik Grunberg (University of Montreal), Jacob Beal (BBN Technologies), Bryan Bartley (University of Washington), Kevin Clancy (ThermoFisher), Michal Galdzicki (University of Washington), Goksel -Misirli (Newcastle University), Ernst Oberortner (Boston University), Matthew Pocock, (Newcastle University), Jacqueline Quinn (Google), Cesar Rodriguez (Autodesk), Mandy Wilson (Virginia Bioinformatics Institute). - -## SBOL Chair and Steering Committee -The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. - -The SBOL Chair is the head of the SBOL Steering Committee. The SBOL Chair is responsible for ensuring regular steering committee meetings are held, for effective moderation of these meetings, and for being an advertised public point of contact for outside organizations. - -The SBOL Chair is elected by a community vote, following the process below. Chairs serve for a four year term. In order to ensure a smooth working relationship between the SBOL Chair and SBOL Editors, the SBOL Editors can remove a chair by a no-confidence vote amongst the SBOL Editors at any time. - -The rest of the SBOL Steering Committee are appointed (and removed) by the SBOL Chair. The Steering Committee has no fixed size or fixed term, but should generally comprise the set of PI-level members who are strongly active, have a strong stake in SBOL, and are willing to assume community leadership responsibilities. - -The SBOL Steering Committee shall hold monthly meetings to coordinate around strategic issues for the community (e.g., funding, setting key priorities and goals). These meetings should be open, and their minutes should be reported to the SBOL Development Group. The SBOL Steering Committee should also convene an external advisory board to help maintain strategic links with other communities and to obtain useful advice in guiding the community. - -The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. - -The SBOL current chair: - -**Chris Myers (May, 2019-), University of Utah** - -Previous Chairs: - -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Kevin Clancy, Synthetic Genomics, Inc. -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Utah -* Ernst Oberortner, DOE Joint Genome Institute (JGI) -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Panel is currently (listed alphabetically): - -* Prof. Matthew Chang, National University of Singapore -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Traci Haddock, iGEM Foundation -* Prof. Richard Kitney, Imperial College London -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University -* Prof. Chris Voigt, Massachusetts Institute of Technology - -## SBOL Industrial Consortium -The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. -As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium shall be free, open, and support the core values of the SBOL community. - -The SBOL Industrial Consortium will organize an Industrial Advisory Board to provide an industrial perspective on SBOL. The SBOL Chair shall hold quarterly meetings with the Industrial Advisory Board. These meetings (which may co-occur with Steering Committee Meetings) should be open and their minutes should be reported to the SBOL Development Group. - -Subject to these constraints, the SBOL Industrial Consortium is otherwise organized independently and operates under its own internal governance. Similarly, membership in the SBOL Industrial Consortium neither implies nor impairs membership in the SBOL Development Group. - -## Voting Procedures - -#### Elections Process: -Before any election, there is a nomination period of 5 working days. -All members of the SBOL Development Group are eligible for all offices (except those that are term-limited). -Any member can self-nominate or can nominate any other member. -Voting runs for 5 working days, starting at the end of the nomination period. All members of the SBOL Development Group are eligible to vote. -Candidates are elected by plurality. - -#### Voting process: -1. Any member of the SBOL Developers Group can submit an SBOL Enhancement Proposal (SEP) to the editors and/or to the community at large. See [SEP #1](https://github.com/SynBioDex/SEPs/issues/1) for a description of when and how to write and submit an SEP. - -2. SBOL editors are expected to move a given SEP draft to a vote once they agree that there has been sufficient debate. However, any member of the SBOL Developers Group can initiate the vote as long as one other member of the group seconds the motion. - -3. SBOL Editors post a voting form (see below), for a final discussion period of 2 working days. - -4. Voting runs for 5 working days, starting at the end of the discussion period. All members of the SBOL Development Group are eligible to vote. - -5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. - -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. - 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. - 2. The reasons for decisions must be recorded with the results of the vote. - 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. - - -#### Voting form must: - -1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” -3. Provide the following options for the vote: - * accept — vote to accept the SEP - * reject — vote to reject the SEP - * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). - -#### Ground-rules for moderating discussions in SBOL breakout sessions - -1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. -2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. -4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” -5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. -6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/.history/hugo_themes/content/community-governance/_index_20201009090401.md b/.history/hugo_themes/content/community-governance/_index_20201009090401.md deleted file mode 100644 index a0b2d9eaf..000000000 --- a/.history/hugo_themes/content/community-governance/_index_20201009090401.md +++ /dev/null @@ -1,179 +0,0 @@ ---- -title: Governance - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: - -* SBOL should be free and open standard, developed by an open and inclusive processes. -* SBOL is a community that believes in fostering, cultivating and preserving a culture of diversity and inclusion. -* Leaders of the SBOL community are expected to actively foster a safe environment where all participants feel comfortable making their voices heard. -* Leadership from new and diverse voices should be actively developed, including by participation in working groups and by public speaking at workshops. - -## SBOL Organization -The SBOL community has the following organization: - -* SBOL Development Group: general body comprising all members of the SBOL community, and ultimate authority -* Ad-Hoc Subgroups: portions of the general development group focused on particular aspects of SBOL development. -* SBOL Editors: operational executives for the community -* SBOL Chair and Steering Committee: strategic planning and guidance for the community -* SBOL Industrial Consortium: a pre-competitive organization of companies (or similar) investing in the SBOL community - -## SBOL Development Group -Membership in the SBOL Development Group is open to all interested parties. Individuals interested in joining the group should contact [the editors](mailto:sbol-editors@googlegroups.com). - -The SBOL Development Group as a whole is the ultimate authority and source of legitimacy for SBOL standards decisions. All elections, standards changes, and governance changes are voted on by the SBOL Development Group according to the procedures below. - -The primary means of communication for the SBOL Development Group is via the sbol-dev Google Group. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list. - -SBOL workshops should be held twice per year. These may be stand-alone workshops or in combination with another event, but must provide ample time for attending members to hold focused discussions on the development of SBOL. - -All members of the SBOL Development Group are encouraged (but not required) to: - -* Attend the SBOL Workshops and other meetings -* Participate in discussions on SBOL mailing lists -* Support the SBOL standard in any tools and systems they work on -* Provide constructive feedback for improving the standard - -## Ad-Hoc Subgroups -Certain activities of the SBOL community are expected to either generate noticeably higher volumes of communication (e.g., software development and support) or to address topics expected to be of interest only to certain special interest groups. When deemed appropriate, ad-hoc subgroups may be created for addressing such topics. - -Subgroups must communicate via open lists that may be readily accessed and joined by any member of the SBOL Development Group. Any communication regarding standards changes, however, should be migrated back to the SBOL Development Group mailing list. - -## SBOL editors -As a matter of pragmatism, many organizational decisions and actions are delegated to an elected group of SBOL Editors, so named because their primary responsibility is ensuring the effective curation of documents for the community. - -The responsibilities of the SBOL Editors are: - -* Equitably representing the community in voting, documents, and guidance of discussion. -* Curation and dissemination of the SBOL standards and related documents (including writing, editing, and coordinating changes). -* Maintaining an open and structured process by which members of the SBOL Development Group can modify and improve SBOL standards (including timely implementation of tracking, processing, responding to, and organizing voting on change proposals). -* Ensuring effective development and maintenance of official SBOL software libraries and associated documentation and tutorials. -* Coordinating scholarly publications and ensuring proper attribution of contributions. -* Running elections and other community votes. -* Organization (or delegation) of SBOL Workshops and other events. -* Maintaining community infrastructure, including: the SBOL web site, source code repositories, mailing lists - -The SBOL Editors shall hold weekly meetings to coordinate their execution of these responsibilities. These meetings should be open, and their minutes should be reported to the SBOL Development Group. - -The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. - -SBOL Editors are elected by a community vote, following the process below. Editors serve for a two year term and cannot serve terms consecutively. To maximize continuity, editors’ terms should be desynchronized. There are 5 editorial positions, currently held by: - -* James McLaughlin, Newcastle University -* Pedro Fontanarrosa, University of Utah -* Vishwesh Kulkarni, University of Warwick -* Prashant Vaidyananthan, Microsoft Research -* Hasan Baig, University of Connecticut - -Previous SBOL Editors include: Zach Palchik (Zymergen), Curtis Madsen (Sandia National Labs), Nicholas Roehner (BBN Technologies), Angel Goñi Moreno (Newcastle University), Umesh P (Kerala Technological University), Tramy Nguyen (University of Utah), James McLaughlin (Newcastle University), Robert Sidney Cox (Kobe University), Raik Grunberg (University of Montreal), Jacob Beal (BBN Technologies), Bryan Bartley (University of Washington), Kevin Clancy (ThermoFisher), Michal Galdzicki (University of Washington), Goksel Misirli (Newcastle University), Ernst Oberortner (Boston University), Matthew Pocock, (Newcastle University), Jacqueline Quinn (Google), Cesar Rodriguez (Autodesk), Mandy Wilson (Virginia Bioinformatics Institute). - -## SBOL Chair and Steering Committee -The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. - -The SBOL Chair is the head of the SBOL Steering Committee. The SBOL Chair is responsible for ensuring regular steering committee meetings are held, for effective moderation of these meetings, and for being an advertised public point of contact for outside organizations. - -The SBOL Chair is elected by a community vote, following the process below. Chairs serve for a four year term. In order to ensure a smooth working relationship between the SBOL Chair and SBOL Editors, the SBOL Editors can remove a chair by a no-confidence vote amongst the SBOL Editors at any time. - -The rest of the SBOL Steering Committee are appointed (and removed) by the SBOL Chair. The Steering Committee has no fixed size or fixed term, but should generally comprise the set of PI-level members who are strongly active, have a strong stake in SBOL, and are willing to assume community leadership responsibilities. - -The SBOL Steering Committee shall hold monthly meetings to coordinate around strategic issues for the community (e.g., funding, setting key priorities and goals). These meetings should be open, and their minutes should be reported to the SBOL Development Group. The SBOL Steering Committee should also convene an external advisory board to help maintain strategic links with other communities and to obtain useful advice in guiding the community. - -The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. - -The SBOL current chair: - -**Chris Myers (May, 2019-), University of Utah** - -Previous Chairs: - -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Kevin Clancy, Synthetic Genomics, Inc. -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Utah -* Ernst Oberortner, DOE Joint Genome Institute (JGI) -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Panel is currently (listed alphabetically): - -* Prof. Matthew Chang, National University of Singapore -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Traci Haddock, iGEM Foundation -* Prof. Richard Kitney, Imperial College London -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University -* Prof. Chris Voigt, Massachusetts Institute of Technology - -## SBOL Industrial Consortium -The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. -As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium shall be free, open, and support the core values of the SBOL community. - -The SBOL Industrial Consortium will organize an Industrial Advisory Board to provide an industrial perspective on SBOL. The SBOL Chair shall hold quarterly meetings with the Industrial Advisory Board. These meetings (which may co-occur with Steering Committee Meetings) should be open and their minutes should be reported to the SBOL Development Group. - -Subject to these constraints, the SBOL Industrial Consortium is otherwise organized independently and operates under its own internal governance. Similarly, membership in the SBOL Industrial Consortium neither implies nor impairs membership in the SBOL Development Group. - -## Voting Procedures - -#### Elections Process: -Before any election, there is a nomination period of 5 working days. -All members of the SBOL Development Group are eligible for all offices (except those that are term-limited). -Any member can self-nominate or can nominate any other member. -Voting runs for 5 working days, starting at the end of the nomination period. All members of the SBOL Development Group are eligible to vote. -Candidates are elected by plurality. - -#### Voting process: -1. Any member of the SBOL Developers Group can submit an SBOL Enhancement Proposal (SEP) to the editors and/or to the community at large. See [SEP #1](https://github.com/SynBioDex/SEPs/issues/1) for a description of when and how to write and submit an SEP. - -2. SBOL editors are expected to move a given SEP draft to a vote once they agree that there has been sufficient debate. However, any member of the SBOL Developers Group can initiate the vote as long as one other member of the group seconds the motion. - -3. SBOL Editors post a voting form (see below), for a final discussion period of 2 working days. - -4. Voting runs for 5 working days, starting at the end of the discussion period. All members of the SBOL Development Group are eligible to vote. - -5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. - -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. - 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. - 2. The reasons for decisions must be recorded with the results of the vote. - 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. - - -#### Voting form must: - -1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” -3. Provide the following options for the vote: - * accept — vote to accept the SEP - * reject — vote to reject the SEP - * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). - -#### Ground-rules for moderating discussions in SBOL breakout sessions - -1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. -2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. -4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” -5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. -6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/.history/hugo_themes/content/community-governance/_index_20201009090413.md b/.history/hugo_themes/content/community-governance/_index_20201009090413.md deleted file mode 100644 index a0b2d9eaf..000000000 --- a/.history/hugo_themes/content/community-governance/_index_20201009090413.md +++ /dev/null @@ -1,179 +0,0 @@ ---- -title: Governance - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: - -* SBOL should be free and open standard, developed by an open and inclusive processes. -* SBOL is a community that believes in fostering, cultivating and preserving a culture of diversity and inclusion. -* Leaders of the SBOL community are expected to actively foster a safe environment where all participants feel comfortable making their voices heard. -* Leadership from new and diverse voices should be actively developed, including by participation in working groups and by public speaking at workshops. - -## SBOL Organization -The SBOL community has the following organization: - -* SBOL Development Group: general body comprising all members of the SBOL community, and ultimate authority -* Ad-Hoc Subgroups: portions of the general development group focused on particular aspects of SBOL development. -* SBOL Editors: operational executives for the community -* SBOL Chair and Steering Committee: strategic planning and guidance for the community -* SBOL Industrial Consortium: a pre-competitive organization of companies (or similar) investing in the SBOL community - -## SBOL Development Group -Membership in the SBOL Development Group is open to all interested parties. Individuals interested in joining the group should contact [the editors](mailto:sbol-editors@googlegroups.com). - -The SBOL Development Group as a whole is the ultimate authority and source of legitimacy for SBOL standards decisions. All elections, standards changes, and governance changes are voted on by the SBOL Development Group according to the procedures below. - -The primary means of communication for the SBOL Development Group is via the sbol-dev Google Group. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list. - -SBOL workshops should be held twice per year. These may be stand-alone workshops or in combination with another event, but must provide ample time for attending members to hold focused discussions on the development of SBOL. - -All members of the SBOL Development Group are encouraged (but not required) to: - -* Attend the SBOL Workshops and other meetings -* Participate in discussions on SBOL mailing lists -* Support the SBOL standard in any tools and systems they work on -* Provide constructive feedback for improving the standard - -## Ad-Hoc Subgroups -Certain activities of the SBOL community are expected to either generate noticeably higher volumes of communication (e.g., software development and support) or to address topics expected to be of interest only to certain special interest groups. When deemed appropriate, ad-hoc subgroups may be created for addressing such topics. - -Subgroups must communicate via open lists that may be readily accessed and joined by any member of the SBOL Development Group. Any communication regarding standards changes, however, should be migrated back to the SBOL Development Group mailing list. - -## SBOL editors -As a matter of pragmatism, many organizational decisions and actions are delegated to an elected group of SBOL Editors, so named because their primary responsibility is ensuring the effective curation of documents for the community. - -The responsibilities of the SBOL Editors are: - -* Equitably representing the community in voting, documents, and guidance of discussion. -* Curation and dissemination of the SBOL standards and related documents (including writing, editing, and coordinating changes). -* Maintaining an open and structured process by which members of the SBOL Development Group can modify and improve SBOL standards (including timely implementation of tracking, processing, responding to, and organizing voting on change proposals). -* Ensuring effective development and maintenance of official SBOL software libraries and associated documentation and tutorials. -* Coordinating scholarly publications and ensuring proper attribution of contributions. -* Running elections and other community votes. -* Organization (or delegation) of SBOL Workshops and other events. -* Maintaining community infrastructure, including: the SBOL web site, source code repositories, mailing lists - -The SBOL Editors shall hold weekly meetings to coordinate their execution of these responsibilities. These meetings should be open, and their minutes should be reported to the SBOL Development Group. - -The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. - -SBOL Editors are elected by a community vote, following the process below. Editors serve for a two year term and cannot serve terms consecutively. To maximize continuity, editors’ terms should be desynchronized. There are 5 editorial positions, currently held by: - -* James McLaughlin, Newcastle University -* Pedro Fontanarrosa, University of Utah -* Vishwesh Kulkarni, University of Warwick -* Prashant Vaidyananthan, Microsoft Research -* Hasan Baig, University of Connecticut - -Previous SBOL Editors include: Zach Palchik (Zymergen), Curtis Madsen (Sandia National Labs), Nicholas Roehner (BBN Technologies), Angel Goñi Moreno (Newcastle University), Umesh P (Kerala Technological University), Tramy Nguyen (University of Utah), James McLaughlin (Newcastle University), Robert Sidney Cox (Kobe University), Raik Grunberg (University of Montreal), Jacob Beal (BBN Technologies), Bryan Bartley (University of Washington), Kevin Clancy (ThermoFisher), Michal Galdzicki (University of Washington), Goksel Misirli (Newcastle University), Ernst Oberortner (Boston University), Matthew Pocock, (Newcastle University), Jacqueline Quinn (Google), Cesar Rodriguez (Autodesk), Mandy Wilson (Virginia Bioinformatics Institute). - -## SBOL Chair and Steering Committee -The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. - -The SBOL Chair is the head of the SBOL Steering Committee. The SBOL Chair is responsible for ensuring regular steering committee meetings are held, for effective moderation of these meetings, and for being an advertised public point of contact for outside organizations. - -The SBOL Chair is elected by a community vote, following the process below. Chairs serve for a four year term. In order to ensure a smooth working relationship between the SBOL Chair and SBOL Editors, the SBOL Editors can remove a chair by a no-confidence vote amongst the SBOL Editors at any time. - -The rest of the SBOL Steering Committee are appointed (and removed) by the SBOL Chair. The Steering Committee has no fixed size or fixed term, but should generally comprise the set of PI-level members who are strongly active, have a strong stake in SBOL, and are willing to assume community leadership responsibilities. - -The SBOL Steering Committee shall hold monthly meetings to coordinate around strategic issues for the community (e.g., funding, setting key priorities and goals). These meetings should be open, and their minutes should be reported to the SBOL Development Group. The SBOL Steering Committee should also convene an external advisory board to help maintain strategic links with other communities and to obtain useful advice in guiding the community. - -The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. - -The SBOL current chair: - -**Chris Myers (May, 2019-), University of Utah** - -Previous Chairs: - -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Kevin Clancy, Synthetic Genomics, Inc. -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Utah -* Ernst Oberortner, DOE Joint Genome Institute (JGI) -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Panel is currently (listed alphabetically): - -* Prof. Matthew Chang, National University of Singapore -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Traci Haddock, iGEM Foundation -* Prof. Richard Kitney, Imperial College London -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University -* Prof. Chris Voigt, Massachusetts Institute of Technology - -## SBOL Industrial Consortium -The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. -As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium shall be free, open, and support the core values of the SBOL community. - -The SBOL Industrial Consortium will organize an Industrial Advisory Board to provide an industrial perspective on SBOL. The SBOL Chair shall hold quarterly meetings with the Industrial Advisory Board. These meetings (which may co-occur with Steering Committee Meetings) should be open and their minutes should be reported to the SBOL Development Group. - -Subject to these constraints, the SBOL Industrial Consortium is otherwise organized independently and operates under its own internal governance. Similarly, membership in the SBOL Industrial Consortium neither implies nor impairs membership in the SBOL Development Group. - -## Voting Procedures - -#### Elections Process: -Before any election, there is a nomination period of 5 working days. -All members of the SBOL Development Group are eligible for all offices (except those that are term-limited). -Any member can self-nominate or can nominate any other member. -Voting runs for 5 working days, starting at the end of the nomination period. All members of the SBOL Development Group are eligible to vote. -Candidates are elected by plurality. - -#### Voting process: -1. Any member of the SBOL Developers Group can submit an SBOL Enhancement Proposal (SEP) to the editors and/or to the community at large. See [SEP #1](https://github.com/SynBioDex/SEPs/issues/1) for a description of when and how to write and submit an SEP. - -2. SBOL editors are expected to move a given SEP draft to a vote once they agree that there has been sufficient debate. However, any member of the SBOL Developers Group can initiate the vote as long as one other member of the group seconds the motion. - -3. SBOL Editors post a voting form (see below), for a final discussion period of 2 working days. - -4. Voting runs for 5 working days, starting at the end of the discussion period. All members of the SBOL Development Group are eligible to vote. - -5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. - -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. - 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. - 2. The reasons for decisions must be recorded with the results of the vote. - 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. - - -#### Voting form must: - -1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” -3. Provide the following options for the vote: - * accept — vote to accept the SEP - * reject — vote to reject the SEP - * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). - -#### Ground-rules for moderating discussions in SBOL breakout sessions - -1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. -2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. -4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” -5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. -6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/.history/hugo_themes/content/community-governance/_index_20201009090415.md b/.history/hugo_themes/content/community-governance/_index_20201009090415.md deleted file mode 100644 index a0b2d9eaf..000000000 --- a/.history/hugo_themes/content/community-governance/_index_20201009090415.md +++ /dev/null @@ -1,179 +0,0 @@ ---- -title: Governance - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: - -* SBOL should be free and open standard, developed by an open and inclusive processes. -* SBOL is a community that believes in fostering, cultivating and preserving a culture of diversity and inclusion. -* Leaders of the SBOL community are expected to actively foster a safe environment where all participants feel comfortable making their voices heard. -* Leadership from new and diverse voices should be actively developed, including by participation in working groups and by public speaking at workshops. - -## SBOL Organization -The SBOL community has the following organization: - -* SBOL Development Group: general body comprising all members of the SBOL community, and ultimate authority -* Ad-Hoc Subgroups: portions of the general development group focused on particular aspects of SBOL development. -* SBOL Editors: operational executives for the community -* SBOL Chair and Steering Committee: strategic planning and guidance for the community -* SBOL Industrial Consortium: a pre-competitive organization of companies (or similar) investing in the SBOL community - -## SBOL Development Group -Membership in the SBOL Development Group is open to all interested parties. Individuals interested in joining the group should contact [the editors](mailto:sbol-editors@googlegroups.com). - -The SBOL Development Group as a whole is the ultimate authority and source of legitimacy for SBOL standards decisions. All elections, standards changes, and governance changes are voted on by the SBOL Development Group according to the procedures below. - -The primary means of communication for the SBOL Development Group is via the sbol-dev Google Group. All significant decisions on governance and the evolution of the standard must be discussed via this mailing list. - -SBOL workshops should be held twice per year. These may be stand-alone workshops or in combination with another event, but must provide ample time for attending members to hold focused discussions on the development of SBOL. - -All members of the SBOL Development Group are encouraged (but not required) to: - -* Attend the SBOL Workshops and other meetings -* Participate in discussions on SBOL mailing lists -* Support the SBOL standard in any tools and systems they work on -* Provide constructive feedback for improving the standard - -## Ad-Hoc Subgroups -Certain activities of the SBOL community are expected to either generate noticeably higher volumes of communication (e.g., software development and support) or to address topics expected to be of interest only to certain special interest groups. When deemed appropriate, ad-hoc subgroups may be created for addressing such topics. - -Subgroups must communicate via open lists that may be readily accessed and joined by any member of the SBOL Development Group. Any communication regarding standards changes, however, should be migrated back to the SBOL Development Group mailing list. - -## SBOL editors -As a matter of pragmatism, many organizational decisions and actions are delegated to an elected group of SBOL Editors, so named because their primary responsibility is ensuring the effective curation of documents for the community. - -The responsibilities of the SBOL Editors are: - -* Equitably representing the community in voting, documents, and guidance of discussion. -* Curation and dissemination of the SBOL standards and related documents (including writing, editing, and coordinating changes). -* Maintaining an open and structured process by which members of the SBOL Development Group can modify and improve SBOL standards (including timely implementation of tracking, processing, responding to, and organizing voting on change proposals). -* Ensuring effective development and maintenance of official SBOL software libraries and associated documentation and tutorials. -* Coordinating scholarly publications and ensuring proper attribution of contributions. -* Running elections and other community votes. -* Organization (or delegation) of SBOL Workshops and other events. -* Maintaining community infrastructure, including: the SBOL web site, source code repositories, mailing lists - -The SBOL Editors shall hold weekly meetings to coordinate their execution of these responsibilities. These meetings should be open, and their minutes should be reported to the SBOL Development Group. - -The SBOL Editors mailing list is [sbol-editors@googlegroups.com](mailto:sbol-editors@googlegroups.com). Editorial communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former editors are kept on the mailing list until they choose to remove themselves. - -SBOL Editors are elected by a community vote, following the process below. Editors serve for a two year term and cannot serve terms consecutively. To maximize continuity, editors’ terms should be desynchronized. There are 5 editorial positions, currently held by: - -* James McLaughlin, Newcastle University -* Pedro Fontanarrosa, University of Utah -* Vishwesh Kulkarni, University of Warwick -* Prashant Vaidyananthan, Microsoft Research -* Hasan Baig, University of Connecticut - -Previous SBOL Editors include: Zach Palchik (Zymergen), Curtis Madsen (Sandia National Labs), Nicholas Roehner (BBN Technologies), Angel Goñi Moreno (Newcastle University), Umesh P (Kerala Technological University), Tramy Nguyen (University of Utah), James McLaughlin (Newcastle University), Robert Sidney Cox (Kobe University), Raik Grunberg (University of Montreal), Jacob Beal (BBN Technologies), Bryan Bartley (University of Washington), Kevin Clancy (ThermoFisher), Michal Galdzicki (University of Washington), Goksel Misirli (Newcastle University), Ernst Oberortner (Boston University), Matthew Pocock, (Newcastle University), Jacqueline Quinn (Google), Cesar Rodriguez (Autodesk), Mandy Wilson (Virginia Bioinformatics Institute). - -## SBOL Chair and Steering Committee -The positions of SBOL Chair and Steering Committee are a means for organizing strategic planning and coordination amongst PI-level members of the SBOL community. - -The SBOL Chair is the head of the SBOL Steering Committee. The SBOL Chair is responsible for ensuring regular steering committee meetings are held, for effective moderation of these meetings, and for being an advertised public point of contact for outside organizations. - -The SBOL Chair is elected by a community vote, following the process below. Chairs serve for a four year term. In order to ensure a smooth working relationship between the SBOL Chair and SBOL Editors, the SBOL Editors can remove a chair by a no-confidence vote amongst the SBOL Editors at any time. - -The rest of the SBOL Steering Committee are appointed (and removed) by the SBOL Chair. The Steering Committee has no fixed size or fixed term, but should generally comprise the set of PI-level members who are strongly active, have a strong stake in SBOL, and are willing to assume community leadership responsibilities. - -The SBOL Steering Committee shall hold monthly meetings to coordinate around strategic issues for the community (e.g., funding, setting key priorities and goals). These meetings should be open, and their minutes should be reported to the SBOL Development Group. The SBOL Steering Committee should also convene an external advisory board to help maintain strategic links with other communities and to obtain useful advice in guiding the community. - -The SBOL Steering Committee mailing list is [sbol-steering@googlegroups.com](mailto:sbol-steering@googlegroups.com). Communications should generally use this list to preserve records and aid organization. To preserve organizational memory, former chairs and members are kept on the mailing list until they choose to remove themselves. - -The SBOL current chair: - -**Chris Myers (May, 2019-), University of Utah** - -Previous Chairs: - -* Anil Wipat (2015-2019), Newcastle University -* Herbert Sauro (2010-2015), University of Washington, Seattle - -The SBOL Steering Committee is currently (listed alphabetically): - -* Jacob Beal, Raytheon BBN Technologies -* Kevin Clancy, Synthetic Genomics, Inc. -* Thomas Gorochowski, University of Bristol -* Goksel Misirli, Keele University -* Chris Myers, University of Utah -* Ernst Oberortner, DOE Joint Genome Institute (JGI) -* Herbert Sauro, University of Washington -* Anil Wipat, Newcastle University - -The SBOL chair has also organized an international advisory panel comprising a range of experts in standards and synthetic biology. The panel will provide an external perspective for SBOL, with advice on how SBOL can grow to meet the needs of the wider community. - -The SBOL Advisory Panel is currently (listed alphabetically): - -* Prof. Matthew Chang, National University of Singapore -* Prof. Victor de Lorenzo, Centro Nacional de Biotecnologia-CSIC -* Dr. Traci Haddock, iGEM Foundation -* Prof. Richard Kitney, Imperial College London -* Dr. Sarah Munro, US National Institute of Standards and Technology / Stanford University -* Prof. Chris Voigt, Massachusetts Institute of Technology - -## SBOL Industrial Consortium -The SBOL Industrial Consortium is a pre-competitive organization of companies (or similar non-company organizations) investing in the SBOL community. -As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium shall be free, open, and support the core values of the SBOL community. - -The SBOL Industrial Consortium will organize an Industrial Advisory Board to provide an industrial perspective on SBOL. The SBOL Chair shall hold quarterly meetings with the Industrial Advisory Board. These meetings (which may co-occur with Steering Committee Meetings) should be open and their minutes should be reported to the SBOL Development Group. - -Subject to these constraints, the SBOL Industrial Consortium is otherwise organized independently and operates under its own internal governance. Similarly, membership in the SBOL Industrial Consortium neither implies nor impairs membership in the SBOL Development Group. - -## Voting Procedures - -#### Elections Process: -Before any election, there is a nomination period of 5 working days. -All members of the SBOL Development Group are eligible for all offices (except those that are term-limited). -Any member can self-nominate or can nominate any other member. -Voting runs for 5 working days, starting at the end of the nomination period. All members of the SBOL Development Group are eligible to vote. -Candidates are elected by plurality. - -#### Voting process: -1. Any member of the SBOL Developers Group can submit an SBOL Enhancement Proposal (SEP) to the editors and/or to the community at large. See [SEP #1](https://github.com/SynBioDex/SEPs/issues/1) for a description of when and how to write and submit an SEP. - -2. SBOL editors are expected to move a given SEP draft to a vote once they agree that there has been sufficient debate. However, any member of the SBOL Developers Group can initiate the vote as long as one other member of the group seconds the motion. - -3. SBOL Editors post a voting form (see below), for a final discussion period of 2 working days. - -4. Voting runs for 5 working days, starting at the end of the discussion period. All members of the SBOL Development Group are eligible to vote. - -5. SBOL Editors may extend the voting period by up to an additional 5 working days when they feel that an insufficient number of votes have been obtained. - -6. SBOL Editors tally and call the vote. First vote will be judged by a 67% majority to indicate “rough consensus”. - 1. If rough consensus is not reached, discussion of 3 working days is to follow. SEP authors can modify or withdraw their proposal during that time. - 2. The reasons for decisions must be recorded with the results of the vote. - 3. Any second followup vote will be ruled by 50% majority and will be treated as the decision. - - -#### Voting form must: - -1. State clearly the SEP number and title being voted on and provide a link to this SEP. -2. State the eligibility criteria for voting, “All members of the SBOL Developers Group are eligible to vote.” -3. Provide the following options for the vote: - * accept — vote to accept the SEP - * reject — vote to reject the SEP - * abstain — no opinion, abstain votes will not be counted when determining majorities - * defer / table for further discussion — keep the SEP in draft stage so that it can be again put to a vote after further discussion and amendment (in contrast to “abstain” this vote will be counted when determining majorities). - -#### Ground-rules for moderating discussions in SBOL breakout sessions - -1. No interruptions; signal to moderator that you wish to speak. If a person goes on too long, however, the moderator may ask them to give the next person a turn to speak. -2. Moderator maintains a queue of speakers, calling on each in turn. -3. Pause periodically for “step back” and explicitly invite comments by less-heard voices, possibly specifically inviting individual people. Spend at least 30 seconds waiting before continuing. -4. Speaking about people or value judgements promotes conflict rather than constructive discussion. Instead, speak about ideas and facts in terms of specific concerns and consequences. - * e.g., “You are wrong” is problematic for communication because it is about people (“you”) and value judgements (“wrong”). It will tend to promote rather than resolve conflict. - * Instead: “I am concerned that proposal X will have negative consequence Y.” -5. Heated conversation suppresses sharing of legitimate concerns. If discussion is getting heated, it should be paused, the emotional concern acknowledged, and restarted with a cooler tone. -6. Side issues should be recorded to revisit later if they become a significant distraction. diff --git a/.history/hugo_themes/content/community/_index_20200819113224.md b/.history/hugo_themes/content/community/_index_20200819113224.md deleted file mode 100644 index c2e31856c..000000000 --- a/.history/hugo_themes/content/community/_index_20200819113224.md +++ /dev/null @@ -1,206 +0,0 @@ ---- -title: The SBOL Community - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL GitHub repository can be accessed here. - -The SBOL community works actively on the SBOL data model and visual standard, participates in online discussions, and meets semi-annually. We represent over 170+ members from 17 different countries, 42 institutions, and 28 different industries. Many of our members are also actively involved in other standards communities, like the Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN). - - -To join our growing community, contact the SBOL Editors at sbol-editors@googlegroups.com. - -### Members - -| Name | Affiliation | Country | -|----------------------------|-----------------------------------------------------------|-----------------| -| Alex McFadden | Zymergen Inc | USA | -| Alexis Casas | Imperial College London | UK | -| Alice Boo | Imperial College London | UK | -| Ana Delgado | University of Oslo | Norway | -| Angel Moreno | Newcastle University | UK | -| Anil Wipat | Newcastle University | UK | -| Anton Kulaga | Computation Biology of Aging Group | Romania | -| Augustin Luna | Dana-Farber Cancer Institute | USA | -| Benjamin Aleritsch | Technical University of Munich | Germany | -| Benjamin Chan | Boston University | USA | -| Bill Yang | Newcastle University | UK | -| Birjesh Kumar | ICGEB, Delhi | India | -| Brad Chapman | Ginkgo Bioworks | USA | -| Brigitte Dreger | BioRender Inc. | Toronto | -| Bryan Bartley | BBN Technologies | USA | -| Bryan Der | MIT | USA | -| Carlog Olguin | Autodesk | USA | -| Cesar Rodriguez | Florida State University | USA | -| Chih-Hsien Yang | National Yang Ming University | Taiwan | -| Chris Anderson | University of California, Berkeley | USA | -| Chris Myers | University of Utah | USA | -| Chris Walker | Macquarie University | Australia | -| Christian Atallah | Newcastle University | UK | -| Christian Nyumbayire | Independent | Italy | -| Christian Olsen | Centers for Disease Control and Prevention | USA | -| Christopher Voigt | MIT | USA | -| Craig Struble | Inscripta Inc. | USA | -| Curtis Madsen | Sandia National Laboratories | USA | -| DA Ball | University of Tennessee | USA | -| Daniel Dixon | University of Bristol | UK | -| Daniel Sutantyo | Macquarie University | USA | -| Dany Entezari | University of Edinburgh | UAE | -| Darren Platt | Amyris | USA | -| David Lomelin | Synthetic Genomics | USA | -| David Ross | NIST | USA | -| David Zong | Rice University | USA | -| Douglas Densmore | Boston University | USA | -| Drew Endy | Stanford University & BIOFAB | USA | -| Eduardo Abeliuk | Teselagen | USA | -| Egils Stalidzans | University of Latvia | Latvia | -| Elizabeth Robinson | UT Austin | USA | -| Elizabeth Strychalsky | NIST | USA | -| Emek Demir | Memorial Sloan Kettering Cancer Center | USA | -| Eric van der Helm | SNIPRBIOME | Denmark | -| Eric Young | Worchester Polytechnic Institute | USA | -| Ernst Oberortner | Lawrence Berkeley National Labs | USA | -| Evan Appleton | Boston University | USA | -| Evren Sirin | Clark & Parsia | USA | -| Falk Schreiber | University of Konstanz | Germany | -| Falk Shreiber | University of Konstanz | Germany | -| Florencio Mazzoldi | Ginkgo Bioworks | USA | -| Gary Bader | University of Toronto | Canada | -| Geoff Baldwin | Imperial College London | USA | -| George McArthur | GenoCAD | USA | -| Goksel Misirli | Keele University | UK | -| Gonzalo Vidal Pena | University of Chile | Chile | -| Grimaldo Elias Urena M. | Technological University of Panama | Panama | -| Guillermo Yanez Feliu | Rudge Lab, PUC. | Chile | -| Guy Bart-Stan | Imperial College London | UK | -| Harold Fellermann | Newcastle University | UK | -| Hasan Baig | Independent | Pakistan | -| Hasan Baig | University of Connecticut | USA | -| Hector Plahar | Joint Bioenergy Institute (JBEI) | USA | -| Henry Holbrook | Benchling | USA | -| Herbert Sauro | University of Washington | USA | -| Hiroyuki Kuwahara | KAUST | Saudi Arabia | -| Huaiyu Mi | USC | USA | -| Igor Durovic | University of Utah | USA | -| Isabel Pötzsch | University of Cambridge | UK | -| Jackie Quinn | Google | USA | -| Jake Beal | BBN Technologies | USA | -| James Diggans | Twist Bioscience | USA | -| James Mglaughlin | Newcastle University | UK | -| James Scott Brown | Imperial College London | UK | -| James Skelton | NEwcastle University | UK | -| Jan Madsen | DTU | Denmark | -| Jared Earl | University of Utah | USA | -| Jason Mohabir | Columbia University | USA | -| Jasper Koehorst | Wageningen University | Netherlands | -| Jean Peccoud | Colorado State University | USA | -| Jeanet Mante | University of Utah | USA | -| Jeffrey Barrick | UT Austin | USA | -| Jeffrey Elhai | Virginia Commonwealth University | USA | -| Jenhan Tao | University of California, San Diego | USA | -| Jennifer Hallinan | Macquarie University | Australia | -| John Gennari | University of Washington | USA | -| John Meng | Lawrence Berkeley National Labs | USA | -| John T. Sexton | Independent | USA | -| Jonathan Karr | Mount Sinai | USA | -| Joseph Hellerstein | University of Washington | USA | -| Joshua Rawlins | UW-Madison | USA | -| Juston Farlow | Serotiny | USA | -| Jyotsna Venkata | St. Joseph's Institute of Technology | India | -| Kelvin Clancy | BioCoder Consulting | USA | -| Kevin Clancy | BioCoder Consulting | USA | -| Kiri Choi | University of Washington | USA | -| Kirtan Dave | Sardar Patel University | India | -| Kyle Medley | University of Washington | USA | -| Laura Adam | Virginia Bioinformatics Institute | USA | -| Linda Kahl | Stanford University | USA | -| Linh Huynh | UC Davis | USA | -| Linhao Meng | Zhejiang University | China | -| Maciek Jacek Swat | CSIRO | Australia | -| Mandy Wilson | Virginia Tech | USA | -| Marc Juul | BIOFAB | USA | -| Marco Castelejin | VTT Technical Research Centre | Finland | -| Mario Marchiso | Tianjin University | China | -| Marta Vazquez-Vilar | CSIC (Consejo Superior de Investigaciones Científicas) | Spain | -| Matthew Crowther | Newcastle University | UK | -| Matthew Lux | Army Research Lab | USA | -| Matthew Pocock | Newcastle University | UK | -| Matthieu Bultelle | Imperial College London | UK | -| Maurice Ling | AdvanceSyn Private Limited | Singapore | -| Maxwell Bates | Autodesk | USA | -| Meher Samineni | REI | USA | -| Michael Zhang | Google | USA | -| Michal Galdzicki | Arzeda | USA | -| Michihiro Araki | Kobe University | Japan | -| Mike Bissell | Shipyard Toolchains | USA | -| Mike Fero | Teselagen | USA | -| Nathan Hillson | Joint Bioenergy Institute | USA | -| Nathan Wilkenson | University of Utah | USA | -| Neil Swainston | Manchester BioFactory Ltd. | UK | -| Neil Thompson | Massachusetts Institute of Technology | USA | -| Nicholas Roehner | BBN Technologies | USA | -| Nicolas Le Novere | EMBL-EBI | UK | -| Owen Gilfellon | Newcastle University | UK | -| Pablo Carbonell | Manchester Institute of Biotechnology | USA | -| Patrick Yizhi | University of Edinburgh | UK | -| Pedro Fontanarrosa | University of Utah | USA | -| Peter Dun | Stanford University | USA | -| Philip Bradley | Newcastle University | UK | -| Prashant Vaidyanathan | Microsoft Inc. | UK | -| Prem Prakash | BITS Pilani | India | -| Rahmi Lale | NTNU | Norway | -| Raik Gruenberg | KAUST | Saudi Arabia | -| Richard Kitney | Imperial College London | UK | -| Robert Cox | Kobe University | Japan | -| Robert Sidney Cox | Robert Sydney Cox III Co. | USA | -| Robin Emig | Augment Bioworks | USA | -| S. Castillo Hair | Rice University | USA | -| Sarah Munro | NIST | USA | -| Sean Leonard | University of Texas at Austin | USA | -| Shamseen Rahman | Boston University | USA | -| Shashank | IIT Delhi | India | -| Shyam Bhakta | UC Berkeley | USA | -| SSBSS Summer School | SSBSS Summer School | Italy | -| Stefan Claesen | Visbion Ltd. | UK | -| Stuart Moodie | Eight Pillars Ltd. | Edinburgh | -| Sunwoo Kang | Stanford University | USA | -| Swapnil Bhatiya | Catalog Inc | USA | -| Thomas Gorochowski | Bio Compute Lab | UK | -| Tim Fiori | University of Australia | Australia | -| Todd Slaby | Lawrence Berkeley National Labs | USA | -| Tramy Nguyen | University of Utah | USA | -| Tyler Camp | University of Texas at Austin | USA | -| Ueno Masayoshi | Kitasato University | Japan | -| Umesh P | University of Kerala | India | -| Vinod Tek | Imperial College London | UK | -| Vishvesh Kulkarni | University of Warwick | UK | -| Vittorio Bartoli | University of Bristol | UK | -| Walid El-Sharoud | Mansoura University | Egypt | -| William Byrd | University of Alabama | USA | -| Xin Gao | KAUST | Saudi Arabia | -| Xuefeng Cui | University of Washington | USA | -| Yaman Sirin | BBN Technologies | USA | -| Yogev Debbi | Genome Compiler | USA | -| Ysis Tarter | Amyris | USA | -| Zach Palchick | Zymergen | USA | -| Zach Zundel | University of Utah | USA | -| Zhen Zhang | University of Utah | USA | -| Zhiyang Ong | Texas A&M University | USA | -| Mudasir Shaikh | Habib University | Pakistan | -| Ritwik Agarwal | Iiit Hyderabad | India | -| Ming Hia | Imperial College | UK | -| Zhiyang Ong | Texas A&M University | USA | -| Ana Delgado | University of Oslo | Norway | -| William Poole | Caltech | USA | -| Stephanie Nicole Call | University of Massachusetts Amherst | USA | diff --git a/.history/hugo_themes/content/community/_index_20201009085048.md b/.history/hugo_themes/content/community/_index_20201009085048.md deleted file mode 100644 index 3b595259b..000000000 --- a/.history/hugo_themes/content/community/_index_20201009085048.md +++ /dev/null @@ -1,206 +0,0 @@ ---- -title: The SBOL Community - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL GitHub repository can be accessed [here](https://github.com/SynBioDex/Community-Media). - -The SBOL community works actively on the SBOL data model and visual standard, participates in online discussions, and meets semi-annually. We represent over 170+ members from 17 different countries, 42 institutions, and 28 different industries. Many of our members are also actively involved in other standards communities, like the Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN). - - -To join our growing community, contact the SBOL Editors at sbol-editors@googlegroups.com. - -### Members - -| Name | Affiliation | Country | -|----------------------------|-----------------------------------------------------------|-----------------| -| Alex McFadden | Zymergen Inc | USA | -| Alexis Casas | Imperial College London | UK | -| Alice Boo | Imperial College London | UK | -| Ana Delgado | University of Oslo | Norway | -| Angel Moreno | Newcastle University | UK | -| Anil Wipat | Newcastle University | UK | -| Anton Kulaga | Computation Biology of Aging Group | Romania | -| Augustin Luna | Dana-Farber Cancer Institute | USA | -| Benjamin Aleritsch | Technical University of Munich | Germany | -| Benjamin Chan | Boston University | USA | -| Bill Yang | Newcastle University | UK | -| Birjesh Kumar | ICGEB, Delhi | India | -| Brad Chapman | Ginkgo Bioworks | USA | -| Brigitte Dreger | BioRender Inc. | Toronto | -| Bryan Bartley | BBN Technologies | USA | -| Bryan Der | MIT | USA | -| Carlog Olguin | Autodesk | USA | -| Cesar Rodriguez | Florida State University | USA | -| Chih-Hsien Yang | National Yang Ming University | Taiwan | -| Chris Anderson | University of California, Berkeley | USA | -| Chris Myers | University of Utah | USA | -| Chris Walker | Macquarie University | Australia | -| Christian Atallah | Newcastle University | UK | -| Christian Nyumbayire | Independent | Italy | -| Christian Olsen | Centers for Disease Control and Prevention | USA | -| Christopher Voigt | MIT | USA | -| Craig Struble | Inscripta Inc. | USA | -| Curtis Madsen | Sandia National Laboratories | USA | -| DA Ball | University of Tennessee | USA | -| Daniel Dixon | University of Bristol | UK | -| Daniel Sutantyo | Macquarie University | USA | -| Dany Entezari | University of Edinburgh | UAE | -| Darren Platt | Amyris | USA | -| David Lomelin | Synthetic Genomics | USA | -| David Ross | NIST | USA | -| David Zong | Rice University | USA | -| Douglas Densmore | Boston University | USA | -| Drew Endy | Stanford University & BIOFAB | USA | -| Eduardo Abeliuk | Teselagen | USA | -| Egils Stalidzans | University of Latvia | Latvia | -| Elizabeth Robinson | UT Austin | USA | -| Elizabeth Strychalsky | NIST | USA | -| Emek Demir | Memorial Sloan Kettering Cancer Center | USA | -| Eric van der Helm | SNIPRBIOME | Denmark | -| Eric Young | Worchester Polytechnic Institute | USA | -| Ernst Oberortner | Lawrence Berkeley National Labs | USA | -| Evan Appleton | Boston University | USA | -| Evren Sirin | Clark & Parsia | USA | -| Falk Schreiber | University of Konstanz | Germany | -| Falk Shreiber | University of Konstanz | Germany | -| Florencio Mazzoldi | Ginkgo Bioworks | USA | -| Gary Bader | University of Toronto | Canada | -| Geoff Baldwin | Imperial College London | USA | -| George McArthur | GenoCAD | USA | -| Goksel Misirli | Keele University | UK | -| Gonzalo Vidal Pena | University of Chile | Chile | -| Grimaldo Elias Urena M. | Technological University of Panama | Panama | -| Guillermo Yanez Feliu | Rudge Lab, PUC. | Chile | -| Guy Bart-Stan | Imperial College London | UK | -| Harold Fellermann | Newcastle University | UK | -| Hasan Baig | Independent | Pakistan | -| Hasan Baig | University of Connecticut | USA | -| Hector Plahar | Joint Bioenergy Institute (JBEI) | USA | -| Henry Holbrook | Benchling | USA | -| Herbert Sauro | University of Washington | USA | -| Hiroyuki Kuwahara | KAUST | Saudi Arabia | -| Huaiyu Mi | USC | USA | -| Igor Durovic | University of Utah | USA | -| Isabel Pötzsch | University of Cambridge | UK | -| Jackie Quinn | Google | USA | -| Jake Beal | BBN Technologies | USA | -| James Diggans | Twist Bioscience | USA | -| James Mglaughlin | Newcastle University | UK | -| James Scott Brown | Imperial College London | UK | -| James Skelton | NEwcastle University | UK | -| Jan Madsen | DTU | Denmark | -| Jared Earl | University of Utah | USA | -| Jason Mohabir | Columbia University | USA | -| Jasper Koehorst | Wageningen University | Netherlands | -| Jean Peccoud | Colorado State University | USA | -| Jeanet Mante | University of Utah | USA | -| Jeffrey Barrick | UT Austin | USA | -| Jeffrey Elhai | Virginia Commonwealth University | USA | -| Jenhan Tao | University of California, San Diego | USA | -| Jennifer Hallinan | Macquarie University | Australia | -| John Gennari | University of Washington | USA | -| John Meng | Lawrence Berkeley National Labs | USA | -| John T. Sexton | Independent | USA | -| Jonathan Karr | Mount Sinai | USA | -| Joseph Hellerstein | University of Washington | USA | -| Joshua Rawlins | UW-Madison | USA | -| Juston Farlow | Serotiny | USA | -| Jyotsna Venkata | St. Joseph's Institute of Technology | India | -| Kelvin Clancy | BioCoder Consulting | USA | -| Kevin Clancy | BioCoder Consulting | USA | -| Kiri Choi | University of Washington | USA | -| Kirtan Dave | Sardar Patel University | India | -| Kyle Medley | University of Washington | USA | -| Laura Adam | Virginia Bioinformatics Institute | USA | -| Linda Kahl | Stanford University | USA | -| Linh Huynh | UC Davis | USA | -| Linhao Meng | Zhejiang University | China | -| Maciek Jacek Swat | CSIRO | Australia | -| Mandy Wilson | Virginia Tech | USA | -| Marc Juul | BIOFAB | USA | -| Marco Castelejin | VTT Technical Research Centre | Finland | -| Mario Marchiso | Tianjin University | China | -| Marta Vazquez-Vilar | CSIC (Consejo Superior de Investigaciones Científicas) | Spain | -| Matthew Crowther | Newcastle University | UK | -| Matthew Lux | Army Research Lab | USA | -| Matthew Pocock | Newcastle University | UK | -| Matthieu Bultelle | Imperial College London | UK | -| Maurice Ling | AdvanceSyn Private Limited | Singapore | -| Maxwell Bates | Autodesk | USA | -| Meher Samineni | REI | USA | -| Michael Zhang | Google | USA | -| Michal Galdzicki | Arzeda | USA | -| Michihiro Araki | Kobe University | Japan | -| Mike Bissell | Shipyard Toolchains | USA | -| Mike Fero | Teselagen | USA | -| Nathan Hillson | Joint Bioenergy Institute | USA | -| Nathan Wilkenson | University of Utah | USA | -| Neil Swainston | Manchester BioFactory Ltd. | UK | -| Neil Thompson | Massachusetts Institute of Technology | USA | -| Nicholas Roehner | BBN Technologies | USA | -| Nicolas Le Novere | EMBL-EBI | UK | -| Owen Gilfellon | Newcastle University | UK | -| Pablo Carbonell | Manchester Institute of Biotechnology | USA | -| Patrick Yizhi | University of Edinburgh | UK | -| Pedro Fontanarrosa | University of Utah | USA | -| Peter Dun | Stanford University | USA | -| Philip Bradley | Newcastle University | UK | -| Prashant Vaidyanathan | Microsoft Inc. | UK | -| Prem Prakash | BITS Pilani | India | -| Rahmi Lale | NTNU | Norway | -| Raik Gruenberg | KAUST | Saudi Arabia | -| Richard Kitney | Imperial College London | UK | -| Robert Cox | Kobe University | Japan | -| Robert Sidney Cox | Robert Sydney Cox III Co. | USA | -| Robin Emig | Augment Bioworks | USA | -| S. Castillo Hair | Rice University | USA | -| Sarah Munro | NIST | USA | -| Sean Leonard | University of Texas at Austin | USA | -| Shamseen Rahman | Boston University | USA | -| Shashank | IIT Delhi | India | -| Shyam Bhakta | UC Berkeley | USA | -| SSBSS Summer School | SSBSS Summer School | Italy | -| Stefan Claesen | Visbion Ltd. | UK | -| Stuart Moodie | Eight Pillars Ltd. | Edinburgh | -| Sunwoo Kang | Stanford University | USA | -| Swapnil Bhatiya | Catalog Inc | USA | -| Thomas Gorochowski | Bio Compute Lab | UK | -| Tim Fiori | University of Australia | Australia | -| Todd Slaby | Lawrence Berkeley National Labs | USA | -| Tramy Nguyen | University of Utah | USA | -| Tyler Camp | University of Texas at Austin | USA | -| Ueno Masayoshi | Kitasato University | Japan | -| Umesh P | University of Kerala | India | -| Vinod Tek | Imperial College London | UK | -| Vishvesh Kulkarni | University of Warwick | UK | -| Vittorio Bartoli | University of Bristol | UK | -| Walid El-Sharoud | Mansoura University | Egypt | -| William Byrd | University of Alabama | USA | -| Xin Gao | KAUST | Saudi Arabia | -| Xuefeng Cui | University of Washington | USA | -| Yaman Sirin | BBN Technologies | USA | -| Yogev Debbi | Genome Compiler | USA | -| Ysis Tarter | Amyris | USA | -| Zach Palchick | Zymergen | USA | -| Zach Zundel | University of Utah | USA | -| Zhen Zhang | University of Utah | USA | -| Zhiyang Ong | Texas A&M University | USA | -| Mudasir Shaikh | Habib University | Pakistan | -| Ritwik Agarwal | Iiit Hyderabad | India | -| Ming Hia | Imperial College | UK | -| Zhiyang Ong | Texas A&M University | USA | -| Ana Delgado | University of Oslo | Norway | -| William Poole | Caltech | USA | -| Stephanie Nicole Call | University of Massachusetts Amherst | USA | diff --git a/.history/hugo_themes/content/contact/_index_20201130160241.md b/.history/hugo_themes/content/contact/_index_20201130160241.md deleted file mode 100644 index d148aa4be..000000000 --- a/.history/hugo_themes/content/contact/_index_20201130160241.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: Contact - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The [sbol-announce](mailto:sbol-announce@googlegroups.com), [sbol-users](mailto:sbol-users@googlegroups.com), [sbol-dev](mailto:sbol-dev@googlegroups.com), and [sbol-visual](mailto:sbol-visual@googlegroups.com) are mailing lists open to all members of the SBOL community to post discussions and ask questions about SBOL. These mailing lists are moderated by the SBOL Editors. If the discussions and comments become inappropriate, the SBOL editors reserve the right to disallow future posting to be made by the community until further notice. - - -| Group | Description | -| ------------------------| ---------------------- | -| **SBOL Editors** | The [SBOL Editors](mailto:sbol-editors@googlegroups.com) are available to help answer any questions that the community may have. | -| **SBOL Announce** | [sbol-announce](mailto:sbol-announce@googlegroups.com) is a mailing list created for the SBOL Editors inform the SBOL community about current news regarding SBOL, community member introduction, SEP voting, and editor elections. This mailing list is also a place where the SBOL community members can post their announcements that they would like to share amongst the community. | -| **SBOL Users** | [sbol-users](mailto:sbol-users@googlegroups.com) is a mailing list created for those who are using SBOL in their software tool and have questions about how they can incorporate features of the SBOL data model and/or sbol-visual glyphs within their tool. | -| **SBOL Developers** | [sbol-dev](mailto:sbol-dev@googlegroups.com) is a mailing list created for those who want to implement the SBOL data model library. All discussions related to proposing a new feature to the SBOL data model and SBOL Enhancement Proposals (SEPs) are taken place in this mailing list. | -| **SBOL Visual** | [sbol-visual](mailto:sbol-visual@googlegroups.com) is a mailing list created for those who want to discuss and propose glyphs to represent engineered biological organisms through diagrams. | -| **SBOL Website Issues** | For website issues, please report them to our [SBOL website GitHub repository](https://github.com/SynBioDex/SBOL_website/issues) by submitting a GitHub issue. | - - - -Please fill in the following form if you would like to **join the SBOL community** or **subscribe** to the sbol-dev, sbol-visual, sbol-users, or sbol-announce mailing list: - - -{{< gdocs src="https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit?usp=sharing" >}} - - -If you are unable to view the form, try this [link](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU). diff --git a/.history/hugo_themes/content/contact/_index_20201202163138.md b/.history/hugo_themes/content/contact/_index_20201202163138.md deleted file mode 100644 index b64b8bd29..000000000 --- a/.history/hugo_themes/content/contact/_index_20201202163138.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: Contact - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The [sbol-announce](mailto:sbol-announce@googlegroups.com), [sbol-users](mailto:sbol-users@googlegroups.com), [sbol-dev](mailto:sbol-dev@googlegroups.com), and [sbol-visual](mailto:sbol-visual@googlegroups.com) are mailing lists open to all members of the SBOL community to post discussions and ask questions about SBOL. These mailing lists are moderated by the SBOL Editors. If the discussions and comments become inappropriate, the SBOL editors reserve the right to disallow future posting to be made by the community until further notice. - - -| Group | Description | -| ------------------------| ---------------------- | -| **SBOL Editors** | The [SBOL Editors](mailto:sbol-editors@googlegroups.com) are available to help answer any questions that the community may have. | -| **SBOL Announce** | [sbol-announce](mailto:sbol-announce@googlegroups.com) is a mailing list created for the SBOL Editors inform the SBOL community about current news regarding SBOL, community member introduction, SEP voting, and editor elections. This mailing list is also a place where the SBOL community members can post their announcements that they would like to share amongst the community. | -| **SBOL Users** | [sbol-users](mailto:sbol-users@googlegroups.com) is a mailing list created for those who are using SBOL in their software tool and have questions about how they can incorporate features of the SBOL data model and/or sbol-visual glyphs within their tool. | -| **SBOL Developers** | [sbol-dev](mailto:sbol-dev@googlegroups.com) is a mailing list created for those who want to implement the SBOL data model library. All discussions related to proposing a new feature to the SBOL data model and SBOL Enhancement Proposals (SEPs) are taken place in this mailing list. | -| **SBOL Visual** | [sbol-visual](mailto:sbol-visual@googlegroups.com) is a mailing list created for those who want to discuss and propose glyphs to represent engineered biological organisms through diagrams. | -| **SBOL Website Issues** | For website issues, please report them to our [SBOL website GitHub repository](https://github.com/SynBioDex/SBOL_website/issues) by submitting a GitHub issue. | - - - -Please fill in the following form if you would like to **join the SBOL community** or **subscribe** to the sbol-dev, sbol-visual, sbol-users, or sbol-announce mailing list: - - -{{< gdocs src="https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit?usp=sharing" >}} - - -If you are unable to view the form, try this [link](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU). Alternatively, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com) along with your name, institution/affiliation, country, your interest in SBOL, and which email list(s) you would like to subscribe to. diff --git a/.history/hugo_themes/content/faq/_index_20201203152331.md b/.history/hugo_themes/content/faq/_index_20201203152331.md deleted file mode 100644 index 8709c6c87..000000000 --- a/.history/hugo_themes/content/faq/_index_20201203152331.md +++ /dev/null @@ -1,212 +0,0 @@ ---- -title: Frequently Asked Questions - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -Didn’t find an answer to your question? Post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. - - -## SBOL - -
- What is Synthetic Biology? - Synthetic biology is a new frontier in biological research where scientists and engineers design and create living systems to carry out useful tasks. In the last half century, the fundamental biochemical pieces and processes that comprise the phenomena of life have been isolated and studied by scientists in the laboratory. This reductionist approach to molecular biology has yielded enormous insight into the basic molecular units that govern life, such as genes encoded on DNA. Today, a new approach, synthetic biology, is possible in which basic units of biochemistry are re-assembled into new living systems, using platform technologies such as DNA synthesis, genome engineering, simulation tools, and computer-aided-design. In the future, important technologies like solar energy, biofuels, and medicines may be synthesized out of “wetware.” -
-
- What is the role of a standard language in synthetic biology? - Standards decrease friction in markets by reducing the cost of translating data and designs. So commercial entities can concentrate on transacting the goods and services in which they create the most value. -
- - -
- What is SBOL? - The design process is fundamental to synthetic biology. The SBOL standard empowers and enables a design-oriented, forward-engineering approach for synthetic biology in the following ways: - -- Facilitates storage of genetic designs in repositories -- Helps synthetic biologists and genetic engineers electronically exchange designs with each other and with biofabrication centers -- Supports development of Genetic Design Automation (GDA) software tools for synthetic biologists -- Represents hierarchically assembled genetic compositions -- Represents abstract genetic compositions without an explicit nucleotide sequence -- Allows expression of genetic designs in publications and thus aids scientific reproducibility -- Captures elements of a design that move beyond DNA Sequences to include RNA, proteins, small molecules and molecular interactions -- SBOL is extensible to allow other kinds of data to be attached to the core data model. This includes, for example, experimental data, host information and mathematical models -- Introductory slides on SBOL can be found {{% staticref "docs/WhatIsSBOL.pdf" "newtab" %}}here{{% /staticref %}}. -
- -
- Is SBOL free? - Yes. SBOL is not patented, has no royalties, and does not cost anything to use. -
- -
- Is SBOL open? - SBOL is open source and licensed under the {{% staticref "http://creativecommons.org/licenses/by/4.0/" "newtab" %}}Creative Commons Attribution 4.0 International License{{% /staticref %}}. -
- -
- How will SBOL help me? - Using the {{% staticref "/data/" "newtab" %}}SBOL data model{{% /staticref %}} will let you download sequence designs from published experiments. You can retrieve SBOL designs from repositories like {{% staticref "http://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}}, and {{% staticref "https://acs-registry.jbei.org/" "newtab" %}}JBEI-ICE{{% /staticref %}}. Take a look at our applications page to see the {{% staticref "/applications/" "newtab" %}}software tools{{% /staticref %}} that currently support SBOL. If you want to support SBOL data in your tool, take a look at the available programming languages that are available to use in your tool. - -You can also express your design using {{% staticref "/visual/" "newtab" %}}SBOL Visual{{% /staticref %}}. If you want to use SBOL visual in your tool, you can download the available SBOL graphical notations {{% staticref "/visual/" "newtab" %}}here{{% /staticref %}}. - -
- -
- What can I do with SBOL? - You can describe the components of a design and the interactions between components like circuit diagrams in the file using {{% staticref "/data/" "newtab" %}}SBOL data{{% /staticref %}}. And you can draw them to prepare publications using {{% staticref "/visual/" "newtab" %}}SBOL Visual{{% /staticref %}}. You can submit genetic designs to include all sequence -information for your paper in one file. You can also attach mathematical models to genetic designs SBOL will let you move your designs and work history between different tools. -
- -
- What kinds of companies should use SBOL? - SynBio software companies, DNA synthesis companies, DNA design companies, really any company that makes or uses genetic materials. -
- -
- I’m a small company. Why should I use the SBOL standard? - Use of the SBOL standard promotes ease of data access across applications and devices. Which means faster development time with fewer resources required, so you can get to market quickly. -
- -
- I’m a large company. Why should I use SBOL? - There are no royalties to pay, and you won’t be sued for using it. Contributes to efficient patent searching. Patented devices can be represented in SBOL, so you can more easily search for comparison to your proposed designs. Use of open standards is also a key element of corporate social responsibility. -
- -
- Why not just store all my sequence data in Word and Excel? - Designs in these tools become ambiguous to other people and are not easily read by, and swapped between software applications. -
- -
- Can I use the SBOL logo in my own work/tools? - Yes, the SBOL Logo is free to use under the Creative Commons license. - - You can get the SBOL logo {{% staticref "img/Logos/SBOLlogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "img/Logos/SBOLlogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Visual logo {{% staticref "img/Logos/SBOLVisualLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "img/Logos/SBOLVisualLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - You can get the SBOL Industrial Consortium logo {{% staticref "img/Logos/SBOLIndustrialLogo.png" "newtab" %}}PNG image file{{% /staticref %}} or {{% staticref "img/Logos/SBOLIndustrialLogo.svg" "newtab" %}}SVG image file{{% /staticref %}}. - - We’d be very flattered if you wanted to use it, but if you like us that much, please consider donating or sponsoring development of SBOL. We’d love to have you. Note, however, that use of the SBOL logo does not convey any kind of endorsement or certification by sbolstandard.org. -
- -
- How is the SBOL standard funded? - SBOL was funded by grants through the National Science Foundation through Collaborative awards #1355909 and #1356401 and EPSRC grant -#EP/J02175X/1. Other sponsorship, support, or endorsements have been provided by the federal agencies, federal research centers, -commercial enterprises, and academic institutions. Please contact the {{% staticref "mailto:sbol-editors@googlegroups.com" "newtab" %}}SBOL Editors{{% /staticref %}} for donation consideration. -
- -
- SBOL vs. GenBank - With the emergence of large-scale DNA sequencing technology in the last few decades, there has also emerged a need to manage and share vast amounts of sequence data. For researchers in the biological sciences, the public GenBank database, data standard, and file format has become a familiar friend. However, there are several reasons why the GenBank standard is insufficient for satisfying the needs of synthetic biologists. While the GenBank standard is used to primarily describe sequences that correspond to an existing DNA sample, the SBOL standard promotes forward-engineering of novel sequences. In other words, SBOL makes it easy to assemble novel sequences from DNA components using computer-aided design and genetic design automation. Moreover, SBOL is able to capture elements of intended design about proteins and small molecules for example, as well as the interactions between them. - - Genbank is a great file format for sequences and unstructured annotations. What can you do with SBOL that you can’t with Genbank? Genbank isn’t meant for designs. It will not represent interactions between components, let you specify undefined components, is not modular and won’t describe designs using proteins and small molecules. -
- -
- Which tools will allow me to build SBOL? - We have summarize a list of SBOL data and SBOL visual tools that were reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Data - -
- Where can I get detailed information on SBOL Data? - SBOL is described in detail in the current {{% staticref "/data/" "newtab" %}}SBOL specification{{% /staticref %}}. -
- -
- What is the difference between SBOL 1.1 and 2.0? - SBOL 1.1 provides users with the ability to specify the structure of their designs. SBOL 2.0 improves upon the expressibility by adding the ability to specify function. More details of the differences can be found by reading the specifications for SBOL 1.1 and SBOL 2.0. -
- -
- Are there repositories that store SBOL data? - Yes, there are several repositories. For instance, the {{% staticref "https://synbiohub.org/" "newtab" %}}SynBioHub{{% /staticref %}} and {{% staticref "https://public-registry.jbei.org/" "newtab" %}}JBEI ICE{{% /staticref %}}. You can have a look at the current repositories that have been reported to us {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Visual - -
- What is SBOL visual? - SBOL visual is a uniform way to draw diagrams of synthetic biology designs. Currently, these designs are depicted at the genetic level. -
- -
- How do I draw SBOL visual designs? - There are a couple of SBOL visual software tools that you can use to draw SBOL visual glyphs such as {{% staticref "http://visbol.org/" "newtab" %}}VisBOL{{% /staticref %}}, {{% staticref "https://github.com/SynBioDex/SBOLDesigner/releases" "newtab" %}}SBOLDesigner{{% /staticref %}}, and {{% staticref "http://pigeon.synbiotools.org/" "newtab" %}}PigeonCAD{{% /staticref %}}. You can view a full list of SBOL visual tools that we have recorded {{% staticref "/applications/" "newtab" %}}here{{% /staticref %}}. -
- -## SBOL Community - -
- How can I contribute to the community? - More information can be found {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. -
- -
- When does the SBOL community meet? - The SBOL community meets approximately every 6 months. A list of previous and upcoming meetings can be found {{% staticref "/community-meetings/" "newtab" %}}here{{% /staticref %}}. -
- -
- Is there a mailing list for the SBOL community? -Yes! There are multiple mailing lists depending on how you'd like to interact with the community and your interests in SBOL. You can find details {{% staticref "/contact/" "newtab" %}}here{{% /staticref %}}. - - -
- -## Citing SBOL - -
- What paper should I cite for SBOL data? - -
    -
  • SBOL 1: - {{< cite page="/publication/galdzicki-synthetic-2014" view="1" >}}
    • -
  • SBOL 2: - {{< cite page="/publication/roehner-sharing-2016" view="1" >}}
    • -
  • SBOL 3: - {{< cite page="/publication/synthetic-biology-open-mclaughlin-2020-a" view="1" >}}
    • -
- -
- -
- What paper should I cite for SBOL Visual? - -
    -
  • SBOL Visual 1: - {{< cite page="/publication/quinn-sbol-2015" view="1" >}}
    • -
  • SBOL Visual 2: - {{< cite page="/publication/beal-communicating-2019" view="1" >}}
    • -
- -
- -
- What papers should I cite for SBOL libraries and utilities? -
    -
  • libSBOLj: - {{< cite page="/publication/lib-sbo-lj-java-library-zhang-2015" view="1" >}}
    • -
  • sboljs: - {{< cite page="/publication/mclaughlin-sboljs-2019" view="1" >}}
    • -
  • pySBOL: - {{< cite page="/publication/bartley-pysbol-2019" view="1" >}}
    • -
  • SBOL Validator: - {{< cite page="/publication/zundel-validator-2017" view="1" >}}
    • -
- -
\ No newline at end of file diff --git a/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115113510.md b/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115113510.md deleted file mode 100644 index 375e9f8a1..000000000 --- a/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115113510.md +++ /dev/null @@ -1,59 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Composable Modular Models for Synthetic Biology -subtitle: '' -summary: '' -authors: -- Goksel Misirli -- Jennifer Hallinan -- Anil Wipat -tags: -- '"composable models"' -- '"database of models"' -- '"model annotation"' -- '"model-driven design"' -- '"standard virtual parts"' -- '"Synthetic biology"' -categories: [] -date: '2015-12-01' -lastmod: 2021-01-15T11:35:11-03:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-01-15T14:35:06.123024Z' -publication_types: -- 2 -abstract: Modelling and computational simulation are crucial for the large-scale engineering - of biological circuits since they allow the system under design to be simulated - prior to implementation in vivo. To support automated, model-driven design it is - desirable that in silico models are modular, composable and use standard formats. - The synthetic biology design process typically involves the composition of genetic - circuits from individual parts. At the most basic level, these parts are representations - of genetic features such as promoters, ribosome binding sites (RBSs), and coding - sequences (CDSs). However, it is also desirable to model the biological molecules - and behaviour that arise when these parts are combined in vivo. Modular models of - parts can be composed and their associated systems simulated, facilitating the process - of model-centred design. The availability of databases of modular models is essential - to support software tools used in the model-driven design process. In this article, - we present an approach to support the development of composable, modular models - for synthetic biology, termed Standard Virtual Parts. We then describe a programmatically - accessible and publicly available database of these models to allow their use by - computational design tools. -publication: '*ACM Journal on Emerging Technologies in Computing Systems*' -doi: 10.1145/2631921 ---- diff --git a/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115123737.md b/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115123737.md deleted file mode 100644 index bdd1b94ba..000000000 --- a/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115123737.md +++ /dev/null @@ -1,59 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Composable Modular Models for Synthetic Biology -subtitle: '' -summary: '' -authors: -- Goksel Misirli -- Jennifer Hallinan -- Anil Wipat -tags: -- '"composable models"' -- '"database of models"' -- '"model annotation"' -- '"model-driven design"' -- '"standard virtual parts"' -- '"Synthetic biology"' -categories: [] -date: '2015-12-01' -lastmod: 2021-01-15T11:35:11-03:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-01-15T14:35:06.123024Z' -publication_types: -- 2 -abstract: Modelling and computational simulation are crucial for the large-scale engineering - of biological circuits since they allow the system under design to be simulated - prior to implementation in vivo. To support automated, model-driven design it is - desirable that in silico models are modular, composable and use standard formats. - The synthetic biology design process typically involves the composition of genetic - circuits from individual parts. At the most basic level, these parts are representations - of genetic features such as promoters, ribosome binding sites (RBSs), and coding - sequences (CDSs). However, it is also desirable to model the biological molecules - and behaviour that arise when these parts are combined in vivo. Modular models of - parts can be composed and their associated systems simulated, facilitating the process - of model-centred design. The availability of databases of modular models is essential - to support software tools used in the model-driven design process. In this article, - we present an approach to support the development of composable, modular models - for synthetic biology, termed Standard Virtual Parts. We then describe a programmatically - accessible and publicly available database of these models to allow their use by - computational design tools. -publication: '*ACM Journal on Emerging Technologies in Computing Systems*' -doi: 10.1145/2631921 ---- diff --git a/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115123818.md b/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115123818.md deleted file mode 100644 index 5db633ad3..000000000 --- a/.history/hugo_themes/content/publication/composable-modular-models-misirli-2015/index_20210115123818.md +++ /dev/null @@ -1,59 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Composable Modular Models for Synthetic Biology -subtitle: '' -summary: '' -authors: -- Goksel Misirli -- Jennifer Hallinan -- Anil Wipat -tags: -- '"composable models"' -- '"database of models"' -- '"model annotation"' -- '"model-driven design"' -- '"standard virtual parts"' -- '"Synthetic biology"' -categories: [] -date: '2015-12-01' -lastmod: 2021-01-15T11:35:11-03:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Smart' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2021-01-15T14:35:06.123024Z' -publication_types: -- 2 -abstract: Modelling and computational simulation are crucial for the large-scale engineering - of biological circuits since they allow the system under design to be simulated - prior to implementation in vivo. To support automated, model-driven design it is - desirable that in silico models are modular, composable and use standard formats. - The synthetic biology design process typically involves the composition of genetic - circuits from individual parts. At the most basic level, these parts are representations - of genetic features such as promoters, ribosome binding sites (RBSs), and coding - sequences (CDSs). However, it is also desirable to model the biological molecules - and behaviour that arise when these parts are combined in vivo. Modular models of - parts can be composed and their associated systems simulated, facilitating the process - of model-centred design. The availability of databases of modular models is essential - to support software tools used in the model-driven design process. In this article, - we present an approach to support the development of composable, modular models - for synthetic biology, termed Standard Virtual Parts. We then describe a programmatically - accessible and publicly available database of these models to allow their use by - computational design tools. -publication: '*ACM Journal on Emerging Technologies in Computing Systems*' -doi: 10.1145/2631921 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20200921103824.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20200921103824.md deleted file mode 100644 index 268a8ea2b..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20200921103824.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124306.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124306.md deleted file mode 100644 index c39413688..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124306.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124326.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124326.md deleted file mode 100644 index 7ffd7ad6a..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124326.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Smart' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124456.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124456.md deleted file mode 100644 index 7ffd7ad6a..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124456.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Smart' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124556.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124556.md deleted file mode 100644 index a907bf3db..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124556.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Center' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124638.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124638.md deleted file mode 100644 index 7ffd7ad6a..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115124638.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Smart' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145523.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145523.md deleted file mode 100644 index 06d6a5bbe..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145523.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: 'test' - focal_point: 'Smart' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145539.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145539.md deleted file mode 100644 index 7ffd7ad6a..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145539.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Smart' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145705.md b/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145705.md deleted file mode 100644 index a907bf3db..000000000 --- a/.history/hugo_themes/content/publication/nguyen-converter-2016/index_20210115145705.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: A Converter from the Systems Biology Markup Language to the Synthetic Biology - Open Language -subtitle: '' -summary: '' -authors: -- Tramy Nguyen -- Nicholas Roehner -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2016-06-17' -lastmod: 2020-09-19T21:28:26+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Center' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:26.531480Z' -publication_types: -- 2 -abstract: 'Standards are important to synthetic biology because they enable exchange - and reproducibility of genetic designs. This paper describes a procedure for converting - between two standards: the Systems Biology Markup Language (SBML) and the Synthetic - Biology Open Language (SBOL). SBML is a standard for behavioral models of biological - systems at the molecular level. SBOL describes structural and basic qualitative - behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent - connection between behavioral and structural information for a biological design. - The conversion process described in this paper leverages Systems Biology Ontology - (SBO) annotations to enable inference of a designs qualitative function.' -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.5b00212 -doi: 10.1021/acssynbio.5b00212 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20200921103824.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20200921103824.md deleted file mode 100644 index e04b992af..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20200921103824.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202744.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202744.md deleted file mode 100644 index 9a00a792f..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202744.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: true - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202800.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202800.md deleted file mode 100644 index e04b992af..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202800.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202806.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202806.md deleted file mode 100644 index 1cfdd6382..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202806.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'center' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202819.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202819.md deleted file mode 100644 index e04b992af..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202819.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202822.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202822.md deleted file mode 100644 index ebd7eec09..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202822.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202929.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202929.md deleted file mode 100644 index e4419fc77..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202929.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Center' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202959.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202959.md deleted file mode 100644 index 92fe6f268..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005202959.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: 'Image test' - focal_point: 'Center' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005203041.md b/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005203041.md deleted file mode 100644 index e4419fc77..000000000 --- a/.history/hugo_themes/content/publication/roehner-specifying-2019/index_20201005203041.md +++ /dev/null @@ -1,55 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL) -subtitle: '' -summary: '' -authors: -- Nicholas Roehner -- Bryan Bartley -- Jacob Beal -- James McLaughlin -- Matthew Pocock -- Michael Zhang -- Zach Zundel -- Chris J. Myers -tags: [] -categories: [] -date: '2019-07-19' -lastmod: 2020-09-19T21:28:28+01:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: 'Center' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-19T20:28:28.600347Z' -publication_types: -- 2 -abstract: As improvements in DNA synthesis technology and assembly methods make combinatorial - assembly of genetic constructs increasingly accessible, methods for representing - genetic constructs likewise need to improve to handle the exponential growth of - combinatorial design space. To this end, we present a community accepted extension - of the SBOL data standard that allows for the efficient and flexible encoding of - combinatorial designs. This extension includes data structures for representing - genetic designs with “variable” components that can be implemented by choosing one - of many linked designs for existing genetic parts or constructs. We demonstrate - the representational power of the SBOL combinatorial design extension through case - studies on metabolic pathway design and genetic circuit design, and we report the - expansion of the SBOLDesigner software tool to support users in creating and modifying - combinatorial designs in SBOL. -publication: '' -url_pdf: https://doi.org/10.1021/acssynbio.9b00092 -doi: 10.1021/acssynbio.9b00092 ---- diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921131328.bib b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921131328.bib deleted file mode 100644 index 230e10439..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921131328.bib +++ /dev/null @@ -1,16 +0,0 @@ -@article{SyntheticBiologyOpen_baig_2020, - abstract = {$<$section class="abstract"$><$h2 class="abstractTitle text-title my-1" id="d801e2"$>$Abstract$<$/h2$><$p$>$Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.$<$/p$><$/section$>$}, - annotation = {00000}, - author = {Baig, Hasan and Fontanarrosa, Pedro and Kulkarni, Vishwesh and McLaughlin, James Alastair and Vaidyanathan, Prashant and Bartley, Bryan and Beal, Jacob and Crowther, Matthew and Gorochowski, Thomas E. and Grünberg, Raik and Misirli, Goksel and Scott-Brown, James and Oberortner, Ernst and Wipat, Anil and Myers, Chris J.}, - chapter = {Journal of Integrative Bioinformatics}, - doi = {10.1515/jib-2020-0017}, - journal = {Journal of Integrative Bioinformatics}, - language = {en}, - month = {June}, - number = {ahead-of-print}, - publisher = {De Gruyter}, - title = {Synthetic Biology Open Language (SBOL) Version 3.0.0}, - volume = {-1}, - year = {2020} -} - diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921131945.bib b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921131945.bib deleted file mode 100644 index 04317c890..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921131945.bib +++ /dev/null @@ -1,16 +0,0 @@ -@article{SyntheticBiologyOpen_baig_2020, - abstract = {Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.}, - annotation = {00000}, - author = {Baig, Hasan and Fontanarrosa, Pedro and Kulkarni, Vishwesh and McLaughlin, James Alastair and Vaidyanathan, Prashant and Bartley, Bryan and Beal, Jacob and Crowther, Matthew and Gorochowski, Thomas E. and Grünberg, Raik and Misirli, Goksel and Scott-Brown, James and Oberortner, Ernst and Wipat, Anil and Myers, Chris J.}, - chapter = {Journal of Integrative Bioinformatics}, - doi = {10.1515/jib-2020-0017}, - journal = {Journal of Integrative Bioinformatics}, - language = {en}, - month = {June}, - number = {ahead-of-print}, - publisher = {De Gruyter}, - title = {Synthetic Biology Open Language (SBOL) Version 3.0.0}, - volume = {-1}, - year = {2020} -} - diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921132011.bib b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921132011.bib deleted file mode 100644 index 04317c890..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921132011.bib +++ /dev/null @@ -1,16 +0,0 @@ -@article{SyntheticBiologyOpen_baig_2020, - abstract = {Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.}, - annotation = {00000}, - author = {Baig, Hasan and Fontanarrosa, Pedro and Kulkarni, Vishwesh and McLaughlin, James Alastair and Vaidyanathan, Prashant and Bartley, Bryan and Beal, Jacob and Crowther, Matthew and Gorochowski, Thomas E. and Grünberg, Raik and Misirli, Goksel and Scott-Brown, James and Oberortner, Ernst and Wipat, Anil and Myers, Chris J.}, - chapter = {Journal of Integrative Bioinformatics}, - doi = {10.1515/jib-2020-0017}, - journal = {Journal of Integrative Bioinformatics}, - language = {en}, - month = {June}, - number = {ahead-of-print}, - publisher = {De Gruyter}, - title = {Synthetic Biology Open Language (SBOL) Version 3.0.0}, - volume = {-1}, - year = {2020} -} - diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921132453.bib b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921132453.bib deleted file mode 100644 index 04317c890..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/cite_20200921132453.bib +++ /dev/null @@ -1,16 +0,0 @@ -@article{SyntheticBiologyOpen_baig_2020, - abstract = {Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.}, - annotation = {00000}, - author = {Baig, Hasan and Fontanarrosa, Pedro and Kulkarni, Vishwesh and McLaughlin, James Alastair and Vaidyanathan, Prashant and Bartley, Bryan and Beal, Jacob and Crowther, Matthew and Gorochowski, Thomas E. and Grünberg, Raik and Misirli, Goksel and Scott-Brown, James and Oberortner, Ernst and Wipat, Anil and Myers, Chris J.}, - chapter = {Journal of Integrative Bioinformatics}, - doi = {10.1515/jib-2020-0017}, - journal = {Journal of Integrative Bioinformatics}, - language = {en}, - month = {June}, - number = {ahead-of-print}, - publisher = {De Gruyter}, - title = {Synthetic Biology Open Language (SBOL) Version 3.0.0}, - volume = {-1}, - year = {2020} -} - diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921131329.md b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921131329.md deleted file mode 100644 index 1ae20c3be..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921131329.md +++ /dev/null @@ -1,70 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Synthetic Biology Open Language (SBOL) Version 3.0.0 -subtitle: '' -summary: '' -authors: -- Hasan Baig -- Pedro Fontanarrosa -- Vishwesh Kulkarni -- James Alastair McLaughlin -- Prashant Vaidyanathan -- Bryan Bartley -- Jacob Beal -- Matthew Crowther -- Thomas E. Gorochowski -- Raik Grünberg -- Goksel Misirli -- James Scott-Brown -- Ernst Oberortner -- Anil Wipat -- Chris J. Myers -tags: [] -categories: [] -date: '2020-06-01' -lastmod: 2020-09-21T13:13:29-03:00 -featured: false -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-21T16:13:29.781775Z' -publication_types: -- 2 -abstract: $<$section class=\"abstract\"$><$h2 class=\"abstractTitle text-title my-1\" - id=\"d801e2\"$>$Abstract$<$/h2$><$p$>$Synthetic biology builds upon genetics, molecular - biology, and metabolic engineering by applying engineering principles to the design - of biological systems. When designing a synthetic system, synthetic biologists need - to exchange information about multiple types of molecules, the intended behavior - of the system, and actual experimental measurements. The Synthetic Biology Open - Language (SBOL) has been developed as a standard to support the specification and - exchange of biological design information in synthetic biology, following an open - community process involving both wet bench scientists and dry scientific modelers - and software developers, across academia, industry, and other institutions. This - document describes SBOL 3.0.0, which condenses and simplifies previous versions - of SBOL based on experiences in deployment across a variety of scientific and industrial - settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part - relationships, (2) renames Component Definition/Component to Component/Sub-Component, - (3) merges Component and Module classes, (4) ensures consistency between data model - and ontology terms, (5) extends the means to define and reference Sub-Components, - (6) refines requirements on object URIs, (7) enables graph-based serialization, - (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence - associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence - Constraints into a general structural Constraint class, and (12) expands the set - of allowed constraints.$<$/p$><$/section$>$ -publication: '*Journal of Integrative Bioinformatics*' -doi: 10.1515/jib-2020-0017 ---- diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921131921.md b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921131921.md deleted file mode 100644 index 3f6271936..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921131921.md +++ /dev/null @@ -1,70 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Synthetic Biology Open Language (SBOL) Version 3.0.0 -subtitle: '' -summary: '' -authors: -- Hasan Baig -- Pedro Fontanarrosa -- Vishwesh Kulkarni -- James Alastair McLaughlin -- Prashant Vaidyanathan -- Bryan Bartley -- Jacob Beal -- Matthew Crowther -- Thomas E. Gorochowski -- Raik Grünberg -- Goksel Misirli -- James Scott-Brown -- Ernst Oberortner -- Anil Wipat -- Chris J. Myers -tags: [] -categories: [] -date: '2020-06-01' -lastmod: 2020-09-21T13:13:29-03:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-21T16:13:29.781775Z' -publication_types: -- 2 -abstract: $<$section class=\"abstract\"$><$h2 class=\"abstractTitle text-title my-1\" - id=\"d801e2\"$>$Abstract$<$/h2$><$p$>$Synthetic biology builds upon genetics, molecular - biology, and metabolic engineering by applying engineering principles to the design - of biological systems. When designing a synthetic system, synthetic biologists need - to exchange information about multiple types of molecules, the intended behavior - of the system, and actual experimental measurements. The Synthetic Biology Open - Language (SBOL) has been developed as a standard to support the specification and - exchange of biological design information in synthetic biology, following an open - community process involving both wet bench scientists and dry scientific modelers - and software developers, across academia, industry, and other institutions. This - document describes SBOL 3.0.0, which condenses and simplifies previous versions - of SBOL based on experiences in deployment across a variety of scientific and industrial - settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part - relationships, (2) renames Component Definition/Component to Component/Sub-Component, - (3) merges Component and Module classes, (4) ensures consistency between data model - and ontology terms, (5) extends the means to define and reference Sub-Components, - (6) refines requirements on object URIs, (7) enables graph-based serialization, - (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence - associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence - Constraints into a general structural Constraint class, and (12) expands the set - of allowed constraints.$<$/p$><$/section$>$ -publication: '*Journal of Integrative Bioinformatics*' -doi: 10.1515/jib-2020-0017 ---- diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132029.md b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132029.md deleted file mode 100644 index 2abdfb76c..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132029.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Synthetic Biology Open Language (SBOL) Version 3.0.0 -subtitle: '' -summary: '' -authors: -- Hasan Baig -- Pedro Fontanarrosa -- Vishwesh Kulkarni -- James Alastair McLaughlin -- Prashant Vaidyanathan -- Bryan Bartley -- Jacob Beal -- Matthew Crowther -- Thomas E. Gorochowski -- Raik Grünberg -- Goksel Misirli -- James Scott-Brown -- Ernst Oberortner -- Anil Wipat -- Chris J. Myers -tags: [] -categories: [] -date: '2020-06-01' -lastmod: 2020-09-21T13:13:29-03:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-21T16:13:29.781775Z' -publication_types: -- 2 -abstract: Abstract$<$/h2$><$p$>$Synthetic biology builds upon genetics, molecular - biology, and metabolic engineering by applying engineering principles to the design - of biological systems. When designing a synthetic system, synthetic biologists need - to exchange information about multiple types of molecules, the intended behavior - of the system, and actual experimental measurements. The Synthetic Biology Open - Language (SBOL) has been developed as a standard to support the specification and - exchange of biological design information in synthetic biology, following an open - community process involving both wet bench scientists and dry scientific modelers - and software developers, across academia, industry, and other institutions. This - document describes SBOL 3.0.0, which condenses and simplifies previous versions - of SBOL based on experiences in deployment across a variety of scientific and industrial - settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part - relationships, (2) renames Component Definition/Component to Component/Sub-Component, - (3) merges Component and Module classes, (4) ensures consistency between data model - and ontology terms, (5) extends the means to define and reference Sub-Components, - (6) refines requirements on object URIs, (7) enables graph-based serialization, - (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence - associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence - Constraints into a general structural Constraint class, and (12) expands the set - of allowed constraints. -publication: '*Journal of Integrative Bioinformatics*' -doi: 10.1515/jib-2020-0017 ---- diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132036.md b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132036.md deleted file mode 100644 index 2abdfb76c..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132036.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Synthetic Biology Open Language (SBOL) Version 3.0.0 -subtitle: '' -summary: '' -authors: -- Hasan Baig -- Pedro Fontanarrosa -- Vishwesh Kulkarni -- James Alastair McLaughlin -- Prashant Vaidyanathan -- Bryan Bartley -- Jacob Beal -- Matthew Crowther -- Thomas E. Gorochowski -- Raik Grünberg -- Goksel Misirli -- James Scott-Brown -- Ernst Oberortner -- Anil Wipat -- Chris J. Myers -tags: [] -categories: [] -date: '2020-06-01' -lastmod: 2020-09-21T13:13:29-03:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-21T16:13:29.781775Z' -publication_types: -- 2 -abstract: Abstract$<$/h2$><$p$>$Synthetic biology builds upon genetics, molecular - biology, and metabolic engineering by applying engineering principles to the design - of biological systems. When designing a synthetic system, synthetic biologists need - to exchange information about multiple types of molecules, the intended behavior - of the system, and actual experimental measurements. The Synthetic Biology Open - Language (SBOL) has been developed as a standard to support the specification and - exchange of biological design information in synthetic biology, following an open - community process involving both wet bench scientists and dry scientific modelers - and software developers, across academia, industry, and other institutions. This - document describes SBOL 3.0.0, which condenses and simplifies previous versions - of SBOL based on experiences in deployment across a variety of scientific and industrial - settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part - relationships, (2) renames Component Definition/Component to Component/Sub-Component, - (3) merges Component and Module classes, (4) ensures consistency between data model - and ontology terms, (5) extends the means to define and reference Sub-Components, - (6) refines requirements on object URIs, (7) enables graph-based serialization, - (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence - associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence - Constraints into a general structural Constraint class, and (12) expands the set - of allowed constraints. -publication: '*Journal of Integrative Bioinformatics*' -doi: 10.1515/jib-2020-0017 ---- diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132112.md b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132112.md deleted file mode 100644 index 3af39790e..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132112.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: Synthetic Biology Open Language (SBOL) Version 3.0.0 -subtitle: '' -summary: '' -authors: -- Hasan Baig -- Pedro Fontanarrosa -- Vishwesh Kulkarni -- James Alastair McLaughlin -- Prashant Vaidyanathan -- Bryan Bartley -- Jacob Beal -- Matthew Crowther -- Thomas E. Gorochowski -- Raik Grünberg -- Goksel Misirli -- James Scott-Brown -- Ernst Oberortner -- Anil Wipat -- Chris J. Myers -tags: [] -categories: [] -date: '2020-06-01' -lastmod: 2020-09-21T13:13:29-03:00 -featured: true -draft: false - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: '' - focal_point: '' - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] -publishDate: '2020-09-21T16:13:29.781775Z' -publication_types: -- 2 -abstract: Synthetic biology builds upon genetics, molecular - biology, and metabolic engineering by applying engineering principles to the design - of biological systems. When designing a synthetic system, synthetic biologists need - to exchange information about multiple types of molecules, the intended behavior - of the system, and actual experimental measurements. The Synthetic Biology Open - Language (SBOL) has been developed as a standard to support the specification and - exchange of biological design information in synthetic biology, following an open - community process involving both wet bench scientists and dry scientific modelers - and software developers, across academia, industry, and other institutions. This - document describes SBOL 3.0.0, which condenses and simplifies previous versions - of SBOL based on experiences in deployment across a variety of scientific and industrial - settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part - relationships, (2) renames Component Definition/Component to Component/Sub-Component, - (3) merges Component and Module classes, (4) ensures consistency between data model - and ontology terms, (5) extends the means to define and reference Sub-Components, - (6) refines requirements on object URIs, (7) enables graph-based serialization, - (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence - associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence - Constraints into a general structural Constraint class, and (12) expands the set - of allowed constraints. -publication: '*Journal of Integrative Bioinformatics*' -doi: 10.1515/jib-2020-0017 ---- diff --git a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132439.md b/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132439.md deleted file mode 100644 index 624d97874..000000000 --- a/.history/hugo_themes/content/publication/synthetic-biology-open-baig-2020/index_20200921132439.md +++ /dev/null @@ -1,47 +0,0 @@ ---- -# Documentation: https://sourcethemes.com/academic/docs/managing-content/ - -title: "Synthetic biology open language (SBOL) version 3.0.0" -subtitle: "" -summary: "" -authors: -- Hasan Baig -- Pedro Fontanarrosa -- Vishwesh Kulkarni -- James McLaughlin -- Prashant Vaidyanathan -- Chris Myers -- Bryan Bartley -- Jacob Beal -- Matthew Crowther -- Thomas Gorochowski -- Raik Grünberg -- Goksel Misirli -- Ernst Oberortner -- James Scott-Brown -- Anil Wipat -categories: [] -date: 2020-04-01T00:00:00Z -publishDate: 2016-04-01T00:00:00Z -featured: true -draft: false -publication_types: ["2"] -tags: [] - -abstract: Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints. - -# Featured image -# To use, add an image named `featured.jpg/png` to your page's folder. -# Focal points: Smart, Center, TopLeft, Top, TopRight, Left, Right, BottomLeft, Bottom, BottomRight. -image: - caption: "" - focal_point: "" - preview_only: false - -# Projects (optional). -# Associate this post with one or more of your projects. -# Simply enter your project's folder or file name without extension. -# E.g. `projects = ["internal-project"]` references `content/project/deep-learning/index.md`. -# Otherwise, set `projects = []`. -projects: [] ---- diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203125907.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203125907.md deleted file mode 100644 index cdb666588..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203125907.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.svg" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203130432.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203130432.md deleted file mode 100644 index 03016f006..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203130432.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.svg" width="500" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203130536.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203130536.md deleted file mode 100644 index d461bebfd..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203130536.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.svg" height="500" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203130618.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203130618.md deleted file mode 100644 index 5293fd975..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203130618.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.png" height="500" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203130627.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203130627.md deleted file mode 100644 index d461bebfd..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203130627.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.svg" height="500" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203131948.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203131948.md deleted file mode 100644 index aadaeb818..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203131948.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.svg" height="500" width="500" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203150535.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203150535.md deleted file mode 100644 index 03016f006..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203150535.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.svg" width="500" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-industrial/_index_20201203150710.md b/.history/hugo_themes/content/sbol-industrial/_index_20201203150710.md deleted file mode 100644 index cdb666588..000000000 --- a/.history/hugo_themes/content/sbol-industrial/_index_20201203150710.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLIndustrialLogo.svg" title="" lightbox="true" >}} - -The SBOL Industrial Consortium is a pre-competitive non-profit organization supporting innovation, dissemination, and integration of SBOL standards, tools and practices for practical applications in an industrial environment. As the SBOL Industrial Consortium operates pre-competitively, all products of activities supported by the SBOL Industrial Consortium are free, open, and intended to support the core values of the SBOL community. - -Specifically, the consortium supports the charitable, educational, and scientific purposes of developing, providing, and promoting education, research, training, and advancement of state-of-the-art technology in the fields of synthetic biology and bio-design automation through SBOL standards and associated tool development. The SBOL Industrial Consortium also provides financial support for projects, activities, and infrastructure within the SBOL community. - -The SBOL Industrial Consortium meets regularly to coordinate its activities, as well as organizing an Industrial Advisory Board to provide an industrial perspective on SBOL. - -For any inquiries, contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) - -### Opportunities - -We will periodically post opportunities for the community to respond to in this space, such as internships, project sponsorship, or infrastructure support. - -- CFP: SBOL Community Critical Infrastructure Support: {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.pdf" "newtab" %}}PDF{{% /staticref %}} {{% staticref "docs/CFP_SBOL_Community_Critical_Infrastructure_Support.docx" "newtab" %}}Word{{% /staticref %}} - -### Member Organizations - -#### Gold -| {{< figure library="true" src="industrial/raytheon.jpeg" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/doulix.png" title="" lightbox="true" width="190" >}} | -|---|---| - -#### Silver -| {{< figure library="true" src="industrial/idt.png" title="" lightbox="true" width="250" >}} | {{< figure library="true" src="industrial/Twist_Logo_cropped.jpeg" title="" lightbox="true" width="200" >}} | -|---|---| - -#### Bronze -| {{< figure library="true" src="industrial/amyris-1.png" title="" lightbox="true" width="240" >}} | {{< figure library="true" src="industrial/Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" title="" lightbox="true" width="320" >}} | -|---|---| - -| {{< figure library="true" src="industrial/Teselagen_300x150-1.png" title="" lightbox="true" width="270" >}} | {{< figure library="true" src="industrial/zymergen.png" title="" lightbox="true" width="70" >}} | -|---|---| - -| {{< figure library="true" src="industrial/shipyard_toolchains_logo_02_338px_matte.png" title="" lightbox="true" width="270" >}} | | -|---|---| - -#### Joining SBOL Industrial - -{{% staticref "docs/SBOL-Industrial-Consortium.pdf" "newtab" %}}Consortium Membership Information and Levels{{% /staticref %}} - -If your organization is interested in joining the SBOL industrial consortium, please contact: [sbol-industrial@googlegroups.com](mailto:sbol-industrial@googlegroups.com) \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-visual-ontology/_index_20201211132740.md b/.history/hugo_themes/content/sbol-visual-ontology/_index_20201211132740.md deleted file mode 100644 index a9282844d..000000000 --- a/.history/hugo_themes/content/sbol-visual-ontology/_index_20201211132740.md +++ /dev/null @@ -1,77 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -*Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -* [http://vows.sbolstandard.org/metadata/CDSGlyph](https://vows.sbolstandard.org/metadata/CDSGlyph) - -### Programmatic access to SBOL-VOWS - -Python and Java examples and related documentation can be found in the following GitHub repository: - -[https://github.com/dissys/sbol-visual-client](https://github.com/dissys/sbol-visual-client) - -The web service returns data using the RDF/JSON format. Hence, any RDF or JSON library can be used to access information regarding the mapping, query, and metadata interfaces. Please note that examples are provided using the RDFLib and Jena libraries for Python and Java programming languages respectively. \ No newline at end of file diff --git a/.history/hugo_themes/content/sbol-visual-ontology/_index_20201215202439.md b/.history/hugo_themes/content/sbol-visual-ontology/_index_20201215202439.md deleted file mode 100644 index 1f5b9a685..000000000 --- a/.history/hugo_themes/content/sbol-visual-ontology/_index_20201215202439.md +++ /dev/null @@ -1,75 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -*Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -* [http://vows.sbolstandard.org/metadata/CDSGlyph](https://vows.sbolstandard.org/metadata/CDSGlyph) - -### Programmatic access to SBOL-VOWS - -Python and Java examples and related documentation can be found in the following GitHub repository: - -[https://github.com/dissys/sbol-visual-client](https://github.com/dissys/sbol-visual-client) - -The web service returns data using the RDF/JSON format. Hence, any RDF or JSON library can be used to access information regarding the mapping, query, and metadata interfaces. Please note that examples are provided using the RDFLib and Jena libraries for Python and Java programming languages respectively. \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-about/_index_20201203125559.md b/.history/hugo_themes/content/visual-about/_index_20201203125559.md deleted file mode 100644 index f9eee1ec3..000000000 --- a/.history/hugo_themes/content/visual-about/_index_20201203125559.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: SBOL Visual - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLVisualLogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/visual-about/_index_20201215202610.md b/.history/hugo_themes/content/visual-about/_index_20201215202610.md deleted file mode 100644 index 15367e22c..000000000 --- a/.history/hugo_themes/content/visual-about/_index_20201215202610.md +++ /dev/null @@ -1,52 +0,0 @@ ---- -title: - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -{{< figure library="true" src="Logos/SBOLVisualLogo.svg" width="500" title="" lightbox="true" >}} - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. - -### Usage - -SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). - -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. - -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). - -### Download Glyphs - -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). - -If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. - -### Proposing a New Feature to the SBOL Data Model - -To propose a new feature to SBOL visual, a standard procedure must be followed. - -1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. -2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). - * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). -3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. -4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/.history/hugo_themes/content/visual-examples/_index_20210114231301.md b/.history/hugo_themes/content/visual-examples/_index_20210114231301.md deleted file mode 100644 index 947b374e9..000000000 --- a/.history/hugo_themes/content/visual-examples/_index_20210114231301.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli_sbol-owl_2019" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - -{{< figure library="true" src="SBOLVisualExamples/example1-1.jpg" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - -{{< figure library="true" src="SBOLVisualExamples/example2.jpg" title="Example 2: Phosphorylation of an inactive transcription factor" lightbox="true" width="670" >}} diff --git a/.history/hugo_themes/content/visual-examples/_index_20210115113726.md b/.history/hugo_themes/content/visual-examples/_index_20210115113726.md deleted file mode 100644 index cd7384ad6..000000000 --- a/.history/hugo_themes/content/visual-examples/_index_20210115113726.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli_sbol-owl_2019" view="3" >}} - -## 2015 (Visual Examples) - -{{< cite page="/publication/ComposableModularModels_misirli_2015" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - -{{< figure library="true" src="SBOLVisualExamples/example1-1.jpg" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - -{{< figure library="true" src="SBOLVisualExamples/example2.jpg" title="Example 2: Phosphorylation of an inactive transcription factor" lightbox="true" width="670" >}} diff --git a/.history/hugo_themes/content/visual-examples/_index_20210115113937.md b/.history/hugo_themes/content/visual-examples/_index_20210115113937.md deleted file mode 100644 index 007edf0e0..000000000 --- a/.history/hugo_themes/content/visual-examples/_index_20210115113937.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Examples - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -## 2020 (Visual Examples) -{{< cite page="/publication/visual2Ontology" view="3" >}} - -{{< cite page="/publication/visualsbol221" view="3" >}} - -## 2019 (Visual Examples) - -{{< cite page="/publication/beal-2019-communicating" view="3" >}} - -{{< cite page="/publication/nguyen-2019-design" view="3" >}} - -{{< cite page="/publication/misirli-sbol-owl_2019" view="3" >}} - -## 2015 (Visual Examples) - -{{< cite page="/publication/composable-modular-models-misirli-2015" view="3" >}} - -
- -Examples to demonstrate the usage of SBOL Visual glyphs is given below. - -Example1: A SBOL visual design of the circuit that contains a promoter, RBS, CDS, and terminator. The promoter is stimulated by CDS that it regulates. - -{{< figure library="true" src="SBOLVisualExamples/example1-1.jpg" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} - -Example2: Phosphorylation of an inactive transcription factor (produced by two different CDSs) by a kinase to form an active transcriptional activator, which then stimulates a promoter. - -{{< figure library="true" src="SBOLVisualExamples/example2.jpg" title="Example 2: Phosphorylation of an inactive transcription factor" lightbox="true" width="670" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820131140.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820131140.md deleted file mode 100644 index 94de26a70..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820131140.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: SBOL Visual - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820143928.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820143928.md deleted file mode 100644 index 600dfab45..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820143928.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: SBOL Visual Glyphs - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820151209.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820151209.md deleted file mode 100644 index 80970862b..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820151209.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: SBOL Visual Glyphs - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191231.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191231.md deleted file mode 100644 index 4a6b85ee0..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191231.md +++ /dev/null @@ -1,19 +0,0 @@ ---- -title: SBOL Visual Glyphs - -{{< ref "Glyphs" >}} - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191256.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191256.md deleted file mode 100644 index 15fc1975b..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191256.md +++ /dev/null @@ -1,19 +0,0 @@ ---- -title: SBOL Visual Glyphs - - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- -{{< ref "Glyphs" >}} -### Glyphs diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191303.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191303.md deleted file mode 100644 index d0cc9452d..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191303.md +++ /dev/null @@ -1,19 +0,0 @@ ---- -title: SBOL Visual Glyphs - - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191312.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191312.md deleted file mode 100644 index 75bb6ab19..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191312.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191402.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191402.md deleted file mode 100644 index 350093c5d..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191402.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -see [test]{{< ref "SBOL-visual" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191450.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191450.md deleted file mode 100644 index 7dc040807..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191450.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -see [test]{{< relref "SBOL-visual" >}} \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191527.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191527.md deleted file mode 100644 index 5f96856d1..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191527.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -see [test]({{< relref "SBOL-visual" >}}) \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200820191548.md b/.history/hugo_themes/content/visual-glyphs/_index_20200820191548.md deleted file mode 100644 index 2bb32db2c..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200820191548.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -see [test]({{< relref "visual-about" >}}) \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102401.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102401.md deleted file mode 100644 index 5c96d2c22..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102401.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release. -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines. -Sample visual glyphs are supported in PDF, PNG, SVG. -Visit our GitHub repository to request features and report issues related to SBOL Visual. -Take a look at the latest software tools that support SBOL Visual glyphs. -Contact the SBOL Visual team for further questions. \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102420.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102420.md deleted file mode 100644 index c578c723f..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102420.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines. -Sample visual glyphs are supported in PDF, PNG, SVG. -Visit our GitHub repository to request features and report issues related to SBOL Visual. -Take a look at the latest software tools that support SBOL Visual glyphs. -Contact the SBOL Visual team for further questions. \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102536.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102536.md deleted file mode 100644 index dd9dc6ee2..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102536.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions.\ diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102549.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102549.md deleted file mode 100644 index e31aac731..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102549.md +++ /dev/null @@ -1,25 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102636.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102636.md deleted file mode 100644 index ee029d8d4..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102636.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - - diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102731.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102731.md deleted file mode 100644 index bdadd98a6..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102731.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="Sequence-Feature-Glyphs-2.png" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102747.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102747.md deleted file mode 100644 index bdadd98a6..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102747.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="Sequence-Feature-Glyphs-2.png" title="Example 1: Promoter stimulated by CDS" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824102756.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824102756.md deleted file mode 100644 index 8691801e7..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824102756.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824103020.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824103020.md deleted file mode 100644 index 8691801e7..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824103020.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824103109.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824103109.md deleted file mode 100644 index 8d3ccde5e..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824103109.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs\Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824103126.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824103126.md deleted file mode 100644 index 2861a00ae..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824103126.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200824103354.md b/.history/hugo_themes/content/visual-glyphs/_index_20200824103354.md deleted file mode 100644 index d436b5e1d..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200824103354.md +++ /dev/null @@ -1,35 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest specification release.\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest software tools that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825131715.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825131715.md deleted file mode 100644 index bb2c0c429..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825131715.md +++ /dev/null @@ -1,35 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825132016.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825132016.md deleted file mode 100644 index 0b67b6555..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825132016.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -{{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}Word{{% /staticref %}} - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825132056.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825132056.md deleted file mode 100644 index a354c0f8a..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825132056.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -{{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" %}}Word{{% /staticref %}} - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825132844.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825132844.md deleted file mode 100644 index 3c8766d65..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825132844.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started.s - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825132851.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825132851.md deleted file mode 100644 index 6c92c720e..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825132851.md +++ /dev/null @@ -1,37 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825133153.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825133153.md deleted file mode 100644 index 1d54466b2..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825133153.md +++ /dev/null @@ -1,39 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825133235.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825133235.md deleted file mode 100644 index 2034d7e02..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825133235.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}} -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}} -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825133357.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825133357.md deleted file mode 100644 index caa439444..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825133357.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}} -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825133405.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825133405.md deleted file mode 100644 index 48fb7a260..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825133405.md +++ /dev/null @@ -1,41 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825133659.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825133659.md deleted file mode 100644 index 789485056..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825133659.md +++ /dev/null @@ -1,45 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-glyphs/_index_20200825133913.md b/.history/hugo_themes/content/visual-glyphs/_index_20200825133913.md deleted file mode 100644 index 782ed6f39..000000000 --- a/.history/hugo_themes/content/visual-glyphs/_index_20200825133913.md +++ /dev/null @@ -1,49 +0,0 @@ ---- -title: SBOL Visual Glyphs - - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Glyphs - -SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}).\ -These glyphs are made to be drawable on a white board but they are not definite, they are guidelines.\ -Sample visual glyphs are supported in PDF, PNG, SVG.\ -Visit our [GitHub repository](https://github.com/SynBioDex/SBOL-visual) to request features and report issues related to SBOL Visual.\ -Take a look at the latest [software tools]({{< relref "applications" >}}) that support SBOL Visual glyphs.\ -Contact the [SBOL Visual team](mailto:sbol-visual@googlegroups.com) for further questions. - -Look at this {{% staticref "docs/SBOL-Visual-2.1-Quickstart.pdf" "newtab" %}}quick introduction to SBOL Visual 2.1{{% /staticref %}} to get started. - -### SBOL Visual 2.0.0 - -{{< figure library="true" src="SBOLVisualGlyphs/Sequence-Feature-Glyphs-2.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Sequence Feature Glyphs PDF.zip" "newtab" %}}Sequence Feature Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs PNG.zip" "newtab" %}}Sequence Feature Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Sequence Feature Glyphs SVG.zip" "newtab" %}}Sequence Feature Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/molecular_species.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/molecular_species_pdf.zip" "newtab" %}}Molecular Species Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/molecular_species_png.zip" "newtab" %}}Molecular Species Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/molecular_species_svg.zip" "newtab" %}}Molecular Species Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Glyphs-768x297.png" title="" lightbox="true" width="470" >}} - -{{% staticref "zip/Interaction Glyphs PDF 2.1.zip" "newtab" %}}Interaction Glyphs PDF{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs PNG 2.1.zip" "newtab" %}}Interaction Glyphs PNG{{% /staticref %}}\ -{{% staticref "zip/Interaction Glyphs SVG 2.1.zip" "newtab" %}}Interaction Glyphs SVG{{% /staticref %}} - -{{< figure library="true" src="SBOLVisualGlyphs/Interaction-Node-Glyphs-768x415.png" title="" lightbox="true" width="470" >}} diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200820131145.md b/.history/hugo_themes/content/visual-ontology/_index_20200820131145.md deleted file mode 100644 index 94de26a70..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200820131145.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: SBOL Visual - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200820143924.md b/.history/hugo_themes/content/visual-ontology/_index_20200820143924.md deleted file mode 100644 index 1afccda58..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200820143924.md +++ /dev/null @@ -1,23 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Purpose - -People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. SBOL Visual aims to organize and systematize such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. At the same time, we aim to make this language simple and easy to use, allowing a high degree of flexibility and freedom in how such diagrams are organized, presented, and styled—in particular, it should be readily possible to create diagrams both by hand and with a wide variety of software programs. Finally, means are provided for extending the language with new and custom diagram elements, and for adoption of useful new elements into the language. For a quick introduction to SBOL Visual, please browse through the [IWBDA 2019 SBOL Visual presentation](https://github.com/SynBioDex/Community-Media/blob/master/2019/IWBDA19/SBOL-Visual.pptx). - -### Vision - -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200820151201.md b/.history/hugo_themes/content/visual-ontology/_index_20200820151201.md deleted file mode 100644 index 1b6a9c10d..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200820151201.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### Ontology \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824090902.md b/.history/hugo_themes/content/visual-ontology/_index_20200824090902.md deleted file mode 100644 index d99b53403..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824090902.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -Terms for glyphs to represent -DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", “AptamerGlyph“, “AssemblyScarGlyph” and “AssemblyScarGlyphAlternative” ) -different types of molecular entities (e.g. ProteinGlyph) -binary molecular interactions (e.g. “InhibitionGlyph“) -molecular interactions with multiple participants (e.g. “AssociationGlyph“). -A base term. The base term in the ontology is called “Glyph”. -Properties. SBOL-VO includes object properties such as “hasGlyph” and “isAlternativeOf” to define the relationships between different terms. -Annotations. Terms are annotated using properties such as “defaultGlyph” and “recommended”. -Ontological axioms. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824091147.md b/.history/hugo_themes/content/visual-ontology/_index_20200824091147.md deleted file mode 100644 index 0d474ddfc..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824091147.md +++ /dev/null @@ -1,29 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", “AptamerGlyph“, “AssemblyScarGlyph” and “AssemblyScarGlyphAlternative” ) - * different types of molecular entities (e.g. ProteinGlyph) - * binary molecular interactions (e.g. “InhibitionGlyph“) - * molecular interactions with multiple participants (e.g. “AssociationGlyph“). -* **A base term**. The base term in the ontology is called “Glyph”. -* **Properties**. SBOL-VO includes object properties such as “hasGlyph” and “isAlternativeOf” to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as “defaultGlyph” and “recommended”. -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824091716.md b/.history/hugo_themes/content/visual-ontology/_index_20200824091716.md deleted file mode 100644 index 66330b48e..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824091716.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -#### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -#### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"} REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824091948.md b/.history/hugo_themes/content/visual-ontology/_index_20200824091948.md deleted file mode 100644 index 265675a1f..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824091948.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -#### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -#### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824092016.md b/.history/hugo_themes/content/visual-ontology/_index_20200824092016.md deleted file mode 100644 index 80fa7ae17..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824092016.md +++ /dev/null @@ -1,44 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -#### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -#### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094029.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094029.md deleted file mode 100644 index 02fafe074..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094029.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -#### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -#### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [(http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094047.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094047.md deleted file mode 100644 index 463f681a1..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094047.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -#### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -#### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094151.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094151.md deleted file mode 100644 index 40530aa08..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094151.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -#### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -#### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"} interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094240.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094240.md deleted file mode 100644 index 3712086c0..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094240.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -#### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -#### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094330.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094330.md deleted file mode 100644 index c0aede755..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094330.md +++ /dev/null @@ -1,57 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094611.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094611.md deleted file mode 100644 index df1c3afdd..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094611.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -*Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - - Retrieving metadata about glyphs: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"} REST interface. Examples: - -http://vows.sbolstandard.org/metadata/CDSGlyph \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094700.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094700.md deleted file mode 100644 index 9144510fd..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094700.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -*Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -http://vows.sbolstandard.org/metadata/CDSGlyph \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094724.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094724.md deleted file mode 100644 index d2876ad20..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094724.md +++ /dev/null @@ -1,69 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -*Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -* [http://vows.sbolstandard.org/metadata/CDSGlyph](https://vows.sbolstandard.org/metadata/CDSGlyph) \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-ontology/_index_20200824094821.md b/.history/hugo_themes/content/visual-ontology/_index_20200824094821.md deleted file mode 100644 index a9282844d..000000000 --- a/.history/hugo_themes/content/visual-ontology/_index_20200824094821.md +++ /dev/null @@ -1,77 +0,0 @@ ---- -title: SBOL Visual Ontology - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -### SBOL Visual Ontology - -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. - -* **Terms for glyphs** to represent - * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssemblyScarGlyphAlternative)" ) - * different types of molecular entities (e.g. "[ProteinGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#ProteinGlyph)") - * binary molecular interactions (e.g. "[InhibitionGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#InhibitionGlyph)") - * molecular interactions with multiple participants (e.g. "[AssociationGlyph](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html#AssociationGlyph)"). -* **A base term**. The base term in the ontology is called "Glyph". -* **Properties**. SBOL-VO includes object properties such as "hasGlyph" and "isAlternativeOf" to define the relationships between different terms. -* **Annotations**. Terms are annotated using properties such as "defaultGlyph" and "recommended". -* **Ontological axioms**. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes. - -### Browse - -[Browse the SBOL-VO terms via an HTML page](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.html). - -The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege. - -### Download - -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/SBOL-visual/Ontology/v2/sbol-vo.rdf) to download the ontology. - -### Computational access: The SBOL-VO web service (SBOL-VOWS) - -**An HTTP-based glyph service**: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The `http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"}` REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO: - -* [http://vows.sbolstandard.org/glyph/AptamerGlyph](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000031](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) -* [http://vows.sbolstandard.org/glyph/SO:0000033](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface : - -* [http://vows.sbolstandard.org/glyph/SO:0000031/svg](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.svg) -* [http://vows.sbolstandard.org/glyph/SO:0000031/png](http://synbiodex.github.io/SBOL-visual/Glyphs/aptamer/aptamer-specification.png) - -**Mapping glyphs to terms from ontologies**: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the `http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"}` interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph. - -* [http://vows.sbolstandard.org/mapping/SO:0000031](https://vows.sbolstandard.org/mapping/SO:0000031) -* [http://vows.sbolstandard.org/mapping/SO:0000033](https://vows.sbolstandard.org/mapping/SO:0000033) - -**Searching for glyphs**: The SBOL-VO-WS can be used to search for glyphs using the `http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"}` REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples: - -*Returning information about the CDSGlyph and CDSAlternativeGlyph terms: - * [http://vows.sbolstandard.org/query/CDSGlyph](https://vows.sbolstandard.org/query/CDSGlyph) - * [http://vows.sbolstandard.org/query/SO:0000316](https://vows.sbolstandard.org/query/SO:0000316) -* Returning information about all glyphs that represent molecular interactions: - * [http://vows.sbolstandard.org/query/SBO:0000231](https://vows.sbolstandard.org/query/SBO:0000231) - -**Retrieving metadata about glyphs**: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the `http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"}` REST interface. Examples: - -* [http://vows.sbolstandard.org/metadata/CDSGlyph](https://vows.sbolstandard.org/metadata/CDSGlyph) - -### Programmatic access to SBOL-VOWS - -Python and Java examples and related documentation can be found in the following GitHub repository: - -[https://github.com/dissys/sbol-visual-client](https://github.com/dissys/sbol-visual-client) - -The web service returns data using the RDF/JSON format. Hence, any RDF or JSON library can be used to access information regarding the mapping, query, and metadata interfaces. Please note that examples are provided using the RDFLib and Jena libraries for Python and Java programming languages respectively. \ No newline at end of file diff --git a/.history/hugo_themes/content/visual-specification/_index_20201215202412.md b/.history/hugo_themes/content/visual-specification/_index_20201215202412.md deleted file mode 100644 index 70d8de975..000000000 --- a/.history/hugo_themes/content/visual-specification/_index_20201215202412.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: SBOL Visual Specification - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" ---- - -[Report an Issue with the Current SBOL Visual Specification](https://github.com/SynBioDex/SBOL-visual/issues) - -___ - - -| **2.x.x Release** | [View Glyphs]({{< relref "visual-glyphs" >}}) | | -|---|---|---| -| **2.3.0**
SBOL Visual 2.3 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.3 enhances the prior SBOL Visual 2.2 standard as follows:
  • Adds higher-level "interactions with interactions", such as an inducer molecule stimulating a repression interaction
  • Binding with a nucleic acid backbone can be shown by overlapping glyphs, as with other molecular complexes
  • Recommends using polypeptide region glyph to show 2A sequences
  • Adds new "unspecified interaction" glyph for visualizing interactions whose nature is unknown
  • Deprecates "insulator" glyph in favor of new "inert DNA spacer" glyph
|{{% staticref "docs/SBOL-Visual-2.3.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.2.0**
SBOL Visual 2.2 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions).

SBOL Visual 2.2 enhances the prior SBOL Visual 2.1 standard as follows:
  • Grounding for molecular species glyphs is changed from BioPAX to SBO (BioPAX terms are retained as deprecated alternatives).
  • New glyphs are added for introns and polypeptide regions (e.g., protein domains).
  • The macromolecule glyph often confused with yeast is deprecated, and a new glyph for proteins added
  • Small polygons are recommended as alternative glyphs for simple chemicals.
| {{% staticref "docs/SBOL-Visual-2.2.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.1.0**
SBOL Visual 2.1 provides a simple and flexible language for diagrams of genetic systems and design, including both structure (e.g., nucleic acid sequence features) and function (e.g., regulatory interactions and reactions). SBOL Visual 2.1 enhances the prior SBOL Visual 2.0 standard with the addition of methods for showing modular structure and mappings between elements of a system, and new glyphs for indicating genomic context (e.g., integration into a plasmid or genome) and for stop codons. Additionally, interactions arrows were modified such that they can split or join, with the glyph at the split or join indicating either superposition or a chemical process. | {{% staticref "docs/SBOL-Visual-2.1.pdf" "newtab" %}}Specification{{% /staticref %}} | | -| **2.0.0**
A diagram language and collection of symbols that can be used to graphically depict a genetic design and its functional interactions. SBOL Visual 2.0 builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs | {{% staticref "docs/SBOLVisual_Specification_2_0_0.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://www.degruyter.com/view/journals/jib/15/1/article-20170074.xml) | - -| **1.x.x Release** | | | -|---|---|---| -| **1.0.0**
A set of symbols that can be used to graphically depict functional information encoded by nucleic acid sequences. Each symbol in the set has three components: a shape, a display name, and a definition. | {{% staticref "docs/BBFRFC93.pdf" "newtab" %}}Specification{{% /staticref %}} | [Cite](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002310) | diff --git a/.history/hugo_themes/layouts/partials/li_card_20201201113555.html b/.history/hugo_themes/layouts/partials/li_card_20201201113555.html deleted file mode 100644 index 753cf2f32..000000000 --- a/.history/hugo_themes/layouts/partials/li_card_20201201113555.html +++ /dev/null @@ -1,70 +0,0 @@ -{{ $item := . }} - - -{{/* Dynamic view adjusts to content type. */}} -{{ $show_buttons := false }} -{{ if eq $item.Type "talk" }} - {{ $show_buttons = true }} -{{ else if eq $item.Type "publication" }} - {{ $show_buttons = true }} -{{ end }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -
- - {{ if eq $item.Type "talk" }} -
- {{ if $item.Params.authors }} -
- {{ partial "page_metadata_authors" $item }} -
- {{ end }} - - {{ partial "functions/get_event_dates" $item }} - - {{ with $item.Params.location }} - - {{ . }} - {{ end }} -
- {{ else }} - {{ partial "page_metadata" (dict "page" $item "is_list" 1) }} - {{ end }} - - {{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} - {{ $anchor := $item.Params.image.focal_point | default "Smart" }} - {{ with $resource }} - {{ $image := .Fill (printf "918x517 q90 %s" $anchor) }} - - {{ $item.Title }} - - {{end}} - -

- {{ $item.Title }} -

- - {{ with $summary }} - -
-

{{.}}

-
- - {{ end }} - - {{ if $show_buttons }} -
- {{ partial "page_links" (dict "page" $item "is_list" 1) }} -
- {{ end }} - -
diff --git a/.history/hugo_themes/layouts/partials/li_card_20201201113617.html b/.history/hugo_themes/layouts/partials/li_card_20201201113617.html deleted file mode 100644 index 11bf5c39c..000000000 --- a/.history/hugo_themes/layouts/partials/li_card_20201201113617.html +++ /dev/null @@ -1,70 +0,0 @@ -{{ $item := . }} - - -{{/* Dynamic view adjusts to content type. */}} -{{ $show_buttons := false }} -{{ if eq $item.Type "talk" }} - {{ $show_buttons = true }} -{{ else if eq $item.Type "publication" }} - {{ $show_buttons = true }} -{{ end }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -
- - {{ if eq $item.Type "talk" }} -
- {{ if $item.Params.authors }} -
- {{ partial "page_metadata_authors" $item }} -
- {{ end }} - - {{ partial "functions/get_event_dates" $item }} - - {{ with $item.Params.location }} - - {{ . }} - {{ end }} -
- {{ else }} - {{ partial "page_metadata" (dict "page" $item "is_list" 1) }} - {{ end }} - - {{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} - {{ $anchor := $item.Params.image.focal_point | default "Smart" }} - {{ with $resource }} - {{ $image := $resource.Fit "20x20" }} - - {{ $item.Title }} - - {{end}} - -

- {{ $item.Title }} -

- - {{ with $summary }} - -
-

{{.}}

-
- - {{ end }} - - {{ if $show_buttons }} -
- {{ partial "page_links" (dict "page" $item "is_list" 1) }} -
- {{ end }} - -
diff --git a/.history/hugo_themes/layouts/partials/li_card_20201201113645.html b/.history/hugo_themes/layouts/partials/li_card_20201201113645.html deleted file mode 100644 index fb419627e..000000000 --- a/.history/hugo_themes/layouts/partials/li_card_20201201113645.html +++ /dev/null @@ -1,70 +0,0 @@ -{{ $item := . }} - - -{{/* Dynamic view adjusts to content type. */}} -{{ $show_buttons := false }} -{{ if eq $item.Type "talk" }} - {{ $show_buttons = true }} -{{ else if eq $item.Type "publication" }} - {{ $show_buttons = true }} -{{ end }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -
- - {{ if eq $item.Type "talk" }} -
- {{ if $item.Params.authors }} -
- {{ partial "page_metadata_authors" $item }} -
- {{ end }} - - {{ partial "functions/get_event_dates" $item }} - - {{ with $item.Params.location }} - - {{ . }} - {{ end }} -
- {{ else }} - {{ partial "page_metadata" (dict "page" $item "is_list" 1) }} - {{ end }} - - {{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} - {{ $anchor := $item.Params.image.focal_point | default "Smart" }} - {{ with $resource }} - {{ $image := $resource.Fit "600x400" }} - - {{ $item.Title }} - - {{end}} - -

- {{ $item.Title }} -

- - {{ with $summary }} - -
-

{{.}}

-
- - {{ end }} - - {{ if $show_buttons }} -
- {{ partial "page_links" (dict "page" $item "is_list" 1) }} -
- {{ end }} - -
diff --git a/.history/hugo_themes/layouts/partials/li_card_20201201114526.html b/.history/hugo_themes/layouts/partials/li_card_20201201114526.html deleted file mode 100644 index fb419627e..000000000 --- a/.history/hugo_themes/layouts/partials/li_card_20201201114526.html +++ /dev/null @@ -1,70 +0,0 @@ -{{ $item := . }} - - -{{/* Dynamic view adjusts to content type. */}} -{{ $show_buttons := false }} -{{ if eq $item.Type "talk" }} - {{ $show_buttons = true }} -{{ else if eq $item.Type "publication" }} - {{ $show_buttons = true }} -{{ end }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -
- - {{ if eq $item.Type "talk" }} -
- {{ if $item.Params.authors }} -
- {{ partial "page_metadata_authors" $item }} -
- {{ end }} - - {{ partial "functions/get_event_dates" $item }} - - {{ with $item.Params.location }} - - {{ . }} - {{ end }} -
- {{ else }} - {{ partial "page_metadata" (dict "page" $item "is_list" 1) }} - {{ end }} - - {{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} - {{ $anchor := $item.Params.image.focal_point | default "Smart" }} - {{ with $resource }} - {{ $image := $resource.Fit "600x400" }} - - {{ $item.Title }} - - {{end}} - -

- {{ $item.Title }} -

- - {{ with $summary }} - -
-

{{.}}

-
- - {{ end }} - - {{ if $show_buttons }} -
- {{ partial "page_links" (dict "page" $item "is_list" 1) }} -
- {{ end }} - -
diff --git a/.history/hugo_themes/layouts/partials/page_author_card_20201202163814.html b/.history/hugo_themes/layouts/partials/page_author_card_20201202163814.html deleted file mode 100644 index dffdc5d2c..000000000 --- a/.history/hugo_themes/layouts/partials/page_author_card_20201202163814.html +++ /dev/null @@ -1,31 +0,0 @@ -{{ $page := .page }} -{{ $author_urlized := .username }} -{{ $site_type := site.Params.site_type | default "Person" }} -{{ $taxonomy := "authors" }} -{{ $profile_page := site.GetPage (printf "/%s/%s" $taxonomy $author_urlized) }} -{{ with $profile_page }} - {{ if isset .Params "superuser" }}{{/* Check an author profile exists. */}} - {{/* If it's a personal site and primary page author is superuser, link to the homepage rather than their profile page. */}} - {{ $profile_url := .RelPermalink }} - {{ if and (eq $site_type "Person") (eq .Params.superuser true) }} - {{ $profile_url = site.BaseURL }} - {{ end }} - {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} - {{ $avatar_shape := site.Params.avatar.shape | default "circle" }} -
- {{ if and site.Params.avatar.gravatar .Params.email }} - {{.Title}} - {{ else if $avatar }} - {{ $avatar_image := $avatar.Fill "270x270 Center" }} - {{.Title}} - {{ end }} - -
-
{{.Title}}
- {{ with .Params.role }}
{{. | markdownify | emojify}}
{{end}} - {{ with .Params.bio }}

{{. | markdownify | emojify}}

{{end}} - {{ partial "social_links" . }} -
-
- {{end}} -{{end}}{{/* Profile page block */}} diff --git a/.history/hugo_themes/layouts/partials/page_author_card_20201202163826.html b/.history/hugo_themes/layouts/partials/page_author_card_20201202163826.html deleted file mode 100644 index 69c0f9856..000000000 --- a/.history/hugo_themes/layouts/partials/page_author_card_20201202163826.html +++ /dev/null @@ -1,31 +0,0 @@ -{{ $page := .page }} -{{ $author_urlized := .username }} -{{ $site_type := site.Params.site_type | default "Person" }} -{{ $taxonomy := "authors" }} -{{ $profile_page := site.GetPage (printf "/%s/%s" $taxonomy $author_urlized) }} -{{ with $profile_page }} - {{ if isset .Params "superuser" }}{{/* Check an author profile exists. */}} - {{/* If it's a personal site and primary page author is superuser, link to the homepage rather than their profile page. */}} - {{ $profile_url := .RelPermalink }} - {{ if and (eq $site_type "Person") (eq .Params.superuser true) }} - {{ $profile_url = site.BaseURL }} - {{ end }} - {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} - {{ $avatar_shape := site.Params.avatar.shape | default "circle" }} -
- {{ if and site.Params.avatar.gravatar .Params.email }} - {{.Title}} - {{ else if $avatar }} - {{ $avatar_image := $avatar.Fit "270x270 Center" }} - {{.Title}} - {{ end }} - -
-
{{.Title}}
- {{ with .Params.role }}
{{. | markdownify | emojify}}
{{end}} - {{ with .Params.bio }}

{{. | markdownify | emojify}}

{{end}} - {{ partial "social_links" . }} -
-
- {{end}} -{{end}}{{/* Profile page block */}} diff --git a/.history/hugo_themes/layouts/partials/page_author_card_20201202163912.html b/.history/hugo_themes/layouts/partials/page_author_card_20201202163912.html deleted file mode 100644 index 8c36b4b66..000000000 --- a/.history/hugo_themes/layouts/partials/page_author_card_20201202163912.html +++ /dev/null @@ -1,31 +0,0 @@ -{{ $page := .page }} -{{ $author_urlized := .username }} -{{ $site_type := site.Params.site_type | default "Person" }} -{{ $taxonomy := "authors" }} -{{ $profile_page := site.GetPage (printf "/%s/%s" $taxonomy $author_urlized) }} -{{ with $profile_page }} - {{ if isset .Params "superuser" }}{{/* Check an author profile exists. */}} - {{/* If it's a personal site and primary page author is superuser, link to the homepage rather than their profile page. */}} - {{ $profile_url := .RelPermalink }} - {{ if and (eq $site_type "Person") (eq .Params.superuser true) }} - {{ $profile_url = site.BaseURL }} - {{ end }} - {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} - {{ $avatar_shape := site.Params.avatar.shape | default "circle" }} -
- {{ if and site.Params.avatar.gravatar .Params.email }} - {{.Title}} - {{ else if $avatar }} - {{ $avatar_image := $avatar.Fit "270x270" }} - {{.Title}} - {{ end }} - -
-
{{.Title}}
- {{ with .Params.role }}
{{. | markdownify | emojify}}
{{end}} - {{ with .Params.bio }}

{{. | markdownify | emojify}}

{{end}} - {{ partial "social_links" . }} -
-
- {{end}} -{{end}}{{/* Profile page block */}} diff --git a/.history/hugo_themes/layouts/partials/page_author_card_20201202164858.html b/.history/hugo_themes/layouts/partials/page_author_card_20201202164858.html deleted file mode 100644 index bed8a4c1c..000000000 --- a/.history/hugo_themes/layouts/partials/page_author_card_20201202164858.html +++ /dev/null @@ -1,31 +0,0 @@ -{{ $page := .page }} -{{ $author_urlized := .username }} -{{ $site_type := site.Params.site_type | default "Person" }} -{{ $taxonomy := "authors" }} -{{ $profile_page := site.GetPage (printf "/%s/%s" $taxonomy $author_urlized) }} -{{ with $profile_page }} - {{ if isset .Params "superuser" }}{{/* Check an author profile exists. */}} - {{/* If it's a personal site and primary page author is superuser, link to the homepage rather than their profile page. */}} - {{ $profile_url := .RelPermalink }} - {{ if and (eq $site_type "Person") (eq .Params.superuser true) }} - {{ $profile_url = site.BaseURL }} - {{ end }} - {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} - {{ $avatar_shape := site.Params.avatar.shape | default "circle" }} -
- {{ if and site.Params.avatar.gravatar .Params.email }} - {{.Title}} - {{ else if $avatar }} - {{ $avatar_image := $avatar.Fit "170x170" }} - {{.Title}} - {{ end }} - -
-
{{.Title}}
- {{ with .Params.role }}
{{. | markdownify | emojify}}
{{end}} - {{ with .Params.bio }}

{{. | markdownify | emojify}}

{{end}} - {{ partial "social_links" . }} -
-
- {{end}} -{{end}}{{/* Profile page block */}} diff --git a/.history/hugo_themes/layouts/partials/page_author_card_20201202164912.html b/.history/hugo_themes/layouts/partials/page_author_card_20201202164912.html deleted file mode 100644 index 400b7b87a..000000000 --- a/.history/hugo_themes/layouts/partials/page_author_card_20201202164912.html +++ /dev/null @@ -1,31 +0,0 @@ -{{ $page := .page }} -{{ $author_urlized := .username }} -{{ $site_type := site.Params.site_type | default "Person" }} -{{ $taxonomy := "authors" }} -{{ $profile_page := site.GetPage (printf "/%s/%s" $taxonomy $author_urlized) }} -{{ with $profile_page }} - {{ if isset .Params "superuser" }}{{/* Check an author profile exists. */}} - {{/* If it's a personal site and primary page author is superuser, link to the homepage rather than their profile page. */}} - {{ $profile_url := .RelPermalink }} - {{ if and (eq $site_type "Person") (eq .Params.superuser true) }} - {{ $profile_url = site.BaseURL }} - {{ end }} - {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} - {{ $avatar_shape := site.Params.avatar.shape | default "circle" }} -
- {{ if and site.Params.avatar.gravatar .Params.email }} - {{.Title}} - {{ else if $avatar }} - {{ $avatar_image := $avatar.Fit "10x10" }} - {{.Title}} - {{ end }} - -
-
{{.Title}}
- {{ with .Params.role }}
{{. | markdownify | emojify}}
{{end}} - {{ with .Params.bio }}

{{. | markdownify | emojify}}

{{end}} - {{ partial "social_links" . }} -
-
- {{end}} -{{end}}{{/* Profile page block */}} diff --git a/.history/hugo_themes/layouts/partials/page_author_card_20201202165330.html b/.history/hugo_themes/layouts/partials/page_author_card_20201202165330.html deleted file mode 100644 index 34f084859..000000000 --- a/.history/hugo_themes/layouts/partials/page_author_card_20201202165330.html +++ /dev/null @@ -1,31 +0,0 @@ -{{ $page := .page }} -{{ $author_urlized := .username }} -{{ $site_type := site.Params.site_type | default "Person" }} -{{ $taxonomy := "authors" }} -{{ $profile_page := site.GetPage (printf "/%s/%s" $taxonomy $author_urlized) }} -{{ with $profile_page }} - {{ if isset .Params "superuser" }}{{/* Check an author profile exists. */}} - {{/* If it's a personal site and primary page author is superuser, link to the homepage rather than their profile page. */}} - {{ $profile_url := .RelPermalink }} - {{ if and (eq $site_type "Person") (eq .Params.superuser true) }} - {{ $profile_url = site.BaseURL }} - {{ end }} - {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} - {{ $avatar_shape := site.Params.avatar.shape | default "circle" }} -
- {{ if and site.Params.avatar.gravatar .Params.email }} - {{.Title}} - {{ else if $avatar }} - {{ $avatar_image := $avatar.Fill "60x60" }} - {{.Title}} - {{ end }} - -
-
{{.Title}}
- {{ with .Params.role }}
{{. | markdownify | emojify}}
{{end}} - {{ with .Params.bio }}

{{. | markdownify | emojify}}

{{end}} - {{ partial "social_links" . }} -
-
- {{end}} -{{end}}{{/* Profile page block */}} diff --git a/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113322.html b/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113322.html deleted file mode 100644 index 8459e9574..000000000 --- a/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113322.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fit "100x80" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113355.html b/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113355.html deleted file mode 100644 index 8459e9574..000000000 --- a/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113355.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fit "100x80" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113409.html b/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113409.html deleted file mode 100644 index edbf89e23..000000000 --- a/.history/hugo_themes/layouts/partials/portfolio_li_card_20201201113409.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fit "20x20" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112511.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112511.html deleted file mode 100644 index 2502fdd11..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112511.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := .Resize (printf "550x q90 %s") }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112536.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112536.html deleted file mode 100644 index e0aa496a7..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112536.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := .Resize (printf "100x q90 %s") }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112641.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112641.html deleted file mode 100644 index 3fa5f377b..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112641.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fill "600x400" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112716.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112716.html deleted file mode 100644 index b97f48d2a..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112716.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fill "400x200" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112822.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112822.html deleted file mode 100644 index b92f66246..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112822.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fill "200x80" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112914.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112914.html deleted file mode 100644 index a5809029f..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112914.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $$resource.Fit "600x400" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112921.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112921.html deleted file mode 100644 index d3e8f1219..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112921.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fit "600x400" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/layouts/portfolio_li_card_20201201112949.html b/.history/hugo_themes/layouts/portfolio_li_card_20201201112949.html deleted file mode 100644 index 8459e9574..000000000 --- a/.history/hugo_themes/layouts/portfolio_li_card_20201201112949.html +++ /dev/null @@ -1,37 +0,0 @@ -{{ $item := .item }} -{{ $widget := .widget }} - -{{ $link := .link }} -{{ $target := .target }} - -{{/* Get summary. */}} -{{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify | truncate (site.Params.abstract_length | default 135) }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} -{{ $js_tag_classes := delimit (apply (apply $item.Params.tags "replace" "." " " "-") "printf" "js-id-%s" ".") " " }} - -
-
- {{ with $resource }} - {{ $image := $resource.Fit "100x80" }} - - - - {{ end }} -
-

{{ $item.Title | markdownify | emojify }}

- {{ with $summary }} -
-

{{ . }}

-
- {{ end }} -
-
-
diff --git a/.history/hugo_themes/themes/academic/layouts/shortcodes/cite_20200826104855.html b/.history/hugo_themes/themes/academic/layouts/shortcodes/cite_20200826104855.html deleted file mode 100644 index e69de29bb..000000000 diff --git a/.history/hugo_themes/themes/academic/layouts/shortcodes/cite_20200826105050.html b/.history/hugo_themes/themes/academic/layouts/shortcodes/cite_20200826105050.html deleted file mode 100644 index 62191e31d..000000000 --- a/.history/hugo_themes/themes/academic/layouts/shortcodes/cite_20200826105050.html +++ /dev/null @@ -1,17 +0,0 @@ -{{ $page := .Get "page" }} - -{{/* Default compact view. */}} -{{ $view := (.Get "view") | default 2 }} -{{ $view = int $view }} - -{{ with site.GetPage $page }} - {{ if eq $view 1 }} - {{ partial "li_list" . }} - {{ else if eq $view 3 }} - {{ partial "li_card" . }} - {{ else if eq $view 4 }} - {{ partial "li_citation" . }} - {{ else }} - {{ partial "li_compact" . }} - {{ end }} -{{ end }} \ No newline at end of file diff --git a/assets/images/logo.svg b/assets/images/logo.svg index f76289512..6a05613a8 100644 --- a/assets/images/logo.svg +++ b/assets/images/logo.svg @@ -1,13 +1,13 @@ + width="408" height="110" viewBox="0 0 407.7 110.2" style="enable-background:new 0 0 407.7 110.2;" xml:space="preserve"> +@media(prefers-color-scheme:dark){.st0{fill:#f8f8f2;}} h1 { font-size: 2.4rem; font-weight: 800; } +.article-style h2 { font-size: 1.6rem; font-weight: 700; margin-top: 2.25rem; } +.article-style h3 { font-size: 1.15rem; font-weight: 700; margin-top: 1.5rem; } +.article-style p, .article-style li { line-height: 1.7; } + +a { color: var(--sbol-green-ink); transition: none; } +.article-title a, h3.article-title a:hover { transition: none; } +a:hover { color: var(--sbol-green-ink); text-decoration: underline; } +.dark a { color: var(--sbol-green-ink); transition: none; } +.article-title a, h3.article-title a:hover { transition: none; } +.text-muted, .article-metadata, .article-date { color: var(--sbol-muted) !important; } +code, pre code { color: var(--sbol-ink-2); background: var(--sbol-code-bg); } +.dark code { color: var(--sbol-ink-2); } +.universal-wrapper h1 { text-align: center; } + +// One container rule at every width: fluid up to --sbol-container with --sbol-gutter on each side. Applies to the page wrapper, +// the theme's Bootstrap containers (navbar, homepage widgets), article pages, bands, panels and the footer. +.universal-wrapper, #navbar-main > .container, .home-section .container, .page-header .container, .search-results > .container { + width: 100%; max-width: var(--sbol-container) !important; margin-left: auto; margin-right: auto; padding-left: var(--sbol-gutter); padding-right: var(--sbol-gutter); +} + +// Shared layout helpers +.sbol-section { margin: var(--sbol-space-5) 0; } +// Rhythm: content starts 2rem below a hero; pages end with 3rem of air unless a band closes them. +.sbol-hero + .universal-wrapper { padding-top: var(--sbol-space-4); } +.sbol-hero + .universal-wrapper > .sbol-features:first-child { margin-top: var(--sbol-space-2); } +.sbol-hero + .universal-wrapper > .sbol-tabs:first-child, .sbol-hero + .universal-wrapper > .sbol-filters:first-child { margin-top: 0; } +// Pages end with air unless a full-bleed band closes them. `:last-of-type` so a trailing (gallery lightbox) does not defeat it. +.page-body .universal-wrapper:last-of-type { padding-bottom: var(--sbol-space-5); } +.page-body .sbol-band:last-of-type + .universal-wrapper { padding-bottom: 0; } +.sbol-section__title { font-size: 1.6rem; font-weight: 700; color: var(--sbol-ink); margin: 0 0 .35rem; padding-bottom: .5rem; border-bottom: 1px solid var(--sbol-rule); } +.sbol-section__desc { color: var(--sbol-ink-3); font-size: .98rem; line-height: 1.7; margin: .5rem 0 1.25rem; max-width: 70ch; } +.sbol-label { font-size: .72rem; font-weight: 700; letter-spacing: .08em; text-transform: uppercase; color: var(--sbol-muted); } +.sbol-lead { font-size: 1.05rem; line-height: 1.65; color: var(--sbol-ink-2); } +.sbol-toc { position: sticky; top: 5rem; font-size: .88rem; } +.sbol-toc nav ul { list-style: none; padding-left: 0; } +.sbol-toc nav ul ul { padding-left: .9rem; } +.sbol-toc a { color: var(--sbol-ink-3); text-decoration: none; display: block; padding: .18rem 0; } +.sbol-toc a:hover { color: var(--sbol-green-ink); } + +// Generic page layout (layouts/_default/sbol-page.html) +.sbol-page { padding-top: var(--sbol-space-4); padding-bottom: var(--sbol-space-5); } +.sbol-page__body { max-width: 78ch; margin: 0; } +.sbol-page--toc { display: grid; grid-template-columns: 220px minmax(0, 1fr); gap: 2.5rem; } +.sbol-page--toc .sbol-page__body { margin: 0; } +@media (max-width: 860px) { .sbol-page--toc { grid-template-columns: 1fr; } .sbol-page--toc .sbol-toc { position: static; } } +.article-style img { max-width: 100%; height: auto; } +.sbol-section__head { display: flex; align-items: flex-start; justify-content: space-between; gap: 1rem; flex-wrap: wrap; .sbol-section__title { border-bottom: 0; padding-bottom: 0; } } diff --git a/assets/scss/sbol/_buttons.scss b/assets/scss/sbol/_buttons.scss new file mode 100644 index 000000000..f22111681 --- /dev/null +++ b/assets/scss/sbol/_buttons.scss @@ -0,0 +1,14 @@ +// Two buttons: primary (black on brand green) and secondary (green-ink outline). Sizes: default, --lg, --sm. +.sbol-btn, .btn-primary, .btn.btn-primary { + display: inline-flex; align-items: center; gap: .45rem; background: var(--sbol-green); color: #000 !important; + border: 1px solid var(--sbol-green); border-radius: var(--sbol-radius-sm); padding: .5rem 1.05rem; font-weight: 700; font-size: .92rem; + line-height: 1.3; text-decoration: none !important; transition: background-color .12s ease, border-color .12s ease; + &:hover, &:focus { background: var(--sbol-green-hover); border-color: var(--sbol-green-hover); color: #000 !important; } +} +.sbol-btn--secondary, .btn-outline-primary, .btn.btn-outline-primary { + background: transparent; color: var(--sbol-green-ink) !important; border: 1px solid var(--sbol-green-ink); + &:hover, &:focus { background: var(--sbol-green-tint); color: var(--sbol-green-ink) !important; } +} +.sbol-btn--lg { padding: .7rem 1.4rem; font-size: 1.02rem; } +.sbol-btn--sm { padding: .35rem .8rem; font-size: .8rem; } +.sbol-link-more { font-weight: 700; color: var(--sbol-green-ink); text-decoration: none; &:hover { text-decoration: underline; } } diff --git a/assets/scss/sbol/_cards.scss b/assets/scss/sbol/_cards.scss new file mode 100644 index 000000000..83ae787db --- /dev/null +++ b/assets/scss/sbol/_cards.scss @@ -0,0 +1,131 @@ +// Cards, feature grids, callouts, bands, split rows, stats, steps, logos: the shared building blocks. +%sbol-card-surface { + background: var(--sbol-card); border: 1px solid var(--sbol-card-border); border-radius: var(--sbol-radius); box-shadow: none; +} +// The one hover accent for interactive surfaces: the border turns brand green and the title turns green ink. No shadow, no motion. +%sbol-hoverable { + transition: border-color .12s ease, background-color .12s ease; + &:hover, &:focus-visible { border-color: var(--sbol-green); background: var(--sbol-green-tint); } + &:hover .sbol-card__title, &:focus-visible .sbol-card__title, &:hover .sbol-lead__title, &:hover .jc-card-label { color: var(--sbol-green-ink); } +} +.sbol-cards { display: grid; grid-template-columns: repeat(auto-fill, minmax(220px, 1fr)); gap: 1rem; margin: 1rem 0; } +.sbol-cards--wide { grid-template-columns: repeat(auto-fill, minmax(290px, 1fr)); gap: 1.5rem; } +.sbol-cards--narrow { grid-template-columns: repeat(auto-fill, minmax(180px, 1fr)); } +.sbol-card { + @extend %sbol-card-surface; + display: flex; flex-direction: column; gap: .35rem; padding: 1.25rem 1.3rem; color: inherit; text-decoration: none; + &:hover { text-decoration: none; color: inherit; } + &.is-link { @extend %sbol-hoverable; } +} +.sbol-card__icon { color: var(--sbol-green); font-size: 1.35rem; margin-bottom: .3rem; } +.sbol-card__title { font-size: 1rem; font-weight: 700; color: var(--sbol-ink); margin: 0; line-height: 1.3; } +.sbol-card__title a { color: inherit; text-decoration: none; &:hover { color: var(--sbol-green-ink); } } +.sbol-card__desc { font-size: .86rem; color: var(--sbol-ink-3); line-height: 1.6; margin: 0; flex: 1; } +.sbol-card__meta { font-size: .78rem; color: var(--sbol-muted); } +.sbol-card__actions { display: flex; flex-wrap: wrap; gap: .5rem; margin-top: .6rem; } +.sbol-card__header { display: flex; align-items: center; justify-content: space-between; gap: .5rem; } +.sbol-card__ext { color: var(--sbol-muted); font-size: .85rem; } +.sbol-card--muted { background: var(--sbol-paper-2); opacity: .9; } +.sbol-card--cta { border: 2px dashed var(--sbol-card-border); background: var(--sbol-paper-2); align-items: center; text-align: center; justify-content: center; } + +// Feature grid: icon, title, description, centered (benefits, reasons) +.sbol-features { display: grid; grid-template-columns: repeat(auto-fit, minmax(210px, 1fr)); gap: var(--sbol-space-4) var(--sbol-space-3); margin: var(--sbol-space-4) 0 var(--sbol-space-5); text-align: center; } +.sbol-feature__icon { color: var(--sbol-green); font-size: 1.6rem; margin-bottom: .6rem; } +.sbol-feature__title { font-size: 1.02rem; font-weight: 700; color: var(--sbol-ink); margin: 0 0 .35rem; } +.sbol-feature__desc { font-size: .9rem; color: var(--sbol-ink-3); line-height: 1.6; margin: 0; } + +// Callout: inline tinted box with icon, text and a button (GenAI prompts) +.sbol-callout { + display: flex; align-items: center; gap: 1.25rem; background: var(--sbol-green-tint); border: 1px solid var(--sbol-band-border); + border-radius: var(--sbol-radius); padding: 1.4rem 1.6rem; margin: 2rem 0; + &__icon { color: var(--sbol-green); font-size: 1.8rem; flex-shrink: 0; } + &__text { flex: 1; } + &__title { font-size: 1.02rem; font-weight: 700; color: var(--sbol-ink); margin: 0 0 .25rem; } + &__desc { font-size: .9rem; color: var(--sbol-ink-3); line-height: 1.6; margin: 0; } + @media (max-width: 640px) { flex-direction: column; align-items: flex-start; } +} + +// Band: full-bleed light section (closing calls to action). One per page at most. +.sbol-band { background: var(--sbol-band); border-top: 1px solid var(--sbol-band-border); padding: var(--sbol-space-5) var(--sbol-space-3); margin-top: var(--sbol-space-5); margin-bottom: 0; } +.sbol-band__inner { max-width: var(--sbol-container); margin: 0 auto; padding: 0 var(--sbol-gutter); } +.sbol-band__inner--center { text-align: center; max-width: 760px; } +.sbol-band__title { font-size: 1.6rem; font-weight: 800; color: var(--sbol-ink); margin: 0 0 .5rem; } +.sbol-band__desc { font-size: .98rem; color: var(--sbol-ink-3); line-height: 1.7; margin: 0 0 1.5rem; } + +// Split row: image beside text, alternating (tool spotlights) +.sbol-split { display: grid; grid-template-columns: 1fr 1fr; gap: 3rem; align-items: center; margin: 3.5rem 0; } +.sbol-split--flip .sbol-split__media { order: 2; } +.sbol-split__media img { width: 100%; height: auto; border-radius: var(--sbol-radius-img); border: 1px solid var(--sbol-card-border); } +.sbol-split__title { font-size: 1.4rem; font-weight: 800; margin: 0 0 .5rem; } +.sbol-split__desc { color: var(--sbol-ink-2); line-height: 1.65; } +.sbol-split ul { padding-left: 1.2rem; color: var(--sbol-ink-2); } +@media (max-width: 760px) { .sbol-split { grid-template-columns: 1fr; gap: 1.5rem; } .sbol-split--flip .sbol-split__media { order: 0; } } + +// Stats +.sbol-stats { display: grid; grid-template-columns: repeat(auto-fit, minmax(140px, 1fr)); gap: 1.5rem; text-align: center; background: var(--sbol-green-tint); border: 1px solid var(--sbol-band-border); border-radius: var(--sbol-radius); padding: 2rem 1.5rem 1.5rem; margin: 2.5rem 0; } +.sbol-stat__number { display: block; font-size: 2.2rem; font-weight: 900; color: var(--sbol-green-ink); line-height: 1; } +.sbol-stat__label { display: block; font-size: .78rem; font-weight: 700; letter-spacing: .08em; text-transform: uppercase; color: var(--sbol-ink-3); margin-top: .35rem; } +.sbol-stats__note { grid-column: 1 / -1; font-size: .88rem; color: var(--sbol-ink-3); margin: 0; max-width: 60ch; justify-self: center; } + +// Numbered steps +.sbol-steps { display: grid; grid-template-columns: repeat(auto-fit, minmax(220px, 1fr)); gap: 1.5rem; margin: 1.5rem 0; } +.sbol-step { display: flex; gap: .9rem; align-items: flex-start; } +.sbol-step__num { flex-shrink: 0; width: 34px; height: 34px; border-radius: 50%; background: var(--sbol-green); color: #000; font-weight: 800; display: flex; align-items: center; justify-content: center; } +.sbol-step h4 { font-size: 1rem; margin: .3rem 0 .3rem; } +.sbol-step p { font-size: .88rem; color: var(--sbol-ink-3); line-height: 1.6; margin: 0; } + +// Logo grid +.sbol-logos { display: grid; grid-template-columns: repeat(auto-fill, minmax(140px, 1fr)); gap: 1.5rem 2rem; align-items: center; margin: 1.5rem 0; } +.sbol-logos img { max-width: 100%; max-height: 48px; width: auto; filter: grayscale(1); opacity: .75; transition: filter .15s, opacity .15s; } +.sbol-logos img:hover { filter: none; opacity: 1; } +.dark .sbol-logos img { filter: grayscale(1) invert(1); } + +// Card variants used across pages (all share %sbol-card-surface and the one hover accent) +.sbol-card--compact { padding: .9rem 1rem; gap: .25rem; } +.sbol-card--figure { padding: 0; overflow: hidden; align-items: stretch; } +// Nested radius rule: image 8px, sitting 4px inside a 12px card, so both corners share the same center in light and dark. +.sbol-card--figure .sbol-card__figure { display: block; width: 100%; padding: 4px 4px 0; overflow: hidden; } +.sbol-card--figure .sbol-card__figure img { display: block; width: 100%; height: auto; border-radius: var(--sbol-radius-img); } +// Contained artwork (gallery figures, logos): the image is letterboxed, so the rounded surface belongs to the panel behind it. +.sbol-card--figure .sbol-card__figure--contain { height: 220px; display: flex; align-items: center; justify-content: center; background: var(--sbol-paper-2); border-radius: var(--sbol-radius-img); } +.sbol-card--figure .sbol-card__figure--contain img { width: auto; height: auto; max-width: calc(100% - 1.5rem); max-height: calc(100% - 1.5rem); object-fit: contain; border-radius: var(--sbol-radius-img); } +.sbol-card--figure .sbol-card__body { padding: .9rem 1rem 1rem; display: flex; flex-direction: column; gap: .25rem; } +.sbol-card--figure .sbol-card__label { padding: .9rem 1rem; font-weight: 700; font-size: 1rem; color: var(--sbol-green-ink); text-align: center; } +.sbol-card--glyph { align-items: center; text-align: center; padding: 1.1rem .6rem .7rem; gap: .5rem; background: var(--sbol-paper-2); } +.sbol-card--glyph img { width: 64px; height: 64px; object-fit: contain; } +.sbol-card--glyph span { font-size: .72rem; color: var(--sbol-ink-3); line-height: 1.3; } +.dark .sbol-card--glyph img { background: #fff; border-radius: var(--sbol-radius-sm); padding: 4px; } +.sbol-card--accent { border-left: 5px solid var(--sbol-green); padding: 1.6rem 1.8rem; gap: .5rem; } +.sbol-card--accent .sbol-card__head { display: flex; align-items: center; gap: .8rem; flex-wrap: wrap; } +.sbol-card--accent .sbol-card__headline { font-size: 1.5rem; font-weight: 800; margin: 0; } +.sbol-card--accent .sbol-card__summary { color: var(--sbol-ink-2); line-height: 1.65; margin: 0; max-width: 80ch; } +// Cards whose title carries the primary link: the whole surface is clickable and takes the shared hover accent. +// Nested links (authors, PDF/Cite/DOI buttons, figure) stay above the overlay. +.sbol-card--linked { + position: relative; + transition: border-color .12s ease, background-color .12s ease; + &:hover, &:focus-within { border-color: var(--sbol-green); background: var(--sbol-green-tint); } + &:hover .sbol-card__title, &:focus-within .sbol-card__title, &:hover .sbol-card__title a { color: var(--sbol-green-ink); } + .sbol-card__title > a::after { content: ""; position: absolute; inset: 0; } + .sbol-card__actions, .sbol-card__figure, .sbol-card__meta a, .sbol-card__ext { position: relative; z-index: 1; } +} + +button.sbol-card { appearance: none; -webkit-appearance: none; font: inherit; text-align: left; cursor: pointer; } +button.sbol-card:focus-visible { outline: 3px solid var(--sbol-focus); outline-offset: 2px; } + +// Lead card (post lists): image beside text +.sbol-lead { + @extend %sbol-card-surface; @extend %sbol-hoverable; + display: grid; grid-template-columns: 1fr 1fr; overflow: hidden; margin: var(--sbol-space-4) 0 2.5rem; text-decoration: none; color: inherit; + &:hover { text-decoration: none; color: inherit; } + &--no-img { grid-template-columns: 1fr; } +} +.sbol-lead__img { overflow: hidden; min-height: 300px; padding: 4px; img { width: 100%; height: 100%; object-fit: cover; display: block; border-radius: var(--sbol-radius-img); } } +.sbol-lead__body { padding: 2.25rem; display: flex; flex-direction: column; justify-content: center; gap: .4rem; } +.sbol-lead__title { font-size: 1.6rem; font-weight: 700; line-height: 1.25; margin: .25rem 0 0; color: var(--sbol-ink); } +.sbol-lead__summary { font-size: 1rem; color: var(--sbol-ink-3); line-height: 1.7; margin: .25rem 0 .75rem; } +@media (max-width: 860px) { .sbol-lead { grid-template-columns: 1fr; } .sbol-lead__img { min-height: 200px; } .sbol-lead__body { padding: 1.5rem; } } +.sbol-card--row { display: grid; grid-template-columns: auto minmax(0, 1fr); gap: .9rem; align-items: start; padding: 1rem 1.25rem; } +.sbol-card--row .sbol-card__rowicon { color: var(--sbol-green-ink); font-size: 1rem; margin-top: .2rem; } +.sbol-card--row .sbol-card__title { font-size: 1.02rem; } +.sbol-cardlist { display: flex; flex-direction: column; } diff --git a/assets/scss/sbol/_fonts.scss b/assets/scss/sbol/_fonts.scss new file mode 100644 index 000000000..f4f2c044c --- /dev/null +++ b/assets/scss/sbol/_fonts.scss @@ -0,0 +1,7 @@ +// Nacelle, self-hosted from static/fonts. Weights used by the site: 400, 700, 900 (with italics). +@font-face { font-family: 'Nacelle'; src: url('/fonts/Nacelle-Regular.woff2') format('woff2'); font-weight: 400; font-style: normal; font-display: swap; } +@font-face { font-family: 'Nacelle'; src: url('/fonts/Nacelle-Italic.woff2') format('woff2'); font-weight: 400; font-style: italic; font-display: swap; } +@font-face { font-family: 'Nacelle'; src: url('/fonts/Nacelle-Bold.woff2') format('woff2'); font-weight: 700; font-style: normal; font-display: swap; } +@font-face { font-family: 'Nacelle'; src: url('/fonts/Nacelle-BoldItalic.woff2') format('woff2'); font-weight: 700; font-style: italic; font-display: swap; } +@font-face { font-family: 'Nacelle'; src: url('/fonts/Nacelle-Heavy.woff2') format('woff2'); font-weight: 900; font-style: normal; font-display: swap; } +@font-face { font-family: 'Nacelle'; src: url('/fonts/Nacelle-HeavyItalic.woff2') format('woff2'); font-weight: 900; font-style: italic; font-display: swap; } diff --git a/assets/scss/sbol/_footer.scss b/assets/scss/sbol/_footer.scss new file mode 100644 index 000000000..c998da00f --- /dev/null +++ b/assets/scss/sbol/_footer.scss @@ -0,0 +1,15 @@ +// Footer: three complementary columns, then license, copyright and build date. +// The theme wraps the footer in .page-footer > .container; release it so the background runs edge to edge. +.page-footer > .container { max-width: none !important; width: 100%; padding-left: 0; padding-right: 0; } +.sbol-footer { background: var(--sbol-paper-2); border-top: 1px solid var(--sbol-rule); padding: var(--sbol-space-5) 0 var(--sbol-space-4); margin-top: 0; font-size: .88rem; text-align: left; } +.sbol-footer__inner { max-width: var(--sbol-container); margin: 0 auto; padding: 0 var(--sbol-gutter); } +.sbol-footer__cols { display: grid; grid-template-columns: repeat(auto-fit, minmax(200px, 1fr)); gap: 2rem 3rem; } +.sbol-footer__heading { font-size: .72rem; font-weight: 700; letter-spacing: .1em; text-transform: uppercase; color: var(--sbol-muted); margin: 0 0 .7rem; text-align: left; } +.sbol-footer ul { list-style: none; padding: 0; margin: 0; } +.sbol-footer li { margin: .3rem 0; } +.sbol-footer a { color: var(--sbol-ink-2); text-decoration: none; &:hover { color: var(--sbol-green-ink); text-decoration: underline; } } +.sbol-footer__connect a i { width: 1.2rem; color: var(--sbol-green-ink); margin-right: .35rem; } +.sbol-footer__bottom { margin-top: var(--sbol-space-4); padding-top: var(--sbol-space-2); border-top: 1px solid var(--sbol-rule); color: var(--sbol-muted); font-size: .8rem; } +.sbol-footer__bottom a { color: var(--sbol-green-ink); } +// Hide the theme's default footer text if it is rendered by another partial +.site-footer .powered-by:empty { display: none; } diff --git a/assets/scss/sbol/_hero.scss b/assets/scss/sbol/_hero.scss new file mode 100644 index 000000000..b09984a41 --- /dev/null +++ b/assets/scss/sbol/_hero.scss @@ -0,0 +1,25 @@ +// Section hero band, shared by every list page, plus the section sub-navigation tabs. +.sbol-hero { + background: linear-gradient(135deg, var(--sbol-hero-a) 0%, var(--sbol-hero-b) 100%); + padding: var(--sbol-space-5) var(--sbol-space-3) 2.75rem; text-align: center; + &--with-subnav { padding-bottom: 0; } +} +.sbol-hero__inner { max-width: 760px; margin: 0 auto; } +.sbol-hero__eyebrow { display: inline-block; background: var(--sbol-green); color: #000; font-size: .72rem; font-weight: 700; letter-spacing: .1em; text-transform: uppercase; padding: .25rem .85rem; border-radius: var(--sbol-radius-pill); margin-bottom: 1rem; } +.sbol-hero__title { font-size: 2.4rem; font-weight: 800; line-height: 1.15; color: var(--sbol-ink); margin: 0 0 .6rem; } +.sbol-hero__sub { font-size: 1.05rem; line-height: 1.65; color: var(--sbol-ink-2); margin: 0 auto; max-width: 62ch; } +.sbol-hero__meta { margin-top: .75rem; font-size: .9rem; color: var(--sbol-ink-3); } +.sbol-hero__actions { display: flex; gap: .6rem; justify-content: center; flex-wrap: wrap; margin-top: 1.4rem; } +.sbol-hero__actions.sbol-hero__actions--tabs { margin-top: 1.4rem; margin-bottom: 0; } +@media (max-width: 560px) { .sbol-hero__title { font-size: 1.9rem; } } + +// Sub-navigation tabs (Data Model, Visual sections) +.sbol-subnav { margin-top: 1.75rem; display: flex; justify-content: center; gap: 0; flex-wrap: wrap; border-bottom: 2px solid transparent; } +.sbol-subnav a { + display: inline-block; padding: .8rem 1.1rem .7rem; font-size: .9rem; font-weight: 700; color: var(--sbol-ink-3); + text-decoration: none; border-bottom: 3px solid transparent; margin-bottom: -2px; white-space: nowrap; + &:hover { color: var(--sbol-ink); text-decoration: none; } + &.active { color: var(--sbol-green-ink); border-bottom-color: var(--sbol-green); } +} +.sbol-subnav-bar { border-bottom: 1px solid var(--sbol-rule); background: var(--sbol-paper); } +.sbol-subnav-bar .sbol-subnav { margin-top: 0; } diff --git a/assets/scss/sbol/_navbar.scss b/assets/scss/sbol/_navbar.scss new file mode 100644 index 000000000..1e5b02818 --- /dev/null +++ b/assets/scss/sbol/_navbar.scss @@ -0,0 +1,103 @@ +// Navbar: brand logo size, right-side call to action rendered from the main_right menu. +.navbar-brand img { max-height: 32px; width: auto; } +@media (max-width: 991.98px) { .navbar-brand img { max-height: 26px; } } +#navbar-main .navbar-nav.ml-md-auto .nav-item .nav-link { + background: var(--sbol-green); color: #000 !important; font-weight: 700; border-radius: var(--sbol-radius-sm); + padding: .45rem 1rem !important; margin: .35rem .5rem; line-height: 1.3; +} +#navbar-main .navbar-nav.ml-md-auto .nav-item .nav-link:hover, #navbar-main .navbar-nav.ml-md-auto .nav-item .nav-link:focus, .dark #navbar-main .navbar-nav.ml-md-auto .nav-item .nav-link:hover { background: var(--sbol-green-hover); color: #000 !important; text-decoration: none; } +.dark #navbar-main .dropdown-menu { background: var(--sbol-card); } +.dark #navbar-main .dropdown-item { color: var(--sbol-ink-2); } + + +// Navbar treatment. Set $sbol-navbar in custom.scss. +// "quiet" (default): white bar, no separator at rest, hairline on scroll, full-width flush panels. From the peer study: +// no line at rest (W3C, Rust, MDN, Allen), hairline only on scroll (Vercel, Kubernetes), panels flush and unshadowed (W3C, MDN, Vercel). +// "stripe": quiet plus a 3px brand stripe on top. "tinted": bar in the hero tint. +$sbol-navbar: "quiet" !default; +$sbol-nav-h: 64px; + +#navbar-main { + height: $sbol-nav-h; background: var(--sbol-paper) !important; box-shadow: none !important; border-bottom: 1px solid transparent; font-size: 15px; + padding-left: 0; padding-right: 0; // the container gutter is the only horizontal offset, same as every page + transition: border-color .15s ease; + &.is-scrolled:not(.is-open) { border-bottom-color: var(--sbol-rule); } +} +body { margin-top: $sbol-nav-h; } +@media (max-width: 991.98px) { #navbar-main { height: 50px; } body { margin-top: 50px; } } +.dark #navbar-main { background: var(--sbol-paper) !important; } +@if $sbol-navbar == "stripe" { #navbar-main { border-top: 3px solid var(--sbol-green); } } +@if $sbol-navbar == "tinted" { #navbar-main { background: var(--sbol-hero-a) !important; } .dark #navbar-main { background: var(--sbol-paper-2) !important; } } + +// Items: 15px medium, darken on hover, 2px green bar at the bar's bottom edge when active or open +#navbar-main .main-menu-item .nav-item { position: relative; } +@media (min-width: 992px) { #navbar-main .main-menu-item .nav-item { height: $sbol-nav-h; display: flex; align-items: center; padding: 0 2px !important; flex-shrink: 0; } } +#navbar-main .main-menu-item .nav-item .nav-link { + position: relative; color: var(--sbol-ink-2) !important; font-weight: 500 !important; padding: 6px 12px !important; border-radius: var(--sbol-radius-sm); + display: inline-flex; align-items: center; gap: .35rem; white-space: nowrap; + &:hover, &:focus-visible { color: var(--sbol-ink) !important; } + &.active { color: var(--sbol-ink) !important; } // same weight as the rest, so the row never reflows between pages +} +#navbar-main .navbar-nav .nav-item, #navbar-main .navbar-nav .nav-link { white-space: nowrap; } +#navbar-main .navbar-nav.ml-md-auto .nav-item { flex-shrink: 0; } +// Between the desktop breakpoint and 1200px the bar is 960px wide: one type step down keeps everything on one line +@media (min-width: 992px) and (max-width: 1199.98px) { + #navbar-main { font-size: 14px; } + #navbar-main .main-menu-item .nav-item .nav-link { padding: 6px 8px !important; } + #navbar-main .navbar-nav.ml-md-auto .nav-item .nav-link { padding: .4rem .75rem !important; margin: .35rem .35rem; } + .navbar-brand img { max-height: 26px; } +} +#navbar-main .dropdown-toggle::after { display: none !important; } // Bootstrap's triangle caret; the chevron replaces it +@media (min-width: 992px) { + #navbar-main .main-menu-item .nav-item .nav-link.active::before, #navbar-main .main-menu-item .nav-item.show > .nav-link::before { + content: ""; position: absolute; left: 12px; right: 12px; bottom: -14px; height: 2px; background: var(--sbol-green); border: 0; + } +} +#navbar-main .nav-chevron { font-size: .6em; opacity: .55; transition: transform .15s ease; } +#navbar-main .nav-item.show .nav-chevron { transform: rotate(180deg); opacity: .9; } +#navbar-main .main-menu-item .nav-item .nav-link .caret { display: none; } + +// Right side: one filled call to action, then icons +#navbar-main .navbar-nav.ml-md-auto .nav-item .nav-link { font-size: 14px; } +#navbar-main .nav-icons .nav-link { color: var(--sbol-ink-2) !important; } + +// Panels: full width, flush under the bar, no gap, no shadow, radius 0, content aligned to the page container +@media (min-width: 992px) { + #navbar-main .main-menu-item .nav-item.dropdown { position: static; } + #navbar-main .sbol-panel { + position: absolute; left: 0; right: 0; top: 100%; margin: 0; padding: 0; border: 0; border-radius: 0; box-shadow: none; + background: var(--sbol-paper); border-bottom: 1px solid var(--sbol-rule); + display: block; opacity: 0; visibility: hidden; transition: opacity .1s ease, visibility .1s; + &.show { opacity: 1; visibility: visible; } + &::before { content: ""; position: absolute; left: 0; right: 0; top: -12px; height: 12px; } // hover bridge + } + #navbar-main .sbol-panel__inner { max-width: var(--sbol-container); margin: 0 auto; padding: 22px var(--sbol-gutter) 28px; } + #navbar-main .sbol-panel__eyebrow { font-size: .72rem; font-weight: 700; letter-spacing: .08em; text-transform: uppercase; color: var(--sbol-muted); margin: 0 0 .9rem; } + #navbar-main .sbol-panel__grid { display: grid; grid-template-columns: repeat(3, minmax(0, 300px)); gap: .25rem 2.5rem; } + #navbar-main .sbol-panel__item { + display: flex; flex-direction: column; gap: .15rem; padding: .55rem .6rem; margin: 0 -.6rem; border-radius: var(--sbol-radius-sm); white-space: normal; color: var(--sbol-ink); + &:hover, &:focus { background: var(--sbol-green-tint); color: var(--sbol-ink); text-decoration: none; } + &.active, &.dropdown-item-active { font-weight: 400; color: var(--sbol-ink) !important; } + } + #navbar-main .sbol-panel__name { font-size: 15px; font-weight: 600; line-height: 1.3; } + #navbar-main .sbol-panel__desc { font-size: 13px; color: var(--sbol-ink-3); line-height: 1.45; } + #navbar-main .sbol-panel__ext { font-size: .7em; color: var(--sbol-muted); margin-left: .2rem; } + @media (prefers-reduced-motion: reduce) { #navbar-main .sbol-panel, #navbar-main .nav-chevron { transition: none; } } +} +@media (max-width: 991.98px) { + #navbar-main .sbol-panel { border: 0; box-shadow: none; padding: 0 0 .5rem 1rem; } + #navbar-main .sbol-panel__eyebrow { display: none; } + #navbar-main .sbol-panel__desc { display: none; } + #navbar-main .sbol-panel__item { padding: .4rem 1rem; } +} + +// Icon dropdowns (language selector; the theme control is disabled and the site follows the system): +// same language as the nav panels, flush under the bar, no floating card. +#navbar-main .nav-icons .nav-item.dropdown { position: relative; } +#navbar-main .nav-icons .dropdown-menu { + left: auto; right: 0; top: 100%; margin: 0; min-width: 13rem; padding: .9rem 0 .6rem; + background: var(--sbol-paper); border: 1px solid var(--sbol-rule); border-top: 0; border-radius: 0; box-shadow: none; +} +#navbar-main .nav-icons .dropdown-item { padding: .55rem 1.15rem; font-size: .92rem; line-height: 1.4; color: var(--sbol-ink-2); } +#navbar-main .nav-icons .dropdown-item:hover, #navbar-main .nav-icons .dropdown-item:focus { background: var(--sbol-green-tint); color: var(--sbol-green-ink); } +#navbar-main .nav-icons .dropdown-item.dropdown-item-active { color: var(--sbol-green-ink) !important; font-weight: 700; } diff --git a/assets/scss/sbol/_pages.scss b/assets/scss/sbol/_pages.scss new file mode 100644 index 000000000..c9f72aa9c --- /dev/null +++ b/assets/scss/sbol/_pages.scss @@ -0,0 +1,47 @@ +// Page-level arrangement only (grids, columns, the gallery lightbox). Every card, badge, button and table on these pages is a shared component. + +// Homepage hero with news feed (shortcode hero-feed) +.hf-wrap { display: flex; gap: var(--sbol-space-5); align-items: flex-start; padding: .5rem 0; } +.hf-left { flex: 1 1 55%; } +.hf-right { flex: 1 1 40%; } +.hf-title { font-size: 2.6rem; font-weight: 800; line-height: 1.2; margin-bottom: 1rem; text-align: left; color: var(--sbol-ink); } +.hf-subtitle { font-size: 1.1rem; color: var(--sbol-ink-2); line-height: 1.65; margin-bottom: 1.75rem; } +.hf-buttons { display: flex; gap: .75rem; flex-wrap: wrap; } +.hf-feed-heading { font-size: .78rem; font-weight: 700; text-transform: uppercase; letter-spacing: .1em; color: var(--sbol-green-ink); border-bottom: 2px solid var(--sbol-green); padding-bottom: .5rem; margin-bottom: 1.1rem; } +.hf-right .sbol-card { margin-bottom: .75rem; } +.hf-empty { font-size: .88rem; color: var(--sbol-muted); } +@media (max-width: 768px) { .hf-wrap { flex-direction: column; gap: var(--sbol-space-4); } .hf-title { font-size: 2rem; } } + +// Homepage journey cards (shortcodes journey-cards, card) +.jc-grid { display: grid; grid-template-columns: repeat(3, minmax(0, 1fr)); gap: var(--sbol-space-3); margin: var(--sbol-space-2) 0; } +@media (max-width: 760px) { .jc-grid { grid-template-columns: 1fr; } } + +// Applications filters +.sbol-filters { display: flex; flex-wrap: wrap; gap: .5rem; margin: 0 0 var(--sbol-space-3); } +.sbol-filter { + display: inline-flex; align-items: center; gap: .4rem; background: var(--sbol-paper-2); border: 1px solid var(--sbol-rule); border-radius: var(--sbol-radius-pill); + padding: .35rem .85rem; font-size: .82rem; font-weight: 700; color: var(--sbol-ink-3); cursor: pointer; font-family: inherit; transition: border-color .12s ease, background-color .12s ease; + &:hover { border-color: var(--sbol-green); color: var(--sbol-green-ink); } + &.active { background: var(--sbol-green); border-color: var(--sbol-green); color: #000; .sbol-tab__count { background: rgba(0,0,0,.12); color: #000; } } +} + +// Glyph grid +.glyph-group-title { margin-top: 2.5rem; } +.glyph-grid { display: grid; grid-template-columns: repeat(auto-fill, minmax(120px, 1fr)); gap: var(--sbol-space-2); margin: var(--sbol-space-3) 0; } + +// Visual gallery grid and native lightbox +.vg-grid { display: grid; grid-template-columns: repeat(auto-fill, minmax(280px, 1fr)); gap: var(--sbol-space-3); margin-top: var(--sbol-space-4); } +.vg-card-title { font-weight: 700; font-size: .88rem; color: var(--sbol-ink); line-height: 1.35; display: -webkit-box; -webkit-line-clamp: 2; -webkit-box-orient: vertical; overflow: hidden; } +.vg-card-byline { font-size: .76rem; color: var(--sbol-muted); } +.vg-lightbox { border: 1px solid var(--sbol-rule); border-radius: var(--sbol-radius); padding: 0; width: unquote("min(880px, 94vw)"); max-height: 92vh; overflow: hidden; background: var(--sbol-card); color: var(--sbol-ink); } +.vg-lightbox::backdrop { background: rgba(0,0,0,.84); } +.vg-lb-wrap { display: flex; flex-direction: column; max-height: 92vh; overflow-y: auto; position: relative; } +.vg-lb-close { position: absolute; top: .75rem; right: .75rem; z-index: 10; background: rgba(0,0,0,.55); color: #fff; border: none; border-radius: 50%; width: 38px; height: 38px; display: flex; align-items: center; justify-content: center; cursor: pointer; &:hover { background: rgba(0,0,0,.85); } } +.vg-lb-img-wrap { background: var(--sbol-paper-2); display: flex; align-items: center; justify-content: center; flex-shrink: 0; } +.vg-lb-img-wrap img { max-width: 100%; max-height: 62vh; object-fit: contain; display: block; } +.vg-lb-info { padding: 1.4rem 1.6rem 1.6rem; } +.vg-lb-title { font-size: 1.05rem; font-weight: 700; margin-bottom: .3rem; } +.vg-lb-byline { font-size: .84rem; color: var(--sbol-ink-3); margin-bottom: .5rem; } +.vg-lb-caption { font-size: .88rem; color: var(--sbol-ink-2); line-height: 1.6; margin-bottom: .9rem; } +.vg-lb-links { display: flex; gap: .6rem; flex-wrap: wrap; align-items: center; } +@media (max-width: 640px) { .vg-grid { grid-template-columns: 1fr; } .vg-lightbox { width: 98vw; } } diff --git a/assets/scss/sbol/_people.scss b/assets/scss/sbol/_people.scss new file mode 100644 index 000000000..18fc1f2dd --- /dev/null +++ b/assets/scss/sbol/_people.scss @@ -0,0 +1,21 @@ +// People roster: initials avatar when no photo exists. +.people-widget .people-person { margin-bottom: 1.5rem; } +.sbol-avatar-initials { + width: 110px; height: 110px; border-radius: 50%; margin: 0 auto .6rem; display: flex; align-items: center; justify-content: center; + background: var(--sbol-green-tint); color: var(--sbol-green-ink); font-weight: 800; font-size: 2rem; letter-spacing: .02em; border: 2px solid var(--sbol-band-border); +} +.people-widget .portrait-title h2 { font-size: 1.05rem; margin: .2rem 0 .1rem; } +.people-widget .portrait-title h2 a { color: var(--sbol-ink); text-decoration: none; &:hover { color: var(--sbol-green-ink); } } +.people-widget .portrait-title h3 { font-size: .82rem; color: var(--sbol-ink-3); font-weight: 400; margin: .1rem 0; } +.people-widget .section-heading h1 { font-size: 1.6rem; font-weight: 700; } +.people-widget h2.mb-4 { font-size: 1.3rem; } +// Roster (shortcode sbol-people) +.sbol-roster { display: grid; grid-template-columns: repeat(auto-fill, minmax(200px, 1fr)); gap: 1.5rem 1.25rem; margin: 1rem 0 2.5rem; } +.sbol-person { text-align: center; } +.sbol-person__photo { width: 110px; height: 110px; border-radius: 50%; object-fit: cover; margin: 0 auto .6rem; display: block; border: 2px solid var(--sbol-band-border); } +.sbol-person__body { display: flex; flex-direction: column; gap: .1rem; } +.sbol-person__name { font-weight: 700; color: var(--sbol-ink); text-decoration: none; font-size: .98rem; &:hover { color: var(--sbol-green-ink); } } +.sbol-person__org, .sbol-person__role { font-size: .8rem; color: var(--sbol-ink-3); } +.sbol-person__social { margin-top: .3rem; font-size: .9rem; a { margin: 0 .2rem; color: var(--sbol-green-ink); } } +.sbol-page__body .sbol-roster { max-width: none; } +.sbol-page__body:has(.sbol-roster) { max-width: none; } diff --git a/assets/scss/sbol/_tables.scss b/assets/scss/sbol/_tables.scss new file mode 100644 index 000000000..80c18499e --- /dev/null +++ b/assets/scss/sbol/_tables.scss @@ -0,0 +1,30 @@ +// One table style for the whole site, plus the tab bar used above tables and library groups. +.sbol-tablewrap { overflow-x: auto; margin: 1.25rem 0; border: 1px solid var(--sbol-rule); border-radius: var(--sbol-radius); } +.sbol-table, .article-style table, .universal-wrapper table:not(.sbol-plain) { + display: table; overflow-x: visible; width: 100%; border-collapse: collapse; font-size: .92rem; margin: 0; word-break: normal; overflow-wrap: normal; + thead th { font-size: .74rem; letter-spacing: .07em; text-transform: uppercase; color: var(--sbol-ink-3); background: var(--sbol-paper-2); text-align: left; padding: .65rem .8rem; border-bottom: 1px solid var(--sbol-rule); position: sticky; top: 0; } + td { padding: .7rem .8rem; vertical-align: top; border-bottom: 1px solid var(--sbol-rule-2); color: var(--sbol-ink-2); text-align: left; } + tbody tr:nth-child(even) td { background: var(--sbol-paper-2); } + tbody tr:hover td { background: var(--sbol-green-tint); } + tbody tr:last-child td { border-bottom: 0; } + td.num, th.num { text-align: right; font-variant-numeric: tabular-nums; } + td.nowrap { white-space: nowrap; } + tr.is-current td { background: var(--sbol-green-tint) !important; font-weight: 600; } +} +.article-style table { border: 1px solid var(--sbol-rule); border-radius: var(--sbol-radius); overflow: hidden; } +// Legacy inline attributes on old event tables lose their effect +.article-style table[style] { width: 100% !important; } + +// Tabs +.sbol-tabs { display: flex; gap: 0; border-bottom: 2px solid var(--sbol-rule); margin: 0 0 1.5rem; flex-wrap: wrap; } +.sbol-tab { + background: none; border: 0; border-bottom: 3px solid transparent; margin-bottom: -2px; padding: .85rem 1.2rem; font-size: .9rem; font-weight: 700; + color: var(--sbol-ink-3); cursor: pointer; font-family: inherit; display: inline-flex; align-items: center; gap: .45rem; text-decoration: none; + &:hover { color: var(--sbol-ink); text-decoration: none; } + &.active, &.is-active { color: var(--sbol-green-ink); border-bottom-color: var(--sbol-green); } +} +.sbol-tab__count { display: inline-block; background: var(--sbol-rule-2); color: var(--sbol-ink-3); font-size: .68rem; font-weight: 700; border-radius: var(--sbol-radius-pill); padding: 0 .4rem; line-height: 1.5; } +.sbol-tab.active .sbol-tab__count { background: var(--sbol-green-tint); color: var(--sbol-green-ink); } +.sbol-tabs--sticky { position: sticky; top: 0; z-index: 10; background: var(--sbol-paper); } +.sbol-panel--hidden { display: none; } +.sbol-empty { font-style: italic; color: var(--sbol-muted); margin: 1rem 0; } diff --git a/assets/scss/sbol/_theme.scss b/assets/scss/sbol/_theme.scss new file mode 100644 index 000000000..34cbe6739 --- /dev/null +++ b/assets/scss/sbol/_theme.scss @@ -0,0 +1,93 @@ +// Theme components (Wowchemy and Bootstrap) brought onto the tokens, so content rendered by the theme +// (publication cards, widgets, markdown, forms, alerts) follows the same shape and hover rules as ours. +.card, .card-simple, .alert, pre, .form-control, .custom-select, .dropdown-menu, .img-thumbnail, .modal-content, .toast, .article-header img, +.article-style img, .article-style figure img, .article-style video, .article-style iframe, .card-image, .card-simple .card-image, .hero-media img, .figure img, +.people-widget img.avatar, .avatar-square { border-radius: var(--sbol-radius-img); } +.card, .card-simple, .alert, .dropdown-menu, .modal-content, .toast { border-radius: var(--sbol-radius); } +.avatar-circle, .avatar { border-radius: 50%; } +.btn, .btn-sm, .btn-lg, .btn-page-header, .form-control, .custom-select, .navbar-toggler, kbd, .pagination, .page-link, .page-item:first-child .page-link, .page-item:last-child .page-link { border-radius: var(--sbol-radius-sm) !important; } +.badge, .badge-pill, .btn-tag, .tag-cloud a { border-radius: var(--sbol-radius-pill) !important; } +.card, .card-simple { border: 1px solid var(--sbol-card-border); box-shadow: none; transition: border-color .12s ease; } +.card:hover, .card-simple:hover { box-shadow: none; transform: none; border-color: var(--sbol-green); background: var(--sbol-green-tint); } +.card .card-image.hover-overlay:before, .card .card-image.hover-overlay:after { display: none; } +.img-hover-zoom:hover img, .tag-cloud a:hover, .tag-cloud a:focus, .tag-cloud a:active, ul.share li:hover i, .network-icon li:hover, a.hero-cta-alt:hover, a.hero-cta-alt:focus, a.hero-cta-alt:active { transform: none; } +.card, .card .card-image.hover-overlay:before, .card .card-image.hover-overlay:after { transition: border-color .12s ease; } +.btn { transition: background-color .12s ease, border-color .12s ease; box-shadow: none !important; } +.article-style img { max-width: 100%; height: auto; } +.article-title a, h3.article-title a:hover, a { transition: none; } + +// Theme switch: no transitions while the theme class changes (custom_js.html adds .sbol-switching for one frame) +html.sbol-switching *, html.sbol-switching *::before, html.sbol-switching *::after { transition: none !important; animation: none !important; } + +// Publication filters (theme markup): tokens for the search box and selects +.filter-search, .pub-filters { border: 1px solid var(--sbol-rule); background: var(--sbol-card); color: var(--sbol-ink-2); border-radius: var(--sbol-radius-sm) !important; padding: .45rem .8rem; font-size: .9rem; height: auto; } +.filter-search:focus, .pub-filters:focus { outline: 2px solid var(--sbol-green); outline-offset: 1px; border-color: var(--sbol-green); box-shadow: none; } +.form-row.mb-4 { margin-top: var(--sbol-space-4); } +.pub-list-item .card-simple, .card-simple { padding: 1.25rem 1.5rem; } +.card-simple .article-title, .article-title a { color: var(--sbol-ink); } + +// One margins rule for theme single pages too: the article container is the site container, text keeps a 78ch measure at the left edge +.article-container { max-width: var(--sbol-container) !important; padding-left: var(--sbol-gutter); padding-right: var(--sbol-gutter); margin: 0 auto; } +.article-container .article-style, .article-container .article-header, .article-container .article-metadata, .article-container .btn-links, .article-container h1, .article-container .page-footer, .article-container .article-footer, .article-container .media { max-width: 78ch; } +.embed-responsive, .article-style .video, .article-style iframe { border-radius: var(--sbol-radius); overflow: hidden; } + +// Publication and talk lists (theme templates + our li_card): consistent vertical rhythm, theme buttons as secondary buttons +// Every list of cards keeps the same vertical rhythm, whichever template emits it (publications, pages widget, +// cite shortcode, author and tag pages). Isotope positions its own wrappers, so the gap goes on the wrapper there. +.sbol-card--pub { margin-bottom: var(--sbol-space-3); } +#container-publications .isotope-item { margin-bottom: var(--sbol-space-3); } +#container-publications .isotope-item .sbol-card--pub { margin-bottom: 0; } +#container-publications { margin-top: var(--sbol-space-3); } +.sbol-card--pub .sbol-card__plain { display: flex; flex-direction: column; gap: .35rem; } +.sbol-card--pub .sbol-card__title { font-size: 1.15rem; } +.sbol-card--pub .article-metadata { margin: 0; font-size: .82rem; } +.sbol-card--pub .article-metadata a { color: var(--sbol-ink-3); } +.btn-page-header, .btn-links .btn, .sbol-card__actions .btn { + display: inline-flex; align-items: center; gap: .35rem; background: transparent; color: var(--sbol-green-ink) !important; border: 1px solid var(--sbol-green-ink); + border-radius: var(--sbol-radius) !important; padding: .3rem .7rem; font-size: .78rem; font-weight: 700; line-height: 1.3; margin: .15rem .35rem .15rem 0; text-decoration: none !important; + &:hover, &:focus { background: var(--sbol-green-tint); color: var(--sbol-green-ink) !important; } +} +.article-metadata, .article-metadata a, .article-date { color: var(--sbol-muted); } +#container-publications .isotope-item.col-lg-12 { padding-left: 0; padding-right: 0; } + +// Disclosure rows (
in content, e.g. the FAQ): one accordion style for the whole site +.article-style details, .sbol-page__body details { + border: 1px solid var(--sbol-card-border); border-radius: var(--sbol-radius); background: var(--sbol-card); margin: .5rem 0; overflow: hidden; + transition: border-color .12s ease, background-color .12s ease; + &[open] { border-color: var(--sbol-rule); } + &:hover { border-color: var(--sbol-green); } +} +.article-style details > summary, .sbol-page__body details > summary { + list-style: none; cursor: pointer; padding: .85rem 1.1rem; font-weight: 700; color: var(--sbol-ink); display: flex; align-items: flex-start; gap: .6rem; + &::-webkit-details-marker { display: none; } + &::before { + content: ""; flex: 0 0 auto; width: .55em; height: .55em; margin-top: .45em; border-right: 2px solid var(--sbol-green-ink); border-bottom: 2px solid var(--sbol-green-ink); + transform: rotate(-45deg); transition: transform .15s ease; + } + b, strong { font-weight: 700; } + &:hover { color: var(--sbol-green-ink); } +} +.article-style details[open] > summary::before, .sbol-page__body details[open] > summary::before { transform: rotate(45deg); } +.article-style details[open] > summary, .sbol-page__body details[open] > summary { border-bottom: 1px solid var(--sbol-rule-2); } +.article-style details, .sbol-page__body details { padding: 0 1.1rem; } +.article-style details[open], .sbol-page__body details[open] { padding-bottom: .9rem; } +.article-style details > summary, .sbol-page__body details > summary { margin: 0 -1.1rem; } +.article-style details > *:not(summary), .sbol-page__body details > *:not(summary) { margin-left: 0; margin-right: 0; } +.article-style details > *:not(summary):first-of-type, .sbol-page__body details > *:not(summary):first-of-type { margin-top: .9rem; } +@media (prefers-reduced-motion: reduce) { .article-style details > summary::before { transition: none; } } + +// Detail pages: featured images are contained, rounded and aligned with the text column +.article-banner, .featured-image { max-height: 380px; width: 100%; object-fit: cover; object-position: center; border-radius: var(--sbol-radius); } +.sbol-single--libraries, .sbol-single--applications, .sbol-single--genai-tools { + // Logos, not hero photos: keep them small, left aligned, and drop the page date + .article-banner, .featured-image { max-height: 180px; width: auto; max-width: unquote("min(100%, 360px)"); object-fit: contain; object-position: left; margin: 0 0 var(--sbol-space-3); display: block; } + .article-header { text-align: left; } + .article-metadata, .article-date { display: none; } +} + +// Content images (markdown `![]()`, figure shortcode): never taller than a screenful, rounded, aligned with the text column +.article-style img, .sbol-page__body img { max-width: 100%; height: auto; border-radius: var(--sbol-radius); } +// Only images without an explicit size get the height cap; a width attribute (figure shortcode) always wins. +.article-style img:not([width]), .sbol-page__body img:not([width]) { max-height: 460px; width: auto; } +.article-style figure, .sbol-page__body figure { margin: var(--sbol-space-3) 0; } +.article-style figure figcaption, .sbol-page__body figure figcaption { font-size: .86rem; color: var(--sbol-ink-3); margin-top: .5rem; } diff --git a/assets/scss/sbol/_tokens.scss b/assets/scss/sbol/_tokens.scss new file mode 100644 index 000000000..34d233f56 --- /dev/null +++ b/assets/scss/sbol/_tokens.scss @@ -0,0 +1,74 @@ +// Design tokens. Light values on :root, dark values under body.dark (the theme's toggle class). +// Components read only these variables; page files add no literal colors. +:root { + --sbol-green: #8cc63f; // fills, rules, badges, primary button; never body text + --sbol-green-ink: #3f6b0d; // links and green text, 6.9:1 on white + --sbol-green-tint: #eef5df; + --sbol-hero-a: #f0f7e8; + --sbol-hero-b: #e8f4d9; + --sbol-band: #f7f9f5; // light full-bleed band (replaces the former navy band) + --sbol-band-border: #e0e8d8; + --sbol-paper: #ffffff; + --sbol-paper-2: #f8f8f8; + --sbol-card: #ffffff; + --sbol-card-border: #e5e7eb; + --sbol-ink: #1a1a1a; + --sbol-ink-2: #444444; + --sbol-ink-3: #666666; // 5.7:1 + --sbol-muted: #6b7280; // dates, captions, 4.8:1 + --sbol-rule: #e5e7eb; + --sbol-rule-2: #eeeeee; + --sbol-code-bg: #f1f3ec; + --sbol-shadow: 0 1px 3px rgba(0, 0, 0, .05); + --sbol-shadow-hover: 0 6px 24px rgba(0, 0, 0, .09); + --sbol-focus: #8cc63f; + // Shape: two radii only. Everything rectangular (cards, panels, buttons, inputs, images, menus, tables) uses the card radius; badges and filters are pills. + // The three names stay so a future change stays central; today they resolve to the same value. + --sbol-radius: 12px; + --sbol-radius-img: var(--sbol-radius); + --sbol-radius-sm: var(--sbol-radius); + --sbol-radius-pill: 999px; + // Layout: one container rule for navbar, content, bands, panels and footer + --sbol-container: 1200px; + --sbol-gutter: 15px; + // Hover accents (no shadow, no motion): cards outline in green, primary buttons darken one step + --sbol-green-hover: #7db536; + --sbol-space-2: 1rem; + --sbol-space-3: 1.5rem; + --sbol-space-4: 2rem; + --sbol-space-5: 3rem; + // Semantic badge set (five hues), tint and ink pairs, all inks >= 4.5:1 on their tint + --sbol-badge-blue-bg: #e6eefc; --sbol-badge-blue-ink: #1d4ed8; + --sbol-badge-purple-bg: #ede9fe; --sbol-badge-purple-ink: #5b21b6; + --sbol-badge-orange-bg: #fdeedd; --sbol-badge-orange-ink: #9a3412; + --sbol-badge-green-bg: #e8f2d5; --sbol-badge-green-ink: #3f6b0d; + --sbol-badge-slate-bg: #e9ebef; --sbol-badge-slate-ink: #374151; +} +body.dark { + --sbol-green: #8cc63f; + --sbol-green-hover: #9ed35a; + --sbol-green-ink: #b7dc7a; + --sbol-green-tint: #2c3a22; + --sbol-hero-a: #2b3a22; + --sbol-hero-b: #232f1c; + --sbol-band: #2b2e3a; + --sbol-band-border: #3b3f4f; + --sbol-paper: #282a36; + --sbol-paper-2: #23252f; + --sbol-card: #2f3140; + --sbol-card-border: #44475a; + --sbol-ink: #f8f8f2; + --sbol-ink-2: #d9dbe4; + --sbol-ink-3: #b3b6c6; + --sbol-muted: #9a9db0; + --sbol-rule: #44475a; + --sbol-rule-2: #383b4a; + --sbol-code-bg: #1f212b; + --sbol-shadow: 0 1px 3px rgba(0, 0, 0, .4); + --sbol-shadow-hover: 0 8px 24px rgba(0, 0, 0, .5); + --sbol-badge-blue-bg: #1e2a4a; --sbol-badge-blue-ink: #a9c4ff; + --sbol-badge-purple-bg: #2c2347; --sbol-badge-purple-ink: #c9b8ff; + --sbol-badge-orange-bg: #402a1a; --sbol-badge-orange-ink: #f4b183; + --sbol-badge-green-bg: #26361a; --sbol-badge-green-ink: #b7dc7a; + --sbol-badge-slate-bg: #33364a; --sbol-badge-slate-ink: #cfd3e0; +} diff --git a/config/_default/config.toml b/config/_default/config.toml index e114c3f4a..4d32f921c 100644 --- a/config/_default/config.toml +++ b/config/_default/config.toml @@ -6,17 +6,17 @@ # Each configuration section is defined by a name in square brackets (e.g. `[outputs]`). # Title of your site -title = "The Synthetic Biology Open Language" +title = "SBOL: Synthetic Biology Open Language" # The URL of your site. # End your URL with a `/` trailing slash, e.g. `https://sbolstandard.org/`. -baseurl = "/" +baseurl = "https://sbolstandard.org/" # Enter a copyright notice to display in the site footer. # To display a copyright symbol, type `©`. For current year, type `{year}`. copyright = "" -relativeURLs = true +enableRobotsTXT = true ############################ ## Advanced options below ## @@ -38,6 +38,9 @@ footnotereturnlinkcontents = "^" ignoreFiles = ["\\.ipynb$", ".ipynb_checkpoints$", "\\.Rmd$", "\\.Rmarkdown$", "_files$", "_cache$"] # Workaround Hugo publishing taxonomy URLs as plurals - consistently use singular across Academic. +[build] + noJSConfigInAssets = true + [permalinks] authors = "/author/:slug/" tags = "/tag/:slug/" diff --git a/config/_default/menus.toml b/config/_default/menus.toml index d891fe681..62d45854d 100644 --- a/config/_default/menus.toml +++ b/config/_default/menus.toml @@ -1,226 +1,176 @@ -# Navigation Links -# To link a homepage widget, specify the URL as a hash `#` followed by the filename of the -# desired widget in your `content/home/` folder. -# The weight parameter defines the order that the links will appear in. - - -[[main]] - name = "SBOL Data Model" - url = "/DataModel" - weight = 20 - identifier = "dom-id" +# Navigation +# Data Model and Visual are direct links to their landing pages; each landing page and its +# sibling pages carry a tab bar (see data/subnav.yaml). Only Ecosystem, News and Community open +# dropdowns. `main_right` renders at the right end of the bar (theme feature) and is styled as a button. [[main]] - name = "About SBOL" - url = "/DataModel-about" - weight = 5 - parent = "dom-id" - -[[main]] - name = "Data Model Specification" - url = "/DataModel-Specification" + name = "Data Model" + url = "/datamodel/" weight = 10 - parent = "dom-id" - [[main]] - name = "SBOL Ontology" - url = "/ontology" + name = "Visual" + url = "/visual/" weight = 20 - parent = "dom-id" - -[[main]] - name = "Examples" - url = "/DataModel-Examples" - weight = 35 - parent = "dom-id" - -[[main]] - name = "SBOL Visual" - url = "/visual" - weight = 25 - identifier = "visual-id" - -[[main]] - name = "About SBOL Visual" - url = "/visual-about" - weight = 5 - parent = "visual-id" - -[[main]] - name = "Visual Specification" - url = "/visual-specification" - weight = 10 - parent = "visual-id" - -[[main]] - name = "Glyphs" - url = "/visual-glyphs" - weight = 15 - parent = "visual-id" - -[[main]] - name = "SBOL Visual Ontology" - url = "/sbol-visual-ontology" - weight = 20 - parent = "visual-id" - -#[[main]] -# name = "Examples from papers" -# url = "/visual-examples" -# weight = 25 -# parent = "visual-id" - -[[main]] - name = "Gallery" - url = "/visual-gallery" - weight = 27 - parent = "visual-id" - -[[main]] - name = "10 Years of SBOL Visual" - url = "/sbolv-10-years" - weight = 30 - parent = "visual-id" [[main]] name = "Ecosystem" - url = "/ecosystem" + url = "/ecosystem/" weight = 30 identifier = "ecosystem-id" - [[main]] name = "Libraries" - url = "/libraries" + url = "/libraries/" weight = 5 parent = "ecosystem-id" - + post = "Official implementations in Python, Java, Rust, JavaScript and C++" [[main]] name = "Applications" - url = "/applications" + url = "/applications/" weight = 10 parent = "ecosystem-id" - - [[main]] + post = "Tools that read, write, design and visualize SBOL" +[[main]] + name = "GenAI Tools" + url = "/genai-tools/" + weight = 15 + parent = "ecosystem-id" + post = "Assistants trained on the SBOL 2 and 3 specifications" +[[main]] name = "Converter" url = "https://converter.sbolstandard.org/" - weight = 15 + weight = 20 parent = "ecosystem-id" - + post = "Convert between SBOL 2, SBOL 3 and GenBank" [[main]] name = "Validator" url = "https://validator.sbolstandard.org/" - weight = 20 - parent = "ecosystem-id" - -[[main]] - name = "GitHub" - url = "https://github.com/SynBioDex/" weight = 25 parent = "ecosystem-id" - + post = "Check that a document is valid SBOL" [[main]] - name = "GenAI Tools" - url = "/genai-tools" + name = "GitHub" + url = "https://github.com/SynBioDex/" weight = 30 parent = "ecosystem-id" - + post = "The SynBioDex organization: specs, libraries, tools" [[main]] name = "Publications" - url = "/publication" + url = "/publication/" weight = 40 [[main]] name = "News" - url = "/news" + url = "/news/" weight = 45 identifier = "news-id" - [[main]] name = "Announcements" - url = "/post" + url = "/post/" weight = 5 parent = "news-id" - + post = "Releases, calls, and meeting news" [[main]] name = "Blog" - url = "/blog" + url = "/blog/" weight = 10 parent = "news-id" - - - + post = "Long-form posts and the SBOLinside video series" [[main]] name = "Community" - url = "/community" + url = "/community/" weight = 50 identifier = "community-id" - [[main]] name = "Leadership" - url = "/community-leadership" + url = "/community-leadership/" weight = 5 parent = "community-id" - + post = "Chair, editors, steering committee" [[main]] name = "Meetings & Outreach" - url = "/community-meetings" + url = "/community-meetings/" weight = 12 parent = "community-id" - -#[[main]] -# name = "Outreach" -# url = "/community-outreach" -# weight = 15 -# parent = "community-id" - - - + post = "COMBINE, HARMONY, workshops and outreach" [[main]] name = "Governance" - url = "/community-governance" + url = "/community-governance/" weight = 20 parent = "community-id" - -#[[main]] -# name = "SBOL Industrial Consortium" -# url = "/sbol-industrial" -# weight = 25 -# parent = "community-id" - + post = "How the community is organized and decides" [[main]] name = "Sponsor SBOL" - url = "/sponsor-sbol" + url = "/sponsor-sbol/" weight = 30 parent = "community-id" + post = "Support the standard through BDAC" -# Footer Links - -[[footer]] - name = "Contact Us" - url = "/contact" +[[main_right]] + name = "Join SBOL" + url = "/join/" weight = 10 -[[footer]] +# Footer: three columns that complement the navigation (nothing here repeats a menu entry). +[[footer_help]] name = "FAQ" - url = "/faq" + url = "/faq/" + weight = 10 +[[footer_help]] + name = "Contact" + url = "/contact/" weight = 20 - -[[footer]] +[[footer_help]] name = "Stack Exchange" url = "https://bioinformatics.stackexchange.com/questions/tagged/sbol" weight = 30 +[[footer_help]] + name = "Announcements list" + url = "https://groups.google.com/g/sbol-announce" + weight = 40 +[[footer_help]] + name = "Slack" + url = "https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg" + weight = 50 -[[footer]] - name = "View Source" +[[footer_contribute]] + name = "Report a website issue" + url = "https://github.com/SynBioDex/SbolStandardWebsite/issues" + weight = 10 +[[footer_contribute]] + name = "View source" url = "https://github.com/SynBioDex/SbolStandardWebsite" + weight = 20 +[[footer_contribute]] + name = "Propose an enhancement (SEP)" + url = "https://github.com/SynBioDex/SEPs" + weight = 30 +[[footer_contribute]] + name = "Submit a tool" + url = "https://github.com/SynBioDex/SbolStandardWebsite/issues/new" weight = 40 - -[[footer]] +[[footer_contribute]] name = "Community Media" url = "https://github.com/SynBioDex/Community-Media" weight = 50 -[[footer]] - name = "Report an Issue" - url = "https://github.com/SynBioDex/SbolStandardWebsite/issues" - weight = 60 +[[footer_connect]] + name = "GitHub" + url = "https://github.com/SynBioDex" + weight = 10 + pre = "github" +[[footer_connect]] + name = "YouTube" + url = "https://www.youtube.com/@syntheticbiologyopenlangua6204" + weight = 20 + pre = "youtube" +[[footer_connect]] + name = "X (Twitter)" + url = "https://twitter.com/sbolstandard" + weight = 30 + pre = "twitter" +[[footer_connect]] + name = "Slack" + url = "https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg" + weight = 40 + pre = "slack" + post = "Support the standard through BDAC" diff --git a/config/_default/params.toml b/config/_default/params.toml index 0600af776..5e776214c 100644 --- a/config/_default/params.toml +++ b/config/_default/params.toml @@ -16,7 +16,7 @@ theme = "sbol" # Enable users to switch between day and night mode? -day_night = false +day_night = true # Override the theme's font set (optional). # Latest font sets (may require updating): https://sourcethemes.com/academic/themes/ @@ -48,7 +48,7 @@ local_business_type = "" org_name = "Synthetic Biology Open Language" # Description for social sharing and search engines. If undefined, superuser role is used in place. -description = "" +description = "SBOL, the Synthetic Biology Open Language, is the free open standard for describing genetic designs: a data model for exchange between software tools and a visual language for diagrams, maintained by an open community." ############################ ## Site Features @@ -124,7 +124,7 @@ contact_links = [ ############################ # Default image for social sharing and search engines. Place image in `static/img/` folder and specify image name here. -sharing_image = "" +sharing_image = "sharing.png" # Twitter username (without @). Used when a visitor shares your site on Twitter. twitter = "" @@ -147,7 +147,7 @@ address_format = "en-us" ############################ # Main menu alignment (l = left, c = center, r = right) and logo options. -main_menu = {align = "l", show_logo = true} +main_menu = {align = "l", show_logo = true, show_day_night = false} # Show estimated reading time for posts? (true/false) reading_time = true diff --git a/content/DataModel-Examples/_index.md b/content/DataModel-Examples/_index.md index 0153ec580..23ab24b50 100644 --- a/content/DataModel-Examples/_index.md +++ b/content/DataModel-Examples/_index.md @@ -12,6 +12,10 @@ view: 3 header: caption: "" image: "" +subtitle: "Example SBOL files and the publications they accompany, by version." +layout: sbol-page +subnav: datamodel +summary: "Example SBOL files and the publications they accompany, by version." --- ### 2019 (Data Model Examples) @@ -45,7 +49,7 @@ header: {{% staticref "zip/sb400135t_si_001.zip" "newtab" %}}Directed Acyclic Genetic Circuit examples{{% /staticref %}} -Further SBOL 2.0 examples are located [here](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. +Further SBOL 2.0 examples are in the [SBOL test suite](https://github.com/SynBioDex/SBOLTestSuite). This comprehensive set of data files includes in addition to more SBOL 2.0 files, SBOL 1.1 files used to test conversion to SBOL 2.0, GenBank files used to test conversion to SBOL 2.0, and invalid SBOL 2.0 files used to test validation. ### SBOL 1.1 Examples diff --git a/content/DataModel-Specification/_index.md b/content/DataModel-Specification/_index.md index 18a10feec..9406fa27c 100644 --- a/content/DataModel-Specification/_index.md +++ b/content/DataModel-Specification/_index.md @@ -1,5 +1,8 @@ --- title: SBOL Data Model Specification +subtitle: "The formal data model for exchanging genetic designs between software tools. The current release is the reference for every SBOL library and validator." +subnav: datamodel +issues_url: https://github.com/SynBioDex/SBOL-specification/issues # View. # 1 = List @@ -12,12 +15,10 @@ view: 3 header: caption: "" image: "" +cascade: + share: false + profile: false +summary: "The formal data model for exchanging genetic designs between software tools. The current release is the reference for every SBOL library and validator." --- -[Report an Issue with the Current SBOL Specification](https://github.com/SynBioDex/SBOL-specification/issues) - \ No newline at end of file + diff --git a/content/DataModel-Specification/version-3.1.0.md b/content/DataModel-Specification/version-3.1.0.md index 9c8f25c91..4feffe17c 100644 --- a/content/DataModel-Specification/version-3.1.0.md +++ b/content/DataModel-Specification/version-3.1.0.md @@ -42,7 +42,7 @@ property on each class. Another enhancement is the generalization of the CombinatorialDeriviation class to allow direct use of Features and Measures. Next, the Participation class now allow Interactions to be participants to describe higher-order interactions. Another change is -the use of Sequence Ontology}terms for Feature orientation. Finally, +the use of Sequence Ontology terms for Feature orientation. Finally, this version of SBOL has generalized from using Unique Reference Identifiers (URIs) to Internationalized Resource Identifiers (IRIs) to support international character sets. diff --git a/content/DataModel-about/_index.md b/content/DataModel-about/_index.md index 490aab391..eb99bf3e1 100644 --- a/content/DataModel-about/_index.md +++ b/content/DataModel-about/_index.md @@ -1,5 +1,5 @@ --- -title: +title: SBOL Data Model # View. # 1 = List @@ -13,13 +13,22 @@ header: caption: "" image: "" -# Provide a short alias (See GitHub #135) +subtitle: "The data model for representing and exchanging genetic designs between software tools, with libraries in Python, Java, Rust, JavaScript and C++." +url: /datamodel/ aliases: - - /datamodel/ + - /datamodel-about/ +layout: sbol-page +subnav: datamodel +toc: true +hero_buttons: + - text: Read the specification + url: /datamodel-specification/ + - text: Get a library + url: /libraries/ + style: secondary +summary: "The data model for representing and exchanging genetic designs between software tools, with libraries in Python, Java, Rust, JavaScript and C++." --- -{{< figure width="600px" library="true" src="Logos/SBOLlogo.svg" title="" lightbox="true" >}} - ### Purpose Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. These principles include standardization, modularity, and design abstraction. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. A common factor of these challenges is the exchange of information about designed systems between laboratories. @@ -34,12 +43,12 @@ The SBOL data standard is a data exchange representation for synthetic biology d SBOL Data is used as a data exchange format to represent genetic designs and its functional interaction. This will allow information to be exchanged between software tools, maintain the integrity of the data, and ensure reproducibility of designs. -To get an idea on how the data model has been used in software tools, view all of the [SBOL Data model tools]({{< relref "applications" >}}) that have been reported to us. -Also take a look at sample papers that have been published online for the SBOL data model, featuring the SBOL data model, and software tools supporting the SBOL data model [here]({{< relref "publication" >}}). +To get an idea on how the data model has been used in software tools, browse the [applications that support SBOL]({{< relref "applications" >}}). +The [publications list]({{< relref "publication" >}}) collects the papers that define the data model, feature it, or describe tools that support it. -### Download SBOL Data Library +### Libraries -We support the SBOL Data models in the following formats: **C/C++**, **Java**, **Javascript**, and **Python**. You can download the SBOL data model [here]({{< relref "libraries" >}}). +Official libraries implement the data model in **Python**, **Java**, **Rust**, **JavaScript**, and **C/C++**; pick one on the [libraries page]({{< relref "libraries" >}}). ### Proposing a New Feature to the SBOL Data Model @@ -47,8 +56,8 @@ To propose a new feature to SBOL, a standard procedure must be followed. 1. Submit a [new issue](https://github.com/SynBioDex/SBOL-specification/issues) on the SBOL Github repository. 2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). + * Read [what an SEP is and how to submit one](https://github.com/SynBioDex/SEPs/issues/1). + * Start from the [SEP template](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). 3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. 4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL. diff --git a/content/applications/_index.md b/content/applications/_index.md index 207efbecc..dc9d7399d 100644 --- a/content/applications/_index.md +++ b/content/applications/_index.md @@ -2,4 +2,8 @@ title: Applications subtitle: Community-contributed software supporting SBOL Core and SBOL Visual, enabling you to design, simulate, visualize, and share genetic designs. submit_url: https://forms.gle/1UmX3CeCb973G9jE9 +cascade: + share: false + profile: false +summary: Community-contributed software supporting SBOL Core and SBOL Visual, enabling you to design, simulate, visualize, and share genetic designs. --- diff --git a/content/applications/boost/index.md b/content/applications/boost/index.md index d38dbc97b..3bd2117e2 100644 --- a/content/applications/boost/index.md +++ b/content/applications/boost/index.md @@ -23,6 +23,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "DOE Joint Genome Institute, Lawrence Berkeley National Labs" + language: "Java" + platform: "Linux/Mac/Win/Web" + availability: "Free for academic users" --- Build-OptimizatiOn Software Tools (BOOST) is a platform of tools to design DNA sequences for manufacturing. Currently, BOOST consists of three tools: (i) The "Juggler" reverse translates protein sequences into DNA sequences and codon juggles DNA sequences, (ii) The "Polisher" verifies DNA sequences against DNA synthesis constraints. In addition, the "Polisher" can modify the protein coding regions of DNA sequences in order to resolve eventual violations of DNA synthesis constraints. (iii) The "Partitioner" decomposes large DNA sequences into synthesizable building blocks with assembly-specific overlap sequences. diff --git a/content/applications/cello/index.md b/content/applications/cello/index.md index 3dbd805a5..da706ce0a 100644 --- a/content/applications/cello/index.md +++ b/content/applications/cello/index.md @@ -31,6 +31,12 @@ url_video: "https://www.youtube.com/watch?v=SLn_SkL7vkQ&feature=youtu.be" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Boston University" + language: "Java/HTML/JS/CSS" + platform: "Web" + availability: "Open-Source" + license: "BSD 2-Clause" --- Cello is a framework that describes what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering. diff --git a/content/applications/device-editor/index.md b/content/applications/device-editor/index.md index 12c942b24..369e4d9c1 100644 --- a/content/applications/device-editor/index.md +++ b/content/applications/device-editor/index.md @@ -27,6 +27,10 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Lawrence Berkeley National Lab" + language: "JavaScript" + platform: "Web" --- diff --git a/content/applications/dnaplotlib/index.md b/content/applications/dnaplotlib/index.md index 0483a9805..0d563cc03 100644 --- a/content/applications/dnaplotlib/index.md +++ b/content/applications/dnaplotlib/index.md @@ -27,6 +27,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "University of Bristol, UK (originally Voigt Lab, MIT)" + language: "Python" + platform: "Linux, Mac, Windows" + availability: "Open-Source" + license: "MIT" --- diff --git a/content/applications/eugene/index.md b/content/applications/eugene/index.md index 3bebb20fe..0ae264a7f 100644 --- a/content/applications/eugene/index.md +++ b/content/applications/eugene/index.md @@ -35,6 +35,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Boston University" + language: "Java" + platform: "Linux, Mac, Windows, Web" + availability: "Open-Source" + license: "CC BY-SA 4.0" --- Eugene is a textual specification language for the rule-based design of synthetic biological systems, devices, parts, and DNA sequences. diff --git a/content/applications/finch/index.md b/content/applications/finch/index.md index becda0551..79c639234 100644 --- a/content/applications/finch/index.md +++ b/content/applications/finch/index.md @@ -28,6 +28,11 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Boston University" + language: "C/Java/Perl" + platform: "Web" + availability: "Free for academic users" --- diff --git a/content/applications/flapjack/index.md b/content/applications/flapjack/index.md index f7b8662f1..70d165a09 100644 --- a/content/applications/flapjack/index.md +++ b/content/applications/flapjack/index.md @@ -31,6 +31,12 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Newcastle University" + language: "Python, JavaScript" + platform: "Linux, MacOS, Windows, Web" + availability: "Open-Source" + license: "MIT License" --- Flapjack is a data management and analysis app for genetic circuit characterization to store, share, mix, analyze and plot your SynBio data.It has a database backend, a webapp as frontend and a Python API, this allows you to access your data remotely using an intuitive user interface and be able to integrate it easily in Python workflows for automation. diff --git a/content/applications/genegenie/index.md b/content/applications/genegenie/index.md index e90bdd697..f5c9ec9a5 100644 --- a/content/applications/genegenie/index.md +++ b/content/applications/genegenie/index.md @@ -23,6 +23,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Manchester Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM)" + language: "Java" + platform: "Web" + availability: "Open-Source" --- GeneGenie supports the design and self-assembly of synthetic genes and constructs. GeneGenie allows for the design of oligonucleotide cohorts encoding the gene sequence optimized for expression in any suitable host through an intuitive, easy-to-use web interface. The tool ensures consistent oligomer overlapping melting temperatures, minimizes the likelihood of misannealing, optimizes codon usage for expression in a selected host, allows for specification of forward and reverse cloning sequences and also provides support for mutagenesis or directed evolution studies. Directed evolution studies are enabled through the construction of variant libraries via the optional specification of ‘variant codons’, containing mixtures of bases, at any position. For example, specifying the variant codon TNT (where N is any nucleotide) will encode a mixture of the amino acids Tyr, Ser, Cys and Phe. diff --git a/content/applications/genetech/index.md b/content/applications/genetech/index.md index 460aa28ad..9676a379f 100644 --- a/content/applications/genetech/index.md +++ b/content/applications/genetech/index.md @@ -27,6 +27,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Denmark Technical University, Habib University, University of Connecticut" + language: "Python, Java" + platform: "MacOS, Windows" + availability: "Open-source, Free for all users" --- diff --git a/content/applications/genocad/index.md b/content/applications/genocad/index.md index 723bff8e6..7586a70ce 100644 --- a/content/applications/genocad/index.md +++ b/content/applications/genocad/index.md @@ -24,6 +24,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "GenoFAB, LLC" + language: "PHP/Java/Prolog/JS" + platform: "Web" + availability: "Commercial" --- GenoCAD is a rule-based DNA design tool. It includes an extensive library of genetic parts derived from the annotation of common plasmids. It allows users to define domain specific languages to design expression systems for particular applications. diff --git a/content/applications/graphviz/index.md b/content/applications/graphviz/index.md index de5da834b..5d4e803a3 100644 --- a/content/applications/graphviz/index.md +++ b/content/applications/graphviz/index.md @@ -23,6 +23,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Graphviz Community" + language: "C" + platform: "Linux, Mac, Windows" + availability: "Open-Source" + license: "Eclipse Public License - v 1.0" --- Graphviz (short for Graph Visualization Software) is a package of open-source tools initiated by AT&T Labs Research for drawing graphs specified in DOT language scripts. It also provides libraries for software applications to use the tools. Graphviz is free software licensed under the Eclipse Public License. Graphviz includes SBOL visual symbols in its set of node shapes, and has edge shapes compatible with proposed regulatory arc shapes. diff --git a/content/applications/ibiosim/index.md b/content/applications/ibiosim/index.md index 328dac936..2a0d04526 100644 --- a/content/applications/ibiosim/index.md +++ b/content/applications/ibiosim/index.md @@ -27,6 +27,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "University of Utah" + language: "Java/C++" + platform: "Linux, Mac, Windows" + availability: "Open-Source" + license: "MIT" --- iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). It can import all levels and versions of SBML and is able to export Level 3 Version 1. It supports all core SBML modeling constructs except some types of fast reactions, and also has support for the hierarchical model composition, layout, flux balance constraints, and arrays packages. It was the first tool to produce correct results for all examples in the SBML benchmark suite. It has also been tested successfully on the stochastic benchmark suite and the curated models in the BioModels database. Finally, it is one of the first tools to also support the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology. diff --git a/content/applications/ice/index.md b/content/applications/ice/index.md index 797549b88..caac7d99c 100644 --- a/content/applications/ice/index.md +++ b/content/applications/ice/index.md @@ -27,6 +27,12 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Lawrence Berkeley National Lab" + language: "Java" + platform: "Web" + availability: "Open-Source" + license: "BSD" --- diff --git a/content/applications/j5/index.md b/content/applications/j5/index.md index ba50ca715..b8c267059 100644 --- a/content/applications/j5/index.md +++ b/content/applications/j5/index.md @@ -27,6 +27,10 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Lawrence Berkeley National Lab" + language: "Perl" + platform: "Web" --- diff --git a/content/applications/mosec/index.md b/content/applications/mosec/index.md index b22b9f525..9e892d164 100644 --- a/content/applications/mosec/index.md +++ b/content/applications/mosec/index.md @@ -23,6 +23,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Newcastle University" + language: "Java" + platform: "Linux, Mac, Windows" + availability: "Free for all users" --- diff --git a/content/applications/partsandpools/index.md b/content/applications/partsandpools/index.md index 28d672039..ef1243237 100644 --- a/content/applications/partsandpools/index.md +++ b/content/applications/partsandpools/index.md @@ -18,9 +18,14 @@ image: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Harbin Institute of Technology" + language: "Perl/Python" + platform: "Linux, Mac, Windows" + availability: "Free for all users" --- -Graphical, drag and drop design of synthetic gene circuit with Standard Biological Parts. Eukaryotic parts are modelled via a rule-based approach. +Graphical, drag and drop design of synthetic gene circuit with Standard Biological Parts. Eukaryotic parts are modeled via a rule-based approach. | | | diff --git a/content/applications/pigeon/index.md b/content/applications/pigeon/index.md index 100dbc443..bc1989a97 100644 --- a/content/applications/pigeon/index.md +++ b/content/applications/pigeon/index.md @@ -27,6 +27,11 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Bhatia Lab at Boston University" + language: "Perl" + platform: "Web" + availability: "Free" --- diff --git a/content/applications/pinecone/index.md b/content/applications/pinecone/index.md index a35b04883..5b2b4876a 100644 --- a/content/applications/pinecone/index.md +++ b/content/applications/pinecone/index.md @@ -25,6 +25,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Serotiny" + language: "JavaScript" + platform: "Web" + availability: "Free for all users" --- Pinecone is Serotiny’s web-based protein design software aimed at researchers doing R&D for therapeutics, materials, as well as those in basic research. Serotiny optimized Pinecone for designing protein constructs by focusing on functional protein domains as the basic unit of design. diff --git a/content/applications/pooldesigner/index.md b/content/applications/pooldesigner/index.md index 8620dec17..d0204a5dd 100644 --- a/content/applications/pooldesigner/index.md +++ b/content/applications/pooldesigner/index.md @@ -23,6 +23,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Biological Design Center, Boston University" + language: "Java/JavaScript" + platform: "Web" + availability: "Open-Source" + license: "BSD 3-Clause" --- The Pool Designer application is capable of analyzing a library of genetic construct variants encoded in SBOL and breaking this library down into pools of genetic parts that can be assembled into any library variant using multiplex assembly methods (see L. Woodruff et al., “Registry in a tube : multiplexed pools of retrievable parts for genetic design space exploration,” Nucl. Acids Res., 2016.). diff --git a/content/applications/protobiocompiler/index.md b/content/applications/protobiocompiler/index.md index eeefbd607..fcdb14400 100644 --- a/content/applications/protobiocompiler/index.md +++ b/content/applications/protobiocompiler/index.md @@ -18,6 +18,12 @@ image: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Raytheon BBN Technologies" + language: "C/C++" + platform: "Linux/Mac/Win/Web" + availability: "Open-Source" + license: "GPL3 with classpath exception" --- Proto BioCompiler generates optimized genetic regulatory network designs from specifications written in a high-level programming language, producing both SBOL specifications, visualization, and ODE models. diff --git a/content/applications/sbolcanvas/index.md b/content/applications/sbolcanvas/index.md index 3912b658d..bc0dc7a8c 100644 --- a/content/applications/sbolcanvas/index.md +++ b/content/applications/sbolcanvas/index.md @@ -31,6 +31,12 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "[Synthetic Biology Knowledge System](http://web.synbioks.org)" + language: "HTML/Java/TypeScript" + platform: "Web" + availability: "Open-Source" + license: "Apache 2.0" --- [SBOLCanvas](https://sbolcanvas.org/) is a web application for diff --git a/content/applications/sboldesigner/index.md b/content/applications/sboldesigner/index.md index f82945f5d..b2be4e43d 100644 --- a/content/applications/sboldesigner/index.md +++ b/content/applications/sboldesigner/index.md @@ -27,6 +27,12 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "University of Colorado, Boulder" + language: "Java/HTML/JS/CSS" + platform: "Web" + availability: "Open-Source" + license: "BSD 2-Clause" --- SBOLDesigner 2.1 is a simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using the Synthetic Biology Open Language (SBOL) 2.0 data model. Throughout the design process, SBOL Visual symbols, a system of schematic glyphs, provide standardized visualizations of individual parts. SBOLDesigner 2.1 completes a workflow for users of genetic design automation tools. It combines a simple user interface with the power of the SBOL standard and serves as a launchpad for more detailed designs involving simulations and experiments. Some new features in SBOLDesigner 2.1 are SBOL Stack integration, local repositories, importing of parts/sequences from existing files, import and export of GenBank and FASTA files, extended role ontology support, the ability to partially open designs with multiple root ComponentDefinitions, backward compatibility with SBOL 1.1, and versioning. SBOLDesigner is made freely available under the Apache 2.0 license. diff --git a/content/applications/sbolgenbank/index.md b/content/applications/sbolgenbank/index.md index ec03e8469..e94995067 100644 --- a/content/applications/sbolgenbank/index.md +++ b/content/applications/sbolgenbank/index.md @@ -23,6 +23,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Berkeley Lab" + language: "Perl" + platform: "Web" + availability: "Free for all users" --- diff --git a/content/applications/sbolme/index.md b/content/applications/sbolme/index.md index ac1dca8ab..f75b4075e 100644 --- a/content/applications/sbolme/index.md +++ b/content/applications/sbolme/index.md @@ -23,6 +23,11 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "KAUST" + language: "HTML/PHP/Python/SQL" + platform: "Web" + availability: "Free for all users" --- diff --git a/content/applications/sbolvalidator/index.md b/content/applications/sbolvalidator/index.md index 45e913e10..4519e5e42 100644 --- a/content/applications/sbolvalidator/index.md +++ b/content/applications/sbolvalidator/index.md @@ -23,6 +23,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "University of Utah" + language: "Python/Java" + platform: "Web" + availability: "Open-Source" + license: "Apache 2.0" --- SBOL Validator/Converter is a simple, easy-to-use software tool that allows for conversion between SBOL/GenBank/FASTA files using the Synthetic Biology Open Language (SBOL) 2.0 data model. The motivation behind the SBOL Validator/Converter is to provide a universally-accepted tool with the capability to check the validity of files. This tool serves as a platform for developers to verify correct implementation of the SBOL data standard, authors to ensure that data is represented properly, and editors to verify SBOL compliance of all software tools and libraries. Some key features of the Validator/Converter include its ability to convert between SBOL, FASTA, and GenBank files and that the tool is web-based which promotes ease of access and allows for central maintenance of validation methods. SBOL Validator/Converter is made freely available under the Apache 2.0 license. diff --git a/content/applications/shortbol/index.md b/content/applications/shortbol/index.md index c2532299c..08b92acc5 100644 --- a/content/applications/shortbol/index.md +++ b/content/applications/shortbol/index.md @@ -32,6 +32,10 @@ url_video: "" # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Newcastle University, Turing Ate My Hamster Ltd" + language: "Scala" + platform: "Linux/Mac/Win/Web" --- diff --git a/content/applications/synbiohub/index.md b/content/applications/synbiohub/index.md index 804ba6a04..0c759b368 100644 --- a/content/applications/synbiohub/index.md +++ b/content/applications/synbiohub/index.md @@ -27,6 +27,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Newcastle University" + language: "JavaScript" + platform: "Linux/Mac/Win/Web" + availability: "Open-Source" + license: "BSD 2-Clause" --- SynBioHub is a registry for storing and sharing genetic circuit designs using the SBOL2 standard. Designs can be uploaded in SBOL or GenBank format, assigned a public link to share with collaborators and for publications, and searched using rich querying functionality. diff --git a/content/applications/tellurium/index.md b/content/applications/tellurium/index.md index 535ef9542..0d31acb8b 100644 --- a/content/applications/tellurium/index.md +++ b/content/applications/tellurium/index.md @@ -26,6 +26,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "University of Washington" + language: "C/C++" + platform: "Linux, Mac, Windows" + availability: "Open-Source" + license: "BSD" --- Tellurium is a Python environment based on spyder2 IDE, designed for systems and synthetic biology simulations. It combines a number of existing libraries, including libRoadRunner, libAntimony, and phraSED-ML, alongside with standards support through libSBML, libSEDML, and pySBOL. Additionally, other Python packages such as matplotlib and NumPy are used to provide extra analysis, optimization, and plotting capabilities. diff --git a/content/applications/tinkercell/index.md b/content/applications/tinkercell/index.md index 56bbedfbb..692c85f8b 100644 --- a/content/applications/tinkercell/index.md +++ b/content/applications/tinkercell/index.md @@ -30,6 +30,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "University of Washington" + language: "C/C++" + platform: "Linux, Mac, Windows" + availability: "Open-Source" + license: "BSD" --- TinkerCell is a widely used open source network design and simulation application tool for synthetic biology (tinkercell.org). The software allows synthetic biologists to design new synthetic circuits and simulate them. TinkerCell is written in C++ and runs on Windows, Mac and Linux. It uses Qt as the GUI framework. Currently TinkerCell only has very limited support for SBOL. diff --git a/content/applications/visbol/index.md b/content/applications/visbol/index.md index 277628a4c..10bdda4d5 100644 --- a/content/applications/visbol/index.md +++ b/content/applications/visbol/index.md @@ -32,6 +32,12 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Newcastle University" + language: "JavaScript" + platform: "Lin/Mac/Win/Web" + availability: "Open-Source" + license: "BSD 2-Clause" --- VisBOL is a JavaScript software library to visualize DNA features from SBOL2 documents using the SBOL Visual standard. A Web interface is also provided to enable end-user access to generate diagrams for presentations and publications. diff --git a/content/applications/vpr/index.md b/content/applications/vpr/index.md index 9b35a5505..9180da791 100644 --- a/content/applications/vpr/index.md +++ b/content/applications/vpr/index.md @@ -23,6 +23,10 @@ links: # E.g. `slides = "example-slides"` references `content/slides/example-slides.md`. # Otherwise, set `slides = ""`. slides: "" +meta: + organization: "Newcastle University" + language: "Java" + platform: "Linux/Web" --- A repository of modular models of biological components. These models are reusable and composable, and facilitate model-driven design of biological systems. diff --git a/content/authors/admin/_index.md b/content/authors/admin/_index.md index b0748933e..f74775949 100644 --- a/content/authors/admin/_index.md +++ b/content/authors/admin/_index.md @@ -74,28 +74,12 @@ email: "" # SBOL is an open standard for the representation of in silico biological designs. # SBOL provides a data format composed of genetic vocabulary terms called SBOL Data. # SBOL also provides schematic glyphs to graphically depict genetic designs called SBOL Visual. -# SBOL standardises data used by synthetic biology practitioners, from users to software developers to wet lab biologists. +# SBOL standardizes data used by synthetic biology practitioners, from users to software developers to wet lab biologists. user_groups: - Researchers - Visitors --- - -
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b/content/biologist/_index.md index ff27c2686..1b944ea14 100644 --- a/content/biologist/_index.md +++ b/content/biologist/_index.md @@ -11,14 +11,14 @@ benefits: description: "Deposit your designs in repositories like SynBioHub and cite them directly in papers with persistent, stable links." - icon: "fas fa-drafting-compass" title: "Speak a Visual Language" - description: "SBOL Visual provides standardised glyphs so your diagrams are immediately understood by any synthetic biologist, worldwide." + description: "SBOL Visual provides standardized glyphs so your diagrams are immediately understood by any synthetic biologist, worldwide." tools: - name: "SBOLCanvas" description: "A web-based tool for creating publication-ready, standards-compliant genetic diagrams - no installation needed." bullets: - "Drag-and-drop interface for building complex designs intuitively" - - "Uses standardised SBOL Visual glyphs for every part type" + - "Uses standardized SBOL Visual glyphs for every part type" - "Export high-quality images ready for manuscripts and presentations" image: "sbolcanvas.png" image_alt: "SBOLCanvas Interface" @@ -38,7 +38,7 @@ tools: flip: true glyphs_title: "The Visual Language of Synthetic Biology" -glyphs_description: "SBOL Visual defines a standardised set of glyphs - symbols for promoters, CDSs, terminators, and more - so diagrams mean the same thing everywhere. Whether you are annotating a figure for a paper or describing a construct to a collaborator, SBOL Visual gives you a shared vocabulary the whole community recognises." +glyphs_description: "SBOL Visual defines a standardized set of glyphs - symbols for promoters, CDSs, terminators, and more - so diagrams mean the same thing everywhere. Whether you are annotating a figure for a paper or describing a construct to a collaborator, SBOL Visual gives you a shared vocabulary the whole community recognizes." glyphs_url: "/visual-glyphs" glyphs_history_url: "/sbolv-10-years" glyphs_gallery_url: "/visual-gallery" @@ -46,4 +46,5 @@ glyphs_gallery_url: "/visual-gallery" genai_title: "Learn SBOL with AI" genai_description: "Not sure where to start? Our SBOL GPT assistants can answer questions about the standard in plain language - no documentation required." genai_url: "/genai-tools" +summary: "No coding required. Give your designs a shared language that tools, collaborators, and journals all understand." --- diff --git a/content/blog/_index.md b/content/blog/_index.md index 3e179853a..9b0169fef 100644 --- a/content/blog/_index.md +++ b/content/blog/_index.md @@ -1,4 +1,7 @@ --- -title: Blog +title: SBOL Blog +subtitle: "Insights, tutorials, and perspectives from the synthetic biology community." +list_badge: blog view: 3 +summary: "Insights, tutorials, and perspectives from the synthetic biology community." --- diff --git a/content/community-governance/_index.md b/content/community-governance/_index.md index 51ef47a74..38637e218 100644 --- a/content/community-governance/_index.md +++ b/content/community-governance/_index.md @@ -12,6 +12,10 @@ view: 3 header: caption: "" image: "" +subtitle: "How the SBOL community is organized, who decides what, and how proposals become part of the standard." +layout: sbol-page +toc: true +summary: "How the SBOL community is organized, who decides what, and how proposals become part of the standard." --- SBOL is being developed by a collegial volunteer organization, which runs primarily by rough consensus. As an organization, the SBOL development community holds the following values: diff --git a/content/community-leadership/10-chair.md b/content/community-leadership/10-chair.md deleted file mode 100644 index cf4abe563..000000000 --- a/content/community-leadership/10-chair.md +++ /dev/null @@ -1,15 +0,0 @@ -+++ -widget = "people" -headless = true -weight = 10 -title = "" - -[content] - user_groups = ["Current Chair"] - -[design] - show_social = true - show_interests = false - show_role = true - show_organizations = true -+++ diff --git a/content/community-leadership/20-editors.md b/content/community-leadership/20-editors.md deleted file mode 100644 index 08f2e08cf..000000000 --- a/content/community-leadership/20-editors.md +++ /dev/null @@ -1,15 +0,0 @@ -+++ -widget = "people" -headless = true -weight = 20 -title = "" - -[content] - user_groups = ["Current Editors"] - -[design] - show_social = true - show_interests = false - show_role = false - show_organizations = true -+++ diff --git a/content/community-leadership/30-steering.md b/content/community-leadership/30-steering.md deleted file mode 100644 index 7023b83ac..000000000 --- a/content/community-leadership/30-steering.md +++ /dev/null @@ -1,15 +0,0 @@ -+++ -widget = "people" -headless = true -weight = 30 -title = "" - -[content] - user_groups = ["Steering Committee"] - -[design] - show_social = true - show_interests = false - show_role = false - show_organizations = true -+++ diff --git a/content/community-leadership/40-past-advisory.md b/content/community-leadership/40-past-advisory.md deleted file mode 100644 index 436b777b6..000000000 --- a/content/community-leadership/40-past-advisory.md +++ /dev/null @@ -1,15 +0,0 @@ -+++ -widget = "people" -headless = true -weight = 40 -title = "" - -[content] - user_groups = ["Past Advisory Board Members"] - -[design] - show_social = true - show_interests = false - show_role = false - show_organizations = true -+++ diff --git a/content/community-leadership/50-past-chairs.md b/content/community-leadership/50-past-chairs.md deleted file mode 100644 index 4a7a16100..000000000 --- a/content/community-leadership/50-past-chairs.md +++ /dev/null @@ -1,15 +0,0 @@ -+++ -widget = "people" -headless = true -weight = 50 -title = "" - -[content] - user_groups = ["Past Chairs"] - -[design] - show_social = false - show_interests = false - show_role = true - show_organizations = true -+++ diff --git a/content/community-leadership/60-past-editors.md b/content/community-leadership/60-past-editors.md deleted file mode 100644 index 2b3a873bf..000000000 --- a/content/community-leadership/60-past-editors.md +++ /dev/null @@ -1,15 +0,0 @@ -+++ -widget = "people" -headless = true -weight = 60 -title = "" - -[content] - user_groups = ["Past Editors"] - -[design] - show_social = false - show_interests = false - show_role = false - show_organizations = true -+++ diff --git a/content/community-leadership/_index.md b/content/community-leadership/_index.md new file mode 100644 index 000000000..c596d3021 --- /dev/null +++ b/content/community-leadership/_index.md @@ -0,0 +1,34 @@ +--- +title: Community Leadership +subtitle: "The people who steer, edit, and advise the SBOL standard. Editors and the chair are elected by the community; see Governance for how." +layout: sbol-page +hero_buttons: + - text: How we are governed + url: /community-governance/ + style: secondary +summary: "The people who steer, edit, and advise the SBOL standard. Editors and the chair are elected by the community; see Governance for how." +--- + +## Current chair + +{{< sbol-people group="Current Chair" role="true" social="true" >}} + +## Current editors + +{{< sbol-people group="Current Editors" role="false" social="true" >}} + +## Steering committee + +{{< sbol-people group="Steering Committee" role="false" social="true" >}} + +## Past advisory board members + +{{< sbol-people group="Past Advisory Board Members" role="false" social="true" >}} + +## Past chairs + +{{< sbol-people group="Past Chairs" role="true" >}} + +## Past editors + +{{< sbol-people group="Past Editors" role="false" sort="name" >}} diff --git a/content/community-leadership/index.md b/content/community-leadership/index.md deleted file mode 100644 index 0de0b351b..000000000 --- a/content/community-leadership/index.md +++ /dev/null @@ -1,4 +0,0 @@ -+++ -title = "Community Leadership" -type = "widget_page" -+++ diff --git a/content/community-meetings/_index.md b/content/community-meetings/_index.md index c310bee3e..07326b49c 100644 --- a/content/community-meetings/_index.md +++ b/content/community-meetings/_index.md @@ -1,9 +1,10 @@ --- title: Meetings & Outreach subtitle: "The SBOL community meets approximately every six months at COMBINE and HARMONY workshops, and actively engages the broader synthetic biology community at conferences worldwide." -hero_btn_text: "Join us on Slack" -hero_btn_icon: "fab fa-slack" -hero_btn_url: "https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg" +hero_buttons: + - text: "Join us on Slack" + icon: "fab fa-slack" + url: "https://join.slack.com/t/sbol-standard/shared_invite/zt-1ukcka8b8-Z4QoyiE_LwwoRBw2DzheSg" connect_text: "SBOL is open-source and thrives on active participation. Contribute code, join working groups, or simply stay informed." connect_links: @@ -15,7 +16,7 @@ connect_links: url: "https://groups.google.com/g/sbol-announce" - name: "Join SBOL" description: "Contact our editors" - url: "https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit" + url: "https://docs.google.com/forms/d/e/1FAIpQLScp8lomURs-y-8BlptY0fFgLSFIl0cKvcMkOBc_JVlEgW22Sw/viewform" - name: "YouTube" description: "View SBOL videos" url: "https://youtube.com/@syntheticbiologyopenlangua6204?si=j5PkGrh_-DSmbl2G" @@ -412,4 +413,5 @@ outreach: date_display: "" location: "University of Washington, Seattle, WA, USA" url: "/event/2018/soundbiolab/" +summary: "The SBOL community meets approximately every six months at COMBINE and HARMONY workshops, and actively engages the broader synthetic biology community at conferences worldwide." --- diff --git a/content/community-outreach/_index.md b/content/community-outreach/_index.md index 2aebafb7f..7c463de05 100644 --- a/content/community-outreach/_index.md +++ b/content/community-outreach/_index.md @@ -1,50 +1,5 @@ --- title: Outreach - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" +layout: redirect +redirect_to: /community-meetings/ --- -Below is a list of outreach events that SBOL has been involved in to educate the community about SBOL and its capability. The presentation materials for many of these outreach events can be found in the SBOL Community Media repository found [here](https://github.com/SynBioDex/Community-Media), and they are made freely available via a Creative Commons license. - -| Events | Date (YYYY/DD/MM) | Location | Agenda + Resources | -|-------------------------------------------------------------------------------|----------------------------|---------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------| -| IWBDA 2023 | 2023/11-14/09 | Boston, Massachusetts, USA | Event | -| SEED 2023 | 2023/30/05 - 2023/02/06 | Hilton Los Angeles/Universal City Hotel, Los Angeles, California, USA | Event | -| IWBDA 2022 | 2022/24-26/10 | Paris, France | Event | -| SEED 2022 | 2022/02-05/05 | Crystal Gateway Marriott, Arlington, VA, USA | Event | -| IWBDA 2021 | 2021/20-24/09 | Virtual | Event | -| SEED 2021 | 2021/15-18/06 | Virtual | Event | -| IWBDA 2020 | 2020/8-10/06 | Worcester Polytechnic Institute, Worcester, MA, US | Link | -| Software for Synthetic Biology Workflows Workshop | 2020/6/22-2020/06/25 | Hyatt Regency, San Francisco, CA, USA | Link | -| IWBDA 2019 | 2019/8-10/07 | Cambridge, UK | Event | -| Software for Synthetic Biology Workflows | 2019/27/06 | New York Hilton - Midtown, New York, NY | Event | -| SEED 2019 | 2019/06/23 - 2019/06/27 | New York Hilton, Midtown, New York City, New York, USA | Event | -| IWBDA 2018 | 2018/31/07 - 2018/01/08 | The David Brower Center in Berkeley, California, USA | Event | -| SEED 2018 | 2018/3-7/06 | JW Marriott Scottsdale Camelback Inn Resort & Spa, Scottsdale, AZ, USA | Link | -| IWBDA 2017 | 2017/11/08 | University of Pittsburgh, PA | Event | -| SEED 2017 | 2017/20-23/06 | Hyatt Regency, Vancouver, British Columbia, Canada | Event | -| SB7.0 | 2017/13-16/07 | National University of Singapore, Singapore | Event | -| Living Computing Project | 2017/12/05 | Boston University, MA, US | Event | -| EMBL-EBI | 2017/02/05 | European Bioinformatics Institute in Cambridge, United Kingdom | Event | -| The 8th International Symposium of Innovative BioProduction Kobe (iBioK) | 2017/2-3/02 | Kobe University Centennial Hall in Japan | Event | -| IET/SynbiCITE | 2016/13-15/12 | Savoy Palace, London, UK | Link | -| IWBDA 2016 | 2016/16-18/08 | Newcastle University in Newcastle upon Tyne, UK | Link | -| Nona | 2016/17/07 | Chicago, IL, USA | Link | -| ISMB 2016 | 2016/8-12/07 | Swan and Dolphin Hotel in Orlando, FL, USA | Link | -| IWBDA 2015 | 2015/19-21/08 | University of Washington in WA, USA | Event | -| SEED 2015 | 2015/10-13/06 | Chicago, IL, USA | Event | -| ICSB 2014 | 2014/14/09 | Melbourne, AU | Event | -| SEED 2014 | 2014/14-17/07 | Manhattan Beach, CA, USA | Event | -| IWBDA 2014 | 2014/11-12/06 | Photonics Center in Boston, MA, USA | Event | -| IWBDA 2013 | 2013/12-13/07 | Imperial College in London,UK | Event | -| SB6.0 | 2013/9-11/07 | Imperial College in London,UK | Event | -| Soundbiolab | | University of Washington in Seattle, WA, USA | Event | diff --git a/content/community/_index.md b/content/community/_index.md index 23aab7fa9..82bd4f3a2 100644 --- a/content/community/_index.md +++ b/content/community/_index.md @@ -1,21 +1,5 @@ --- title: The SBOL Community - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -# 4 = Citation -view: 3 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" +layout: redirect +redirect_to: /join/ --- - - -The SBOL community works actively on the SBOL data model and visual standard, participates in online discussions, and meets semi-annually. We represent over 170+ members from 17 different countries, 42 institutions, and 28 different industries. Many of our members are also actively involved in other standards communities, like the Systems Biology Markup Language (SBML) and Systems Biology Graphical Notation (SBGN). - - -To join our growing community, contact the SBOL Editors [here](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit). diff --git a/content/contact/_index.md b/content/contact/_index.md index 5dc21d762..340d66868 100644 --- a/content/contact/_index.md +++ b/content/contact/_index.md @@ -12,8 +12,15 @@ view: 3 header: caption: "" image: "" +subtitle: "Reach the SBOL editors and the community." +layout: sbol-page +summary: "Reach the SBOL editors and the community." --- +For questions about SBOL, the specifications, or the tools, email the [SBOL Editors](mailto:sbol-editors@googlegroups.com). They answer directly and can point you to the right part of the community. + +## Mailing lists + The [sbol-announce](mailto:sbol-announce@googlegroups.com), [sbol-users](mailto:sbol-users@googlegroups.com), [sbol-dev](mailto:sbol-dev@googlegroups.com), and [sbol-visual](mailto:sbol-visual@googlegroups.com) are mailing lists open to all members of the SBOL community to post discussions and ask questions about SBOL. These mailing lists are moderated by the SBOL Editors. If the discussions and comments become inappropriate, the SBOL editors reserve the right to disallow future posting to be made by the community until further notice. @@ -24,13 +31,15 @@ The [sbol-announce](mailto:sbol-announce@googlegroups.com), [sbol-users](mailto: | **SBOL Users** | [sbol-users](mailto:sbol-users@googlegroups.com) is a mailing list created for those who are using SBOL in their software tool and have questions about how they can incorporate features of the SBOL data model and/or sbol-visual glyphs within their tool. | | **SBOL Developers** | [sbol-dev](mailto:sbol-dev@googlegroups.com) is a mailing list created for those who want to implement the SBOL data model library. All discussions related to proposing a new feature to the SBOL data model and SBOL Enhancement Proposals (SEPs) are taken place in this mailing list. | | **SBOL Visual** | [sbol-visual](mailto:sbol-visual@googlegroups.com) is a mailing list created for those who want to discuss and propose glyphs to represent engineered biological organisms through diagrams. | -| **SBOL Website Issues** | For website issues, please report them to our [SBOL website GitHub repository](https://github.com/SynBioDex/SBOL_website/issues) by submitting a GitHub issue. | +| **SBOL Website Issues** | For website issues, please report them to our [SBOL website GitHub repository](https://github.com/SynBioDex/SbolStandardWebsite/issues) by submitting a GitHub issue. | + +## Join or subscribe -Please fill in the following form if you would like to **join the SBOL community** or **subscribe** to the sbol-dev, sbol-visual, sbol-users, or sbol-announce mailing list: +The form below registers you as a member of the SBOL community and subscribes you to the mailing lists you choose. It is not a contact form: for questions, email the [SBOL Editors](mailto:sbol-editors@googlegroups.com) instead. {{< gdocs src="https://docs.google.com/forms/d/e/1FAIpQLScp8lomURs-y-8BlptY0fFgLSFIl0cKvcMkOBc_JVlEgW22Sw/viewform?embedded=true" >}} -If you are unable to view the form, try this [link](https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU). Alternatively, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com) along with your name, institution/affiliation, country, your interest in SBOL, and which email list(s) you would like to subscribe to. +If the form does not load, [open it in a new tab](https://docs.google.com/forms/d/e/1FAIpQLScp8lomURs-y-8BlptY0fFgLSFIl0cKvcMkOBc_JVlEgW22Sw/viewform). You can also email the [SBOL Editors](mailto:sbol-editors@googlegroups.com) with your name, institution or affiliation, country, your interest in SBOL, and the lists you would like to join. diff --git a/content/developer/_index.md b/content/developer/_index.md index 477a5746f..934e53284 100644 --- a/content/developer/_index.md +++ b/content/developer/_index.md @@ -75,4 +75,5 @@ contribute_links: description: "Developer discussions and announcements" icon: "fas fa-envelope" url: "https://groups.google.com/g/sbol-dev" +summary: "A precise data model, official libraries in multiple languages, and an active open-source community. Everything you need to build SBOL-native tools." --- diff --git a/content/event/2013/iwbda/index.md b/content/event/2013/iwbda/index.md index 88b1ec3b5..50d753532 100644 --- a/content/event/2013/iwbda/index.md +++ b/content/event/2013/iwbda/index.md @@ -20,24 +20,23 @@ An international workshop on Bio-Design Automation. ## SBOL Materials: - - - - - - - - - - +
-   Michal Galdzicki - -   Recent Advances in the Synthetic Biology Open Language -
-   Jacqueline Quinn - -   Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology -
+ + + + + + + +
+  Michal Galdzicki + +  Recent Advances in the Synthetic Biology Open Language +
+  Jacqueline Quinn + +  Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology +
**** diff --git a/content/event/2013/sb6/index.md b/content/event/2013/sb6/index.md index 39383037a..f284983b6 100644 --- a/content/event/2013/sb6/index.md +++ b/content/event/2013/sb6/index.md @@ -20,33 +20,31 @@ An international synthetic biology conference. ## SBOL Talks: - - - - - - - - - - - - - - - +
-   Chris Myers - -   Development of the Synthetic Biology Open Language -
-   Jacqueline Quinn - -   Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology -
-   Michal Galdzicki - -   The Synthetic Biology Open Language Standard: Sharing Design Information in Synthetic Biology -
+ + + + + + + + + + + +
+  Chris Myers + +  Development of the Synthetic Biology Open Language +
+  Jacqueline Quinn + +  Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology +
+  Michal Galdzicki + +  The Synthetic Biology Open Language Standard: Sharing Design Information in Synthetic Biology +
**** \ No newline at end of file diff --git a/content/event/2014/combine/index.md b/content/event/2014/combine/index.md index 07ecedc6d..dc1abca4d 100644 --- a/content/event/2014/combine/index.md +++ b/content/event/2014/combine/index.md @@ -22,147 +22,124 @@ A conference where the COMBINE community come together to present their work and **Monday, August 18th** - - - - - - - - +
-   [14:30PM – 15:00PM GMT] - -   Developing Standards in Synthetic Biology: the needs for a broad new engineering discipline - - Herbert Sauro -
+ + + + +
+  [14:30PM – 15:00PM GMT] + +  Developing Standards in Synthetic Biology: the needs for a broad new engineering discipline + +Herbert Sauro +
**** **Tuesday, August 19th** - - - - - - - - - - - - - - - - +
-   [12:00PM – 12:30PM GMT] - -   Synthetic Biology Open Language Visual: graphical notation for forward engineering of biology - - Jackie Quinn -
-   [16:00PM – 16:30PM GMT] - -   SBOL Visual 2.0 - - Jackie Quinn -
+ + + + + + + + + +
+  [12:00PM – 12:30PM GMT] + +  Synthetic Biology Open Language Visual: graphical notation for forward engineering of biology + +Jackie Quinn +
+  [16:00PM – 16:30PM GMT] + +  SBOL Visual 2.0 + +Jackie Quinn +
**** **Wednesday, August 20th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [09:00AM – 09:30PM GMT] - -   Generating SBML models from SBOL - - Nicholas Roehner -
-   [09:00AM – 09:30PM GMT] - -   Vector NTI Express Designer as a demonstration of SBOL interoperability with COMBINE standards - - Kevin Clancy -
-   [10:00AM – 10:30AM GMT] - -   SBOL Stack: The One-stop-shop to Storing and Publishing SBOL Data - - Curtis Madsen -
-   [14:00PM – 14:30PM GMT] - -   SBOL 2.0 Hierarchical Composition - - Nicholas Roehner -
-   [16:00PM – 17:30PM GMT] - -   SBOL 2.0 Interactions and Other Issues - - Nicholas Roehner -
+ + + + + + + + + + + + + + + + + + + + + + + + +
+  [09:00AM – 09:30PM GMT] + +  Generating SBML models from SBOL + +Nicholas Roehner +
+  [09:00AM – 09:30PM GMT] + +  Vector NTI Express Designer as a demonstration of SBOL interoperability with COMBINE standards + +Kevin Clancy +
+  [10:00AM – 10:30AM GMT] + +  SBOL Stack: The One-stop-shop to Storing and Publishing SBOL Data + +Curtis Madsen +
+  [14:00PM – 14:30PM GMT] + +  SBOL 2.0 Hierarchical Composition + +Nicholas Roehner +
+  [16:00PM – 17:30PM GMT] + +  SBOL 2.0 Interactions and Other Issues + +Nicholas Roehner +
**** **Friday, August 22nd** - - - - - - - - +
-   [16:00PM – 17:00PM GMT] - -   SBOL 2.0 finalization - - Nicholas Roehner -
+ + + + +
+  [16:00PM – 17:00PM GMT] + +  SBOL 2.0 finalization + +Nicholas Roehner +
**** diff --git a/content/event/2014/icsb/index.md b/content/event/2014/icsb/index.md index a4b7bf25b..c7b2ae98c 100644 --- a/content/event/2014/icsb/index.md +++ b/content/event/2014/icsb/index.md @@ -20,15 +20,15 @@ A conference that invites speakers from industry and academia to present their w ## SBOL Talk: - - - - - +
-   Chris Myers - -   The Synthetic Biology Open Language (SBOL) -
+ + + +
+  Chris Myers + +  The Synthetic Biology Open Language (SBOL) +
**** diff --git a/content/event/2014/iwbda/index.md b/content/event/2014/iwbda/index.md index f31f61cd2..260b7bb33 100644 --- a/content/event/2014/iwbda/index.md +++ b/content/event/2014/iwbda/index.md @@ -20,24 +20,23 @@ An international workshop on Bio-Design Automation. ## SBOL Materials: - - - - - - - - - - +
-   Nicholas Roehner - -   Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language -
-   Christian Olsen - -   Synthetic Biology Open Language Designer -
+ + + + + + + +
+  Nicholas Roehner + +  Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language +
+  Christian Olsen + +  Synthetic Biology Open Language Designer +
**** diff --git a/content/event/2014/seed/index.md b/content/event/2014/seed/index.md index 4b54afa90..17ee85aa1 100644 --- a/content/event/2014/seed/index.md +++ b/content/event/2014/seed/index.md @@ -20,15 +20,15 @@ A synthetic biology conference that brings together synthetic biologist from ind ## SBOL Talk: - - - - - +
-   Nicholas Roehner - -   A Proposed Data Model for the Next Version of the Synthetic Biology Open Language -
+ + + +
+  Nicholas Roehner + +  A Proposed Data Model for the Next Version of the Synthetic Biology Open Language +
**** \ No newline at end of file diff --git a/content/event/2015/combine/index.md b/content/event/2015/combine/index.md index 33578a756..3e0c261c0 100644 --- a/content/event/2015/combine/index.md +++ b/content/event/2015/combine/index.md @@ -23,211 +23,178 @@ A conference where the COMBINE community come together to present their work and **Monday, October 12th** - - - - - - - - +
-   [03:30PM – 04:15PM MDT] - -   The Synthetic Biology Open Language (SBOL) – recent developments in SBOL tools and repositories - - Anil Wipat -
+ + + + +
+  [03:30PM – 04:15PM MDT] + +  The Synthetic Biology Open Language (SBOL) – recent developments in SBOL tools and repositories + +Anil Wipat +
**** **Tuesday, October 13th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [08:30AM – 10:00AM MDT] - -   SBOL - - Anil Wipat -
-   [08:30AM – 08:45AM MDT] - -   Multiplicity of Representation in SBOL 2.0 - - Nicholas Roehner -
-   [08:45AM – 09:00AM MDT] - -   libSBOLj 2.0: A Java Library to Support SBOL 2.0 - - Zhen Zhang -
-   [09:00AM – 09:15AM MDT] - -   A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language - - Tramy Nguyen -
-   [09:00AM – 09:15AM MDT] - -   SBOL visual: introduction, recent developments, and current challenges - - Jacob Beal -
-   [11:15AM – 11:30AM MDT] - -   VisBOL: Web-based tooling for synthetic biology design visualization - - James McLaughlin -
-   [01:30PM – 03:00PM MDT] - -   SBOL Community Discussion - - Herbert Sauro -
-   [03:30PM – 05:00PM MDT] - -   SBOL Visual 2.0/SBGN Discussion - - Jake Beal/Augustin Luna -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+  [08:30AM – 10:00AM MDT] + +  SBOL + +Anil Wipat +
+  [08:30AM – 08:45AM MDT] + +  Multiplicity of Representation in SBOL 2.0 + +Nicholas Roehner +
+  [08:45AM – 09:00AM MDT] + +  libSBOLj 2.0: A Java Library to Support SBOL 2.0 + +Zhen Zhang +
+  [09:00AM – 09:15AM MDT] + +  A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language + +Tramy Nguyen +
+  [09:00AM – 09:15AM MDT] + +  SBOL visual: introduction, recent developments, and current challenges + +Jacob Beal +
+  [11:15AM – 11:30AM MDT] + +  VisBOL: Web-based tooling for synthetic biology design visualization + +James McLaughlin +
+  [01:30PM – 03:00PM MDT] + +  SBOL Community Discussion + +Herbert Sauro +
+  [03:30PM – 05:00PM MDT] + +  SBOL Visual 2.0/SBGN Discussion + +Jake Beal/Augustin Luna +
**** **Wednesday, October 14th** - - - - - - - - +
-   [03:30PM – 05:00PM MDT] - -   SBOL Extension Discussion - - Raik Gruenberg -
+ + + + +
+  [03:30PM – 05:00PM MDT] + +  SBOL Extension Discussion + +Raik Gruenberg +
**** **Thursday, October 15th** - - - - - - - - +
-   [01:30PM – 03:00PM MDT] - -   SBOL Infrastructure Discussion - - Chris Myers -
+ + + + +
+  [01:30PM – 03:00PM MDT] + +  SBOL Infrastructure Discussion + +Chris Myers +
**** **Friday, October 16th** - - - - - - - - +
-   [10:45AM – 11:00AM MDT] - -   On the Adoption of Standards at the DOE Joint Genome Institute - - Ernst Oberortner -
+ + + + +
+  [10:45AM – 11:00AM MDT] + +  On the Adoption of Standards at the DOE Joint Genome Institute + +Ernst Oberortner +
**** **Poster Session** - - - - - - - - +
-   Monday – Friday Break Sessions - -   Analysis of Weaknesses in SBOL/SBML Modeling through Creation of Use Cases - - Zach Zundel -
+ + + + +
+  Monday – Friday Break Sessions + +  Analysis of Weaknesses in SBOL/SBML Modeling through Creation of Use Cases + +Zach Zundel +
diff --git a/content/event/2015/iwbda/index.md b/content/event/2015/iwbda/index.md index 3eb5d2b21..abff46583 100644 --- a/content/event/2015/iwbda/index.md +++ b/content/event/2015/iwbda/index.md @@ -22,65 +22,63 @@ An international workshop on Bio-Design Automation. **Thursday, August 20th** - - - - - - - - - - - - - - - - - - - - - - - -
-   - -   Introduction to SBOL - - Chris Myers -
-   [09:00AM – 09:20AM PDT] - -   The Synthetic Biology Open Language 2.0 - - Bryan Bartley -
-   [09:20AM – 09:40AM PDT] - -   A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language - Tramy Nguyen -
-   [09:40AM – 10:00AM PDT] - -   SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs - Curtis Madsen -
+ + + + + + + + + + + + + + + + + + + + + +
+  + +  Introduction to SBOL + +Chris Myers +
+  [09:00AM – 09:20AM PDT] + +  The Synthetic Biology Open Language 2.0 + +Bryan Bartley +
+  [09:20AM – 09:40AM PDT] + +  A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language +Tramy Nguyen +
+  [09:40AM – 10:00AM PDT] + +  SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs +Curtis Madsen +


Friday, August 21st

- - - - -
-   [04:00PM – 04:20PM PDT] - -   SynBad: An SVP Design Framework - Owen Gilfellon -
+ + + + +
+  [04:00PM – 04:20PM PDT] + +  SynBad: An SVP Design Framework +Owen Gilfellon +

diff --git a/content/event/2015/seed/index.md b/content/event/2015/seed/index.md index ebbed4d81..678f999ad 100644 --- a/content/event/2015/seed/index.md +++ b/content/event/2015/seed/index.md @@ -20,42 +20,39 @@ A synthetic biology conference that brings together synthetic biologist from ind ## SBOL Talk: - - - - - - - - - - - - - - - - - - - - +
-   Jake Beal - -   Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communication of Synthetic Biology Designs -
-   Aaron Adlerl - -   Sbol Visual: Standard Schematic Diagrams for Synthetic Genetic Constructs -
-   Jacqueline Quinn - -   Standardized Design Description Language for Synthetic Biological Constructs -
-   Jacqueline Quinn - -   Sbol Visual: Standard Schematic Diagrams for Synthetic Genetic Constructs -
+ + + + + + + + + + + + + + + +
+  Jake Beal + +  Synthetic Biology Open Language (SBOL): Community-Driven Standard for Communication of Synthetic Biology Designs +
+  Aaron Adlerl + +  Sbol Visual: Standard Schematic Diagrams for Synthetic Genetic Constructs +
+  Jacqueline Quinn + +  Standardized Design Description Language for Synthetic Biological Constructs +
+  Jacqueline Quinn + +  Sbol Visual: Standard Schematic Diagrams for Synthetic Genetic Constructs +
**** \ No newline at end of file diff --git a/content/event/2017/combine/index.md b/content/event/2017/combine/index.md index 212342541..a3f73159c 100644 --- a/content/event/2017/combine/index.md +++ b/content/event/2017/combine/index.md @@ -22,212 +22,174 @@ A conference where the COMBINE community come together to present their work and **Tuesday, October 10th** - - - - - - - - +
-   [16:00PM – 17:30PM GMT] - -   SBOL Visual Specification Writing - -
+ + + + +
+  [16:00PM – 17:30PM GMT] + +  SBOL Visual Specification Writing + +
**** **Wednesday, October 11th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [09:00AM – 09:15AM GMT] - -   Automated Coupling of Circuit and Chassis for Synthetic Biology - - Bryan Bartley, Herbert Sauro and John Gennari -
-   [09:15AM – 09:30PM GMT] - -   Standards for Data Integration in Synthetic Biology - - James Alastair McLaughlin, Göksel Mısırlı and Anil Wipat -
-   [09:30AM – 10:00AM GMT] - -   Encoding recipes for experimental implementation in SBOL - - Alasdair Humphries, James Alastair McLaughlin and Anil Wipat -
-   [10:00AM – 10:15AM GMT] - -   Representing the Design-Build-Test-Learn Cycle with the Synthetic Biology Open Language - - Bryan Bartley, Jacob Beal, John Gennari, and et al. -
-   [10:15AM – 10:30AM GMT] - -   Recent Updates to the SynBioHub Data Repository - - Zach Zundel, James McLaughlin, Chris Myers and Anil Wipat -
-   [16:00PM – 17:30PM GMT] - -   Encoding design-build-test - -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+  [09:00AM – 09:15AM GMT] + +  Automated Coupling of Circuit and Chassis for Synthetic Biology + +Bryan Bartley, Herbert Sauro and John Gennari +
+  [09:15AM – 09:30PM GMT] + +  Standards for Data Integration in Synthetic Biology + +James Alastair McLaughlin, Göksel Mısırlı and Anil Wipat +
+  [09:30AM – 10:00AM GMT] + +  Encoding recipes for experimental implementation in SBOL + +Alasdair Humphries, James Alastair McLaughlin and Anil Wipat +
+  [10:00AM – 10:15AM GMT] + +  Representing the Design-Build-Test-Learn Cycle with the Synthetic Biology Open Language + +Bryan Bartley, Jacob Beal, John Gennari, and et al. +
+  [10:15AM – 10:30AM GMT] + +  Recent Updates to the SynBioHub Data Repository + +Zach Zundel, James McLaughlin, Chris Myers and Anil Wipat +
+  [16:00PM – 17:30PM GMT] + +  Encoding design-build-test + +
**** **Thursday, October 12th** - - - - - - - - +
-   [16:00PM – 17:30PM GMT] - -   Combinatorial Design Specification and Library Hacking - -
+ + + + +
+  [16:00PM – 17:30PM GMT] + +  Combinatorial Design Specification and Library Hacking + +
**** **Friday, October 13th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [09:00AM – 09:15AM GMT] - -   An Infobiotics Workbench Conversion Tool for SBOL and SBML - - Boyang Dun, Chris Myers and Harold Fellermann -
-   [09:15AM – 09:30AM GMT] - -   Representing Combinatorial Genetic Designs - - Nicholas Roehner and Jacob Beal -
-   [09:30AM – 09:45AM GMT] - -   DNA Specifications and Codon: Expressing Combinatorial Designs at Scale - - Zachary Palchick, Barbara Frewen and Aaron Kimball -
-   [09:45AM – 10:00AM GMT] - -   Genetic networks in 3D – Requirements for an SBOL spatial package - - Ruud Stoof and Ángel Goñi Moreno -
-   [10:00AM – 10:15AM GMT] - -   Improving the SBOL Visual Glyph Collection - - Bryan Bartley, Jacob Beal, Robert Sidney Cox, and et al. -
-   [10:15AM – 10:30AM GMT] - -   Tawny-SBOL: Using ontologies to design and constrain genetic circuits - - Goksel Misirli, James Alastair Mclaughlin, Angel Goni-Moreno and et al. -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+  [09:00AM – 09:15AM GMT] + +  An Infobiotics Workbench Conversion Tool for SBOL and SBML + +Boyang Dun, Chris Myers and Harold Fellermann +
+  [09:15AM – 09:30AM GMT] + +  Representing Combinatorial Genetic Designs + +Nicholas Roehner and Jacob Beal +
+  [09:30AM – 09:45AM GMT] + +  DNA Specifications and Codon: Expressing Combinatorial Designs at Scale + +Zachary Palchick, Barbara Frewen and Aaron Kimball +
+  [09:45AM – 10:00AM GMT] + +  Genetic networks in 3D – Requirements for an SBOL spatial package + +Ruud Stoof and Ángel Goñi Moreno +
+  [10:00AM – 10:15AM GMT] + +  Improving the SBOL Visual Glyph Collection + +Bryan Bartley, Jacob Beal, Robert Sidney Cox, and et al. +
+  [10:15AM – 10:30AM GMT] + +  Tawny-SBOL: Using ontologies to design and constrain genetic circuits + +Goksel Misirli, James Alastair Mclaughlin, Angel Goni-Moreno and et al. +
diff --git a/content/event/2017/embl-ebi/index.md b/content/event/2017/embl-ebi/index.md index f4bfda526..966b3d52c 100644 --- a/content/event/2017/embl-ebi/index.md +++ b/content/event/2017/embl-ebi/index.md @@ -21,15 +21,15 @@ A EMBL-EBI event that teaches attendees the skills and knowledge in bioinformati **Monday, May 22nd** - - - - - +
-   Anil Wipat - -   The Synthetic Biology Open Language (SBOL) and recent developments in tools and repositories -
+ + + +
+  Anil Wipat + +  The Synthetic Biology Open Language (SBOL) and recent developments in tools and repositories +
**** \ No newline at end of file diff --git a/content/event/2017/harmony/index.md b/content/event/2017/harmony/index.md index 8bbf07545..33439b45a 100644 --- a/content/event/2017/harmony/index.md +++ b/content/event/2017/harmony/index.md @@ -24,269 +24,219 @@ A registration fee are applied for attendees who are attending in person. Howeve **Monday, June 26th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [9:30AM – 10:30AM PST] - -   Model generation in iBioSim using SBOL and SBML - - Chris Myers -
-   [09:30AM – 10:30AM PST] - -   SBOL.assembly: Automated Design to Build Transition using SBOL 2.0 - - Ernst Oberortner -
-   [9:30AM – 10:30AM PST] - -   SynBioHub: A Design Repository for Synthetic Biology - - James McLaughlin -
-   [10:30AM – 12:30PM PST] - -   SBOL Visual 2.0 - - Jacob Beal -
-   [14:00PM – 15:30PM PST] - -   Combinatorial Design - - Nicholas Roehner -
-   [16:00PM – 17:30PM PST] - -   Combinatorial Design - - Nicholas Roehner -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+  [9:30AM – 10:30AM PST] + +  Model generation in iBioSim using SBOL and SBML + +Chris Myers +
+  [09:30AM – 10:30AM PST] + +  SBOL.assembly: Automated Design to Build Transition using SBOL 2.0 + +Ernst Oberortner +
+  [9:30AM – 10:30AM PST] + +  SynBioHub: A Design Repository for Synthetic Biology + +James McLaughlin +
+  [10:30AM – 12:30PM PST] + +  SBOL Visual 2.0 + +Jacob Beal +
+  [14:00PM – 15:30PM PST] + +  Combinatorial Design + +Nicholas Roehner +
+  [16:00PM – 17:30PM PST] + +  Combinatorial Design + +Nicholas Roehner +
**** **Tuesday, June 27th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [9:30AM – 10:30AM PST] - -   iGEM Vision - - Vinoo Selvarajah -
-   [10:30AM – 12:30PM PST] - -   iGEM Vision - - Vinoo Selvarajah -
-   [14:00PM – 15:30PM PST] - -   Workflow Hacking - -
-   [16:00PM – 17:30PM PST] - -   Workflow Hacking - -
+ + + + + + + + + + + + + + + + + + + +
+  [9:30AM – 10:30AM PST] + +  iGEM Vision + +Vinoo Selvarajah +
+  [10:30AM – 12:30PM PST] + +  iGEM Vision + +Vinoo Selvarajah +
+  [14:00PM – 15:30PM PST] + +  Workflow Hacking + +
+  [16:00PM – 17:30PM PST] + +  Workflow Hacking + +
**** **Wednesday, June 28th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [09:30AM – 10:30AM PST] - -   Provenance/Assembly - - James McLaughlin -
-   [10:30AM – 12:30PM PST] - -   Provenance/Assembly - - James McLaughlin -
-   [14:00PM – 15:30PM PST] - -   Experimental Data - - Sidney Cox III -
-   [16:00PM – 17:30PM PST] - -   Experimental Data - - Sidney Cox III -
+ + + + + + + + + + + + + + + + + + + +
+  [09:30AM – 10:30AM PST] + +  Provenance/Assembly + +James McLaughlin +
+  [10:30AM – 12:30PM PST] + +  Provenance/Assembly + +James McLaughlin +
+  [14:00PM – 15:30PM PST] + +  Experimental Data + +Sidney Cox III +
+  [16:00PM – 17:30PM PST] + +  Experimental Data + +Sidney Cox III +
**** **Thursday, June 29th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [09:30AM – 10:30AM PST] - -   SBOL Hacking - -
-   [10:30AM – 12:30PM PST] - -   SBOL Hacking - -
-   [14:00PM – 15:30PM PST] - -   SBOL Visual 2 - - Jacob Beal -
-   [16:00PM – 17:00PM PST] - -   SBOL Visual 2 - - Jacob Beal -
+ + + + + + + + + + + + + + + + + + + +
+  [09:30AM – 10:30AM PST] + +  SBOL Hacking + +
+  [10:30AM – 12:30PM PST] + +  SBOL Hacking + +
+  [14:00PM – 15:30PM PST] + +  SBOL Visual 2 + +Jacob Beal +
+  [16:00PM – 17:00PM PST] + +  SBOL Visual 2 + +Jacob Beal +
**** diff --git a/content/event/2017/ibiok/index.md b/content/event/2017/ibiok/index.md index 7bb103359..098933705 100644 --- a/content/event/2017/ibiok/index.md +++ b/content/event/2017/ibiok/index.md @@ -16,24 +16,24 @@ Date: February 2nd – 3rd, 2017 ## Description: The 8th International Symposium of Innovative BioProduction Kobe (iBioK) hosts an annual symposium every year to educate the scientific community on their latest technology to produce biofuels, bio-plastics, bio-fibers, bio-chemicals from biomass using carbon dioxide as a recyclable resources. -A complete description of the symposium can be found [here](http://www.kobe-u.ac.jp/documents/NEWS/event/stin/2017_02_02_1.pdf). +Read the [complete description of the symposium](http://www.kobe-u.ac.jp/documents/NEWS/event/stin/2017_02_02_1.pdf). ## SBOL Talk: **Friday, February 3rd** - - - - - - +
-   [14:50AM – 12:00PM JST] - -   Enabling synthetic biology workflows using biological data standards - - Anil Wipat -
+ + + + +
+  [14:50AM – 12:00PM JST] + +  Enabling synthetic biology workflows using biological data standards + +Anil Wipat +
**** \ No newline at end of file diff --git a/content/event/2017/iwbda/index.md b/content/event/2017/iwbda/index.md index 5982a0237..03ca845b9 100644 --- a/content/event/2017/iwbda/index.md +++ b/content/event/2017/iwbda/index.md @@ -24,123 +24,119 @@ There will be a one-day workshop to introduce software developers to SBOL on Aug **Wednesday, August 9th** - - - - - - - - - - - +
-   [16:00PM – 16:20PM EDT] - -   Mapping Genetic Design Space with Phylosemantics - - Bryan Bartley -
-   [16:20PM – 16:40PM EDT] - -   Large-Scale Genetic Design: Moving From Designs to Design Spaces - - Nicholas Roehner -
+ + + + + + + + + +
+  [16:00PM – 16:20PM EDT] + +  Mapping Genetic Design Space with Phylosemantics + +Bryan Bartley +
+  [16:20PM – 16:40PM EDT] + +  Large-Scale Genetic Design: Moving From Designs to Design Spaces + +Nicholas Roehner +
**** **Thursday, August 10th** - - - - - - +
-   [08:50AM – 09:10AM EDT] - -   Standard Enabled Model Generator for Genetic Circuit Design - - Tramy Nguyen -
+ + + + +
+  [08:50AM – 09:10AM EDT] + +  Standard Enabled Model Generator for Genetic Circuit Design + +Tramy Nguyen +
- - - - - - +
-   [08:50AM – 09:10AM EDT] - -   A Test Suite for Compliance Testing of Software Support for the Synthetic Biology Open Language - - Meher Samineni -
+ + + + +
+  [08:50AM – 09:10AM EDT] + +  A Test Suite for Compliance Testing of Software Support for the Synthetic Biology Open Language + +Meher Samineni +
**** **Friday, August 11th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
-   [09:00AM – 12:00PM EDT] - -   Introduction to SBOL - - Jacob Beal -
-   [09:00AM – 12:00PM EDT] - -   Introduction to libSBOLj and sboljs - - Chris Myers -
-   [09:00AM – 12:00PM EDT] - -   Introduction to libSBOL and pySBOL - - Bryan Bartley -
-   [12:00PM – 01:00PM EDT] - -   Lunch Break - -
-   [01:00PM – 05:00PM EDT] - -   Hands on experience to integrate SBOL into user’s Software - -
+ + + + + + + + + + + + + + + + + + + + + + + + +
+  [09:00AM – 12:00PM EDT] + +  Introduction to SBOL + +Jacob Beal +
+  [09:00AM – 12:00PM EDT] + +  Introduction to libSBOLj and sboljs + +Chris Myers +
+  [09:00AM – 12:00PM EDT] + +  Introduction to libSBOL and pySBOL + +Bryan Bartley +
+  [12:00PM – 01:00PM EDT] + +  Lunch Break + +
+  [01:00PM – 05:00PM EDT] + +  Hands on experience to integrate SBOL into user’s Software + +
**** \ No newline at end of file diff --git a/content/event/2017/lcp/index.md b/content/event/2017/lcp/index.md index 0e2f3d134..3f7efc8b9 100644 --- a/content/event/2017/lcp/index.md +++ b/content/event/2017/lcp/index.md @@ -15,21 +15,21 @@ Date: May 12th, 2017 ## Description: -A synthetic biology project funded by the National Science Foundation’s Expedition in Computing Program. A complete description of the project can be found [here](https://www.programmingbiology.org). +A synthetic biology project funded by the National Science Foundation’s Expedition in Computing Program. A complete description of the project is available in [this document](https://www.programmingbiology.org). ## SBOL Talk: **Friday, July 12th** - - - - - +
-   Chris Myers - -   Data Management Workflow -
+ + + +
+  Chris Myers + +  Data Management Workflow +
**** \ No newline at end of file diff --git a/content/event/2017/sb7/index.md b/content/event/2017/sb7/index.md index 560ea3e29..9b7156ef5 100644 --- a/content/event/2017/sb7/index.md +++ b/content/event/2017/sb7/index.md @@ -22,18 +22,18 @@ An international synthetic biology conference. **Friday, July 13th – 1** - - - - - - +
-   [08:30AM – 10:00AM SGT] - -   Foundational Engineering - - Anil Wipat -
+ + + + +
+  [08:30AM – 10:00AM SGT] + +  Foundational Engineering + +Anil Wipat +
**** \ No newline at end of file diff --git a/content/event/2017/seed/index.md b/content/event/2017/seed/index.md index 0a7cc522a..fc7500bb7 100644 --- a/content/event/2017/seed/index.md +++ b/content/event/2017/seed/index.md @@ -22,18 +22,18 @@ A synthetic biology conference that brings together synthetic biologist from ind **Friday, June 23rd** - - - - - - +
-   [11:30AM – 12:00PM PDT] - -   A Synthetic Biology Workflow Using Sbol - - Chris Myers -
+ + + + +
+  [11:30AM – 12:00PM PDT] + +  A Synthetic Biology Workflow Using Sbol + +Chris Myers +
**** \ No newline at end of file diff --git a/content/event/2018/combine/index.md b/content/event/2018/combine/index.md index 4b328eb99..9ade066f5 100644 --- a/content/event/2018/combine/index.md +++ b/content/event/2018/combine/index.md @@ -9,7 +9,7 @@ permalink: /combine-2018/ categories: - Announcements --- -## Location: [Center for Integrated Life Sciences and Engineering at Boston University](http://www.bu.edu/facilities/project/center-for-integrated-life-sciences-engineering){.freelinking.external} in Boston, MA USA +## Location: [Center for Integrated Life Sciences and Engineering at Boston University](http://www.bu.edu/facilities/project/center-for-integrated-life-sciences-engineering) in Boston, MA USA Date: October 8th – 12th, 2018 Complete COMBINE Agenda:  @@ -21,225 +21,184 @@ A conference where the COMBINE community come together to present their work and **Tuesday, October 9th** - - - - - - - - - - - - - - - - - - - - - - - - +
- [10:00AM – 12:00PM ET] - - SBOL Breakout Session - -   -
- [1:30PM – 3:00PM ET] - - SBOL Breakout Session - -   -
- [3:30PM – 5:00PM ET] - - SBOL Breakout Session - -   -
+ + + + + + + + + + + + + + +
+[10:00AM – 12:00PM ET] + +SBOL Breakout Session + +  +
+[1:30PM – 3:00PM ET] + +SBOL Breakout Session + +  +
+[3:30PM – 5:00PM ET] + +SBOL Breakout Session + +  +
  **Wednesday, October 10th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
- [08:45AM – 09:00AM ET] - - Rendering Complex Genetic Design with DNAplotlib and pySBOL2 - - Sunwoo Kang -
- [09:00AM – 09:15AM ET] - - VisBOL enhancements for SBOL 2 - - Arezoo Sadeghi -
- [11:15AM – 11:30AM ET] - - A Web-based CAD tool for the Synthetic Biology Open Language - - James Alastair Mclaughlin -
- [1:30PM – 3:00PM ET] - - SBOL Breakout Session - -
- [3:30PM – 5:00PM ET] - - SBOL Breakout Session - -
+ + + + + + + + + + + + + + + + + + + + + + + + +
+[08:45AM – 09:00AM ET] + +Rendering Complex Genetic Design with DNAplotlib and pySBOL2 + +Sunwoo Kang +
+[09:00AM – 09:15AM ET] + +VisBOL enhancements for SBOL 2 + +Arezoo Sadeghi +
+[11:15AM – 11:30AM ET] + +A Web-based CAD tool for the Synthetic Biology Open Language + +James Alastair Mclaughlin +
+[1:30PM – 3:00PM ET] + +SBOL Breakout Session + +
+[3:30PM – 5:00PM ET] + +SBOL Breakout Session + +
** Thursday, October 11th** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
- [10:30AM – 10:45AM ET] - - Software Tools for Next-Gen Genetic Design - - Nicholas Roehner -
- [11:00AM – 11:15AM ET] - - Sharing COMBINE Archives using SynBioHub - - Zach Zundel -
- [11:15AM – 11:30AM ET] - - SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories - - Michael Zhang -
- [1:30PM – 3:00PM ET] - - SBOL Breakout Session - -
- [3:30PM – 5:00PM ET] - - SBOL Breakout Session - -
+ + + + + + + + + + + + + + + + + + + + + + + + +
+[10:30AM – 10:45AM ET] + +Software Tools for Next-Gen Genetic Design + +Nicholas Roehner +
+[11:00AM – 11:15AM ET] + +Sharing COMBINE Archives using SynBioHub + +Zach Zundel +
+[11:15AM – 11:30AM ET] + +SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories + +Michael Zhang +
+[1:30PM – 3:00PM ET] + +SBOL Breakout Session + +
+[3:30PM – 5:00PM ET] + +SBOL Breakout Session + +
  **Friday, October 12th** - - - - - - - - - - - - - - - - +
- [1:30PM – 3:00PM ET] - - SBOL Breakout Session - -
- [3:30PM – 5:00PM ET] - - SBOL Breakout Session - -
+ + + + + + + + + +
+[1:30PM – 3:00PM ET] + +SBOL Breakout Session + +
+[3:30PM – 5:00PM ET] + +SBOL Breakout Session + +
diff --git a/content/event/2018/harmony/index.md b/content/event/2018/harmony/index.md index 8349bf91c..bf3c227d2 100644 --- a/content/event/2018/harmony/index.md +++ b/content/event/2018/harmony/index.md @@ -17,159 +17,134 @@ categories: **Monday, June 18th** - - - - - - - - - - - - - - - - +
-   [11:00AM – 12:00PM GMT] - -   Goals for meetings and future directions of SBOL - - Anil Wipat -
-   [02:00PM – 05:00PM GMT] - -   SBOL Data Model v2.2.1 - - Chris Myers -
+ + + + + + + + + +
+  [11:00AM – 12:00PM GMT] + +  Goals for meetings and future directions of SBOL + +Anil Wipat +
+  [02:00PM – 05:00PM GMT] + +  SBOL Data Model v2.2.1 + +Chris Myers +
**** **Tuesday, June 19th** - - - - - - - - - - - - - - - - +
-   [09:15AM – 12:00PM GMT] - -   SBOL paper and tool hacking - -
-   [02:00PM – 05:00PM GMT] - -   Encoding Experimental Data - - Ernst Oberortner -
+ + + + + + + + + +
+  [09:15AM – 12:00PM GMT] + +  SBOL paper and tool hacking + +
+  [02:00PM – 05:00PM GMT] + +  Encoding Experimental Data + +Ernst Oberortner +
**** **Wednesday, June 20th** - - - - - - - - - - - - - - - - +
-   [09:15AM – 12:00PM GMT] - -   SBOL paper and tool hacking - -
-   [02:00PM – 05:00PM GMT] - -   [SBOL Visual v2.1] [MapsTo] [Parametrisation] - - Thomas Gorochowski -
+ + + + + + + + + +
+  [09:15AM – 12:00PM GMT] + +  SBOL paper and tool hacking + +
+  [02:00PM – 05:00PM GMT] + +  [SBOL Visual v2.1] [MapsTo] [Parametrisation] + +Thomas Gorochowski +
**** **Thursday, June 21st** - - - - - - - - - - - - - - - - +
-   [09:15AM – 12:00PM GMT] - -   SBOL data model v3.0 - - James McLaughlin -
-   [02:00PM – 05:00PM GMT] - -   SBOL paper and tool hacking - -
+ + + + + + + + + +
+  [09:15AM – 12:00PM GMT] + +  SBOL data model v3.0 + +James McLaughlin +
+  [02:00PM – 05:00PM GMT] + +  SBOL paper and tool hacking + +
**** **Friday, June 22nd** - - - - - - - - - - - - - - - - +
-   [02:00PM – 05:00PM GMT] - -   SBOL paper and tool hacking - -
-   [02:00PM – 05:00PM GMT] - -   SBOL paper and tool hacking - -
+ + + + + + + + + +
+  [02:00PM – 05:00PM GMT] + +  SBOL paper and tool hacking + +
+  [02:00PM – 05:00PM GMT] + +  SBOL paper and tool hacking + +
\ No newline at end of file diff --git a/content/event/2018/harmony/sbol-breakout-sessions/index.md b/content/event/2018/harmony/sbol-breakout-sessions/index.md index 1909d0c5a..8e42f2951 100644 --- a/content/event/2018/harmony/sbol-breakout-sessions/index.md +++ b/content/event/2018/harmony/sbol-breakout-sessions/index.md @@ -21,159 +21,134 @@ A registration fee are applied for attendees who are attending in person. Howeve **Monday, June 18th** - - - - - - - - - - - - - - - - +
-   [11:00AM – 12:00PM GMT] - -   Goals for meetings and future directions of SBOL - - Anil Wipat -
-   [02:00PM – 05:00PM GMT] - -   SBOL Data Model v2.2.1 - - Chris Myers -
+ + + + + + + + + +
+  [11:00AM – 12:00PM GMT] + +  Goals for meetings and future directions of SBOL + +Anil Wipat +
+  [02:00PM – 05:00PM GMT] + +  SBOL Data Model v2.2.1 + +Chris Myers +
**** **Tuesday, June 19th** - - - - - - - - - - - - - - - - +
-   [09:15AM – 12:00PM GMT] - -   SBOL paper and tool hacking - -
-   [02:00PM – 05:00PM GMT] - -   Encoding Experimental Data - - Ernst Oberortner -
+ + + + + + + + + +
+  [09:15AM – 12:00PM GMT] + +  SBOL paper and tool hacking + +
+  [02:00PM – 05:00PM GMT] + +  Encoding Experimental Data + +Ernst Oberortner +
**** **Wednesday, June 20th** - - - - - - - - - - - - - - - - +
-   [09:15AM – 12:00PM GMT] - -   SBOL paper and tool hacking - -
-   [02:00PM – 05:00PM GMT] - -   SBOL Visual v2.1 - - Thomas Gorochowski -
+ + + + + + + + + +
+  [09:15AM – 12:00PM GMT] + +  SBOL paper and tool hacking + +
+  [02:00PM – 05:00PM GMT] + +  SBOL Visual v2.1 + +Thomas Gorochowski +
**** **Thursday, June 21st** - - - - - - - - - - - - - - - - +
-   [09:15AM – 12:00PM GMT] - -   SBOL data model v3.0 - - James McLaughlin -
-   [02:00PM – 05:00PM GMT] - -   SBOL paper and tool hacking - -
+ + + + + + + + + +
+  [09:15AM – 12:00PM GMT] + +  SBOL data model v3.0 + +James McLaughlin +
+  [02:00PM – 05:00PM GMT] + +  SBOL paper and tool hacking + +
**** **Friday, June 22nd** - - - - - - - - - - - - - - - - +
-   [02:00PM – 05:00PM GMT] - -   SBOL paper and tool hacking - -
-   [02:00PM – 05:00PM GMT] - -   SBOL paper and tool hacking - -
+ + + + + + + + + +
+  [02:00PM – 05:00PM GMT] + +  SBOL paper and tool hacking + +
+  [02:00PM – 05:00PM GMT] + +  SBOL paper and tool hacking + +
diff --git a/content/event/2018/nona/index.md b/content/event/2018/nona/index.md index ce2834a37..d847912df 100644 --- a/content/event/2018/nona/index.md +++ b/content/event/2018/nona/index.md @@ -21,31 +21,29 @@ A online software used to host academic tools. **Monday, July 17th** - - - - - - +
-   Ernst Oboerortner - -   Synthetic Biology Open Language -
+ + + +
+  Ernst Oboerortner + +  Synthetic Biology Open Language +
**** **Monday, July 17th** - - - - - - +
-   Michael Zhang - -   SBOLDesigner -
+ + + +
+  Michael Zhang + +  SBOLDesigner +
**** \ No newline at end of file diff --git a/content/event/2018/sbol-workshop/2018-06-29-sbol-10.md b/content/event/2018/sbol-workshop/2018-06-29-sbol-10.md index 8414965d7..21a8cc873 100644 --- a/content/event/2018/sbol-workshop/2018-06-29-sbol-10.md +++ b/content/event/2018/sbol-workshop/2018-06-29-sbol-10.md @@ -11,7 +11,7 @@ categories: --- The 10th SBOL workshop took place in UC Berkeley, CA, USA. Materials that were presented at the workshop are linked below. -The full agenda of the workshop can be found [here](https://docs.google.com/document/d/1qP6WK-eUUB41Upt38vN0LmulLcoG9yEEr1gHEyJaiVQ/edit). +See the [full agenda of the workshop](https://docs.google.com/document/d/1qP6WK-eUUB41Upt38vN0LmulLcoG9yEEr1gHEyJaiVQ/edit). * Jackie Quinn: Brief Intro to SBOL and the Workshop * Matthew Pocock: [Taking Stock, Code base tour](https://github.com/SynBioDex/Community-Media/blob/master/2014/SBOL10/RDF%20Pickling.pptx) diff --git a/content/event/2018/sbol-workshop/2018-06-29-sbol-8.md b/content/event/2018/sbol-workshop/2018-06-29-sbol-8.md index ddca620ab..bec474f00 100644 --- a/content/event/2018/sbol-workshop/2018-06-29-sbol-8.md +++ b/content/event/2018/sbol-workshop/2018-06-29-sbol-8.md @@ -11,7 +11,7 @@ categories: --- The 8th SBOL workshop took place in Boston University in Boston, MA, USA Materials that were presented at the workshop are linked below. -The full agenda of the workshop can be found [here](https://docs.google.com/document/d/1TqUqovny1-4esIiVZJKPHAAdlcDnVL0kAqIqpycfLYc/edit#heading=h.2i3m39ieoijr). +See the [full agenda of the workshop](https://docs.google.com/document/d/1TqUqovny1-4esIiVZJKPHAAdlcDnVL0kAqIqpycfLYc/edit#heading=h.2i3m39ieoijr). * Aaron Adler and Fusun Yaman: [Synthetic Biology Tools from BBN](https://github.com/SynBioDex/Community-Media/blob/master/2012/SBOL8/BBN_Tools.pdf) * Michal Galdzicki and Bryan Bartley: [Host Context](https://github.com/SynBioDex/Community-Media/blob/master/2012/SBOL8/HostContextPresentation.pptx) diff --git a/content/event/2018/software-for-synthetic-biology-workflows/index.md b/content/event/2018/software-for-synthetic-biology-workflows/index.md index eba9ebd36..7576176e8 100644 --- a/content/event/2018/software-for-synthetic-biology-workflows/index.md +++ b/content/event/2018/software-for-synthetic-biology-workflows/index.md @@ -22,20 +22,18 @@ SEED is a conference where synthetic biologist from different areas of the field **Monday, June 18th** - - - - - - - - +
-   [12:30PM – 12:50PM MST] - -   SBOL Visual 2.0 - - Jacob Beal -
+ + + + +
+  [12:30PM – 12:50PM MST] + +  SBOL Visual 2.0 + +Jacob Beal +
### Software for Synthetic Biology Workflows Workshop Description: @@ -80,84 +78,69 @@ Location: SEED 2018 @ JW Marriott Scottsdale Camelback Inn Resort & Spa **2:00PM – 3:30PM – Presentations to introduce the tools** - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
- ●   Introduction to workflows [10min] - - Jacob Beal -
- ●   SBOL, its libraries, converter, and validator [10min] - - Jacob Beal -
- ●   JBEI ICE [10min] - - Nathan J. Hillson -
- ●   SynBioHub/iBioSim/SBOLDesigner [20min] - - Tramy Nguyen -
- ●   Cello [10min] - - Shuyi Zhang -
- ●   Operon Calculator and RBS Library Calculator [10min] - - Howard Salis -
- ●   BOOST [10min] - - Ernst Oberortner -
- ●   TASBE [10min] - - Jacob Beal -
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+●   Introduction to workflows [10min] + +Jacob Beal +
+●   SBOL, its libraries, converter, and validator [10min] + +Jacob Beal +
+●   JBEI ICE [10min] + +Nathan J. Hillson +
+●   SynBioHub/iBioSim/SBOLDesigner [20min] + +Tramy Nguyen +
+●   Cello [10min] + +Shuyi Zhang +
+●   Operon Calculator and RBS Library Calculator [10min] + +Howard Salis +
+●   BOOST [10min] + +Ernst Oberortner +
+●   TASBE [10min] + +Jacob Beal +
**** @@ -166,14 +149,13 @@ Location: SEED 2018 @ JW Marriott Scottsdale Camelback Inn Resort & Spa **** **4:00PM – 5:30PM Hands-on work with the tools** - - - - - - +
- ●   Hands-on tools and workflows (Part 1)(Part 2) - - Kevin Clancy -
+ + + +
+●   Hands-on tools and workflows (Part 1)(Part 2) + +Kevin Clancy +
\ No newline at end of file diff --git a/content/event/_index.md b/content/event/_index.md index a950193f0..790ece750 100644 --- a/content/event/_index.md +++ b/content/event/_index.md @@ -1,14 +1,8 @@ --- -title: Recent & Upcoming Talks - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -view: 2 - -# Optional header image (relative to `static/media/` folder). -header: - caption: "" - image: "" ---- \ No newline at end of file +title: Events +layout: redirect +redirect_to: /community-meetings/ +cascade: + share: false + profile: false +--- diff --git a/content/faq/_index.md b/content/faq/_index.md index 5a806882b..5c9b4367b 100644 --- a/content/faq/_index.md +++ b/content/faq/_index.md @@ -12,6 +12,9 @@ view: 3 header: caption: "" image: "" +subtitle: "Answers to common questions about SBOL, its tools, and how to take part." +layout: sbol-page +summary: "Answers to common questions about SBOL, its tools, and how to take part." --- Didn't find an answer to your question? Post your question to our [sbol-dev](mailto:sbol-dev@googlegroups.com) e-mailing list. diff --git a/content/genai-tools/_index.md b/content/genai-tools/_index.md index 0cbc5a14d..5ef6038cc 100644 --- a/content/genai-tools/_index.md +++ b/content/genai-tools/_index.md @@ -1,4 +1,8 @@ --- title: "GenAI Tools" subtitle: "AI-powered tools and assistants built around the SBOL standard. These resources can help you explore specifications, write SBOL documents, and learn the standard faster." +cascade: + share: false + profile: false +summary: "AI-powered tools and assistants built around the SBOL standard. These resources can help you explore specifications, write SBOL documents, and learn the standard faster." --- diff --git a/content/home/get-started.md b/content/home/get-started.md index 8ae5a75ec..fe1c2a299 100644 --- a/content/home/get-started.md +++ b/content/home/get-started.md @@ -10,8 +10,8 @@ subtitle = "" [design] columns = "1" -[design.background] - color = "white" +[design.spacing] + padding = ["10px", "0", "40px", "0"] [advanced] css_class = "" diff --git a/content/home/sbol.md b/content/home/sbol.md index c447d9976..bbf650da7 100644 --- a/content/home/sbol.md +++ b/content/home/sbol.md @@ -10,11 +10,8 @@ subtitle = "" [design] columns = "1" -[design.background] - color = "white" - [design.spacing] - padding = ["20px", "0", "20px", "0"] + padding = ["40px", "0", "10px", "0"] [advanced] css_class = "" diff --git a/content/join/_index.md b/content/join/_index.md index 42f27759b..df2238b6a 100644 --- a/content/join/_index.md +++ b/content/join/_index.md @@ -39,16 +39,16 @@ connect_links: description: "Contribute code, file issues, and propose SEPs" icon: "fab fa-github" url: "https://github.com/SynBioDex" - - label: "Formal Membership" - description: "Fill in our form to officially join the community" + - label: "Register as a member" + description: "Join the community and pick the mailing lists you want" icon: "fas fa-user-plus" - url: "https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit" + url: "https://docs.google.com/forms/d/e/1FAIpQLScp8lomURs-y-8BlptY0fFgLSFIl0cKvcMkOBc_JVlEgW22Sw/viewform" meetings_title: "Attend a Meeting" meetings_description: "The SBOL community meets semi-annually at COMBINE and HARMONY workshops, and engages the broader synthetic biology community at conferences worldwide. All meetings are open to attend." meetings_url: "/community-meetings" -structure_title: "How We Are Organised" +structure_title: "How We Are Organized" structure_description: "SBOL is governed by a steering committee of elected members and managed by a chair and editors who oversee the standard." structure_links: - label: "Leadership" @@ -65,7 +65,8 @@ structure_links: url: "/sbol-industrial" cta_title: "Ready to Join?" -cta_description: "Fill in our membership form and we will be in touch. No obligations - just a way for us to know you are part of the community." +cta_description: "Register with the community and we will add you to the mailing lists you choose. No obligations, just a way for us to know you are part of the community." cta_btn_text: "Join the Community" -cta_btn_url: "https://docs.google.com/forms/d/12OfLZ05guthLVvdapwxHWq7JSBaTPr_O3QXIeiGDfPU/edit" +cta_btn_url: "https://docs.google.com/forms/d/e/1FAIpQLScp8lomURs-y-8BlptY0fFgLSFIl0cKvcMkOBc_JVlEgW22Sw/viewform" +summary: "SBOL is built by the community, for the community. Whether you contribute code, attend workshops, or simply stay informed - there is a place for you." --- diff --git a/content/libraries/_index.md b/content/libraries/_index.md index 24a76c4ee..a449feba1 100644 --- a/content/libraries/_index.md +++ b/content/libraries/_index.md @@ -6,4 +6,8 @@ tabs: label: "SBOL 3" - id: "2" label: "SBOL 2" +cascade: + share: false + profile: false +summary: Community-contributed libraries implementing SBOL Core across languages and platforms. --- diff --git a/content/libraries/sbol2-py/_index.md b/content/libraries/sbol2-py/_index.md index 14e2b2151..5163003c3 100644 --- a/content/libraries/sbol2-py/_index.md +++ b/content/libraries/sbol2-py/_index.md @@ -58,7 +58,7 @@ pySBOL2 provides Python interfaces and their implementation for Synthetic Biolog -The repository of the latest version of pySBOL3 library can be accessed [here](https://github.com/SynBioDex/pySBOL3). +The latest version lives in the [pySBOL3 repository](https://github.com/SynBioDex/pySBOL3). diff --git a/content/libraries/sbol3-py/index.md b/content/libraries/sbol3-py/index.md index 07f4c9b06..74ecbafdf 100644 --- a/content/libraries/sbol3-py/index.md +++ b/content/libraries/sbol3-py/index.md @@ -68,5 +68,5 @@ License](https://opensource.org/licenses/MIT). **Cite:** Mitchell, Tom, Jacob Beal, and Bryan Bartley. "[pySBOL3: SBOL3 for Python Programmers.](https://doi.org/10.1021/acssynbio.2c00249)" ACS Synthetic Biology 11, no. 7 (2022): 2523-2526. -# Older Versions +## Older Versions - [pySBOL2 for SBOL2](pysbol2) diff --git a/content/ontology/_index.md b/content/ontology/_index.md index e49fbc42d..0c5b38793 100644 --- a/content/ontology/_index.md +++ b/content/ontology/_index.md @@ -12,12 +12,16 @@ view: 3 header: caption: "" image: "" +subtitle: "Controlled terms and constraints for the SBOL data model, provided as an OWL ontology with tooling for semantic reasoning." +layout: sbol-page +subnav: datamodel +summary: "Controlled terms and constraints for the SBOL data model, provided as an OWL ontology with tooling for semantic reasoning." --- -The SBOL-OWL ontology provides a set of controlled terms that are used to describe genetic circuit designs using SBOL. Terms are included for the followings. +The SBOL-OWL ontology provides a set of controlled terms that are used to describe genetic circuit designs using SBOL. Terms are included for the following. * Descriptions of SBOL entities (e.g. [“ComponentDefinition“](https://dissys.github.io/sbol-owl/sbol-owl.html#ComponentDefinition)) that are exchanged electronically. Constraints and validation rules that are enforced on SBOL entities are also captured as part of the ontology. -* SBOL entities (e.g. [“TopLevel“](https://dissys.github.io/sbol-owl/sbol-owl.html#TopLevel)) that are not serialised but are used to group different SBOL entities. SBOL-OWL exposes these entities to semantic reasoning tools via parent-child relationships. +* SBOL entities (e.g. [“TopLevel“](https://dissys.github.io/sbol-owl/sbol-owl.html#TopLevel)) that are not serialized but are used to group different SBOL entities. SBOL-OWL exposes these entities to semantic reasoning tools via parent-child relationships. * Terms (e.g. [“inline“](https://dissys.github.io/sbol-owl/sbol-owl.html#inline)) that are used to restrict values of SBOL entities. * Properties (e.g. [“sequence“](https://dissys.github.io/sbol-owl/sbol-owl.html#sequence)) linking SBOL entities to accepted values. * Metadata terms (e.g. [“Promoter“](https://dissys.github.io/sbol-owl/sbol-owl.html#Promoter)) for commonly used descriptions of design entities. Such terms may require the use of several SBOL entities and properties. @@ -38,7 +42,7 @@ SBOL-OWL is available in different formats. SBOL-OWL can be combined with any SBOL document to query genetic circuit designs using semantic queries. The semanticSBOL Java library has been developed to facilitate this process. The resulting files can then be submitted to existing reasoners for semantic inferencing. The library also includes methods to check the consistency of SBOL files, to execute semantic queries, and to list inconsistencies programmatically. -[Click here](https://github.com/dissys/sbol-owl) to access the documentation and examples to use the library programmatically. +See the [semanticSBOL documentation and examples](https://github.com/dissys/sbol-owl) to use the library programmatically. The semanticSBOL library can be used from the command line to merge SBOL files with the SBOL-OWL ontology. @@ -54,5 +58,5 @@ Example: ### Download semanticSBOL -{{% staticref "zip/semanticSBOL-1.0-SNAPSHOT-jar-with-dependencies.jar" "newtab" %}}Click here{{% /staticref %}} to download the standalone sbol-sem Java library as a single file including all the dependencies.\ -{{% staticref "zip/semanticSBOL-1.0-SNAPSHOT.jar" "newtab" %}}Click here{{% /staticref %}} to download the sbol-sem Java library only. Dependencies are not included. \ No newline at end of file +{{% staticref "zip/semanticSBOL-1.0-SNAPSHOT-jar-with-dependencies.jar" "newtab" %}}Download the standalone sbol-sem Java library{{% /staticref %}} as a single file including all the dependencies.\ +{{% staticref "zip/semanticSBOL-1.0-SNAPSHOT.jar" "newtab" %}}Download the sbol-sem Java library only{{% /staticref %}} (dependencies not included). \ No newline at end of file diff --git a/content/post/SBOLinside-Announcement/index.md b/content/post/SBOLinside-Announcement/index.md index bb94b771a..de07eea47 100644 --- a/content/post/SBOLinside-Announcement/index.md +++ b/content/post/SBOLinside-Announcement/index.md @@ -13,7 +13,7 @@ tags: {{< figure src="SBOLinside_Banner.png" title="" lightbox="true" >}} Alongside our day-to-day editorial work, we have been developing something special for the SBOL community. -We asked ourselves: how can we offer deeper insights into SBOL and our organisation while making it easier for the community to follow our ongoing work? +We asked ourselves: how can we offer deeper insights into SBOL and our organization while making it easier for the community to follow our ongoing work? Our answer is **SBOLinside**. SBOLinside is a video podcast format specifically focusing on providing inside stories from our work on SBOL and our organization. diff --git a/content/publication/_index.md b/content/publication/_index.md index f6554b038..7b8c074f9 100644 --- a/content/publication/_index.md +++ b/content/publication/_index.md @@ -12,4 +12,6 @@ view: 3 header: caption: "" image: "" +subtitle: "Papers that define SBOL, extend it, or describe the tools that use it. Filter by type or year, or search by title and author." +summary: "Papers that define SBOL, extend it, or describe the tools that use it." --- diff --git a/content/sbol-industrial/_index.md b/content/sbol-industrial/_index.md index 77b969d41..9b1fef90e 100644 --- a/content/sbol-industrial/_index.md +++ b/content/sbol-industrial/_index.md @@ -1,5 +1,5 @@ --- -title: +title: SBOL Industrial Consortium # View. # 1 = List @@ -12,6 +12,9 @@ view: 3 header: caption: "" image: "" +subtitle: "The pre-competitive non-profit that supports SBOL adoption in industry." +layout: sbol-page +summary: "The pre-competitive non-profit that supports SBOL adoption in industry." --- {{< figure src="SBOLIndustrialLogo.png" title="" lightbox="true" >}} diff --git a/content/sbol-visual-ontology/_index.md b/content/sbol-visual-ontology/_index.md index 4aa37a11d..c79b52e5d 100644 --- a/content/sbol-visual-ontology/_index.md +++ b/content/sbol-visual-ontology/_index.md @@ -12,9 +12,13 @@ view: 3 header: caption: "" image: "" +subtitle: "Terms that define SBOL Visual glyphs and their relationships, for tools that reason about diagrams." +layout: sbol-page +subnav: visual +summary: "Terms that define SBOL Visual glyphs and their relationships, for tools that reason about diagrams." --- -The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. +The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organized based on their descriptions in community-edited [Markdown](https://github.com/SynBioDex/SBOL-visual/tree/master/Glyphs) files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items. * **Terms for glyphs** to represent * DNA sequence features (e.g. "[CDSGlyph](http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.html#CDSGlyph)", "[AptamerGlyph](http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.html#AptamerGlyph)", "[AssemblyScarGlyph](http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.html#AssemblyScarGlyph)" and "[AssemblyScarGlyphAlternative](http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.html#AssemblyScarGlyphAlternative)" ) @@ -34,7 +38,7 @@ The ontology can also be viewed after downloading and opening in an ontology edi ### Download -SBOL-VO is available as an RDF file. Click [here](http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.rdf) to download the ontology (**please note** that your browser may not allow direct downloads. If it does not, please copy and paste the following link on a new tab: http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.rdf ). +SBOL-VO is available as an RDF file: [download the ontology](http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.rdf) (**please note** that your browser may not allow direct downloads. If it does not, please copy and paste the following link on a new tab: http://synbiodex.github.io/sbol-visual-ontology/sbol-vo.rdf ). ### Computational access: The SBOL-VO web service (SBOL-VOWS) diff --git a/content/sbolv-10-years/_index.md b/content/sbolv-10-years/_index.md index 8ab86b0bb..3b8dae8fb 100644 --- a/content/sbolv-10-years/_index.md +++ b/content/sbolv-10-years/_index.md @@ -15,6 +15,9 @@ cascade: header: caption: "" image: "" +layout: sbol-page +subnav: visual +summary: 10 Years of Standardized Genetic Design Diagrams --- ## Welcome to the SBOL Community’s retrospective on SBOL Visual! diff --git a/content/sbolv-10-years/acs-2012/index.md b/content/sbolv-10-years/acs-2012/index.md index 994a411b2..10b04062e 100644 --- a/content/sbolv-10-years/acs-2012/index.md +++ b/content/sbolv-10-years/acs-2012/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 63 - **Total Figures in All Articles:** 340 - **Figures Compatible with SBOL Visual:** 87 (25.59%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 36 (41.38%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 18 (20.69%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2013/index.md b/content/sbolv-10-years/acs-2013/index.md index ba3244cdd..8b43f63e9 100644 --- a/content/sbolv-10-years/acs-2013/index.md +++ b/content/sbolv-10-years/acs-2013/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 80 - **Total Figures in All Articles:** 408 - **Figures Compatible with SBOL Visual:** 99 (24.26%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 61 (61.62%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 36 (36.36%) -# Individual issues +## Individual issues ## February diff --git a/content/sbolv-10-years/acs-2014/index.md b/content/sbolv-10-years/acs-2014/index.md index 219dc3cd6..0c57d32a9 100644 --- a/content/sbolv-10-years/acs-2014/index.md +++ b/content/sbolv-10-years/acs-2014/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 118 - **Total Figures in All Articles:** 531 - **Figures Compatible with SBOL Visual:** 113 (21.28%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 53 (46.9%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 27 (23.89%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2015/index.md b/content/sbolv-10-years/acs-2015/index.md index c4e2f5b4d..8c85f009a 100644 --- a/content/sbolv-10-years/acs-2015/index.md +++ b/content/sbolv-10-years/acs-2015/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 145 - **Total Figures in All Articles:** 743 - **Figures Compatible with SBOL Visual:** 177 (23.82%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 107 (60.45%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 38 (21.47%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2016/index.md b/content/sbolv-10-years/acs-2016/index.md index 7c824d727..639403a06 100644 --- a/content/sbolv-10-years/acs-2016/index.md +++ b/content/sbolv-10-years/acs-2016/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 169 - **Total Figures in All Articles:** 886 - **Figures Compatible with SBOL Visual:** 217 (24.49%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 136 (62.67%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 90 (41.47%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2017/index.md b/content/sbolv-10-years/acs-2017/index.md index ca6f2c91c..bf0a0d1bd 100644 --- a/content/sbolv-10-years/acs-2017/index.md +++ b/content/sbolv-10-years/acs-2017/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 242 - **Total Figures in All Articles:** 1266 - **Figures Compatible with SBOL Visual:** 285 (22.51%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 187 (65.61%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 115 (40.35%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2018/index.md b/content/sbolv-10-years/acs-2018/index.md index 302a87879..a7ceea9f4 100644 --- a/content/sbolv-10-years/acs-2018/index.md +++ b/content/sbolv-10-years/acs-2018/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 305 - **Total Figures in All Articles:** 1615 - **Figures Compatible with SBOL Visual:** 429 (26.56%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 242 (56.41%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 98 (22.84%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2019/index.md b/content/sbolv-10-years/acs-2019/index.md index e6b22cce8..255fb44d2 100644 --- a/content/sbolv-10-years/acs-2019/index.md +++ b/content/sbolv-10-years/acs-2019/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 287 - **Total Figures in All Articles:** 1512 - **Figures Compatible with SBOL Visual:** 432 (28.57%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 219 (50.69%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 126 (29.17%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2020/index.md b/content/sbolv-10-years/acs-2020/index.md index 6ef626015..96308cad2 100644 --- a/content/sbolv-10-years/acs-2020/index.md +++ b/content/sbolv-10-years/acs-2020/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 302 - **Total Figures in All Articles:** 1455 - **Figures Compatible with SBOL Visual:** 339 (23.3%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 275 (81.12%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 128 (37.76%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2021/index.md b/content/sbolv-10-years/acs-2021/index.md index a5ef58c83..07a50dd58 100644 --- a/content/sbolv-10-years/acs-2021/index.md +++ b/content/sbolv-10-years/acs-2021/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 327 - **Total Figures in All Articles:** 1759 - **Figures Compatible with SBOL Visual:** 457 (25.98%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 382 (83.59%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 262 (57.33%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2022/index.md b/content/sbolv-10-years/acs-2022/index.md index b33476f63..4be82875e 100644 --- a/content/sbolv-10-years/acs-2022/index.md +++ b/content/sbolv-10-years/acs-2022/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 393 - **Total Figures in All Articles:** 2068 - **Figures Compatible with SBOL Visual:** 595 (28.77%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 487 (81.85%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 245 (41.18%) -# Individual issues +## Individual issues ## January diff --git a/content/sbolv-10-years/acs-2023/index.md b/content/sbolv-10-years/acs-2023/index.md index 30bf12620..51ce961ce 100644 --- a/content/sbolv-10-years/acs-2023/index.md +++ b/content/sbolv-10-years/acs-2023/index.md @@ -14,14 +14,14 @@ header: caption: "" image: "" --- -# Summary +## Summary - **Total Articles Analyzed:** 344 - **Total Figures in All Articles:** 1766 - **Figures Compatible with SBOL Visual:** 378 (21.4%) - **Figures Compatible with SBOL Visual & Fully Compliant:** 279 (73.81%) - **Figures Compatible with SBOL Visual & Following Best Practices:** 138 (36.51%) -# Individual issues +## Individual issues ## January diff --git a/content/sponsor-sbol/_index.md b/content/sponsor-sbol/_index.md index 3e795c464..89c5ffa04 100644 --- a/content/sponsor-sbol/_index.md +++ b/content/sponsor-sbol/_index.md @@ -3,6 +3,9 @@ title: Support SBOL subtitle: "SBOL is a free, open standard maintained by a global volunteer community. Supporting the Bio-Design Automation Consortium (BDAC) is how you help keep SBOL active, visible, and growing." bdac_url: "https://bio-design-automation.org" +hero_buttons: + - text: "Support via BDAC" + url: "https://bio-design-automation.org" benefits: - icon: "fas fa-chalkboard-teacher" @@ -33,4 +36,5 @@ past_sponsors: logo: "Inscripta_Brandmark-with-Tagline_R3-FINAL_RGB.png" - name: "Teselagen" logo: "Teselagen_300x150-1.png" +summary: "SBOL is a free, open standard maintained by a global volunteer community. Supporting the Bio-Design Automation Consortium (BDAC) is how you help keep SBOL active, visible, and growing." --- diff --git a/content/talk/_index.md b/content/talk/_index.md index 7d27cb39b..9c0c7060d 100644 --- a/content/talk/_index.md +++ b/content/talk/_index.md @@ -1,14 +1,5 @@ --- -title: Recent & Upcoming Talks - -# View. -# 1 = List -# 2 = Compact -# 3 = Card -view: 2 - -# Optional header image (relative to `static/img/` folder). -header: - caption: "" - image: "" +title: Talks +layout: redirect +redirect_to: /community-meetings/ --- diff --git a/content/visual-about/_index.md b/content/visual-about/_index.md index fc57b99ca..e941e16ff 100644 --- a/content/visual-about/_index.md +++ b/content/visual-about/_index.md @@ -1,5 +1,5 @@ --- -title: +title: SBOL Visual # View. # 1 = List @@ -13,12 +13,23 @@ header: caption: "" image: "" -# Provide a short alias (See GitHub #135) +subtitle: "The visual language for genetic design diagrams: standard glyphs, defined semantics and best practices that tools and journals share." +url: /visual/ aliases: - - /visual/ + - /visual-about/ +layout: sbol-page +subnav: visual +toc: true +hero_buttons: + - text: Read the specification + url: /visual-specification/ + - text: Browse the glyphs + url: /visual-glyphs/ + style: secondary +summary: "The visual language for genetic design diagrams: standard glyphs, defined semantics and best practices that tools and journals share." --- -{{< figure width="600px" library="true" src="Logos/SBOLVisualLogo.svg" title="" lightbox="true" >}} +{{< figure width="320px" library="true" src="Logos/SBOLVisualLogo.svg" title="" lightbox="true" >}} ### Purpose @@ -26,31 +37,31 @@ People who are engineering biological organisms often find it useful to communic ### Vision -In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. +In order to ground SBOL Visual with precise definitions, we reference its visual elements to data models with a well-defined semantics. SBOL Visual glyphs are defined in terms of their relation to the SBOL 2 data model, and terms in the Sequence Ontology, the Systems Biology Ontology, and BioPAX. ### Usage SBOL Visual acts as a guideline to graphically depict genetic designs and its functional interaction. -A quick introduction can be found [here]({{< relref "visual-glyphs" >}}). +The [glyph library]({{< relref "visual-glyphs" >}}) is the quickest introduction. -To get an idea on how these glyphs has been used in software tools, view all of the [SBOL Visual tools]({{< relref "applications" >}}) that have been reported to us. +To see how tools use these glyphs, browse the [applications that support SBOL Visual]({{< relref "applications" >}}). -Also take a look at sample papers that have been published online for SBOL visual, featuring SBOL visual, and software tools supporting SBOL visual [here]({{< relref "publication" >}}). +The [publications list]({{< relref "publication" >}}) collects the papers that define SBOL Visual, feature it, or describe tools that support it. ### Download Glyphs -We support SBOL Visual glyphs in the following formats: PNG, SVG, and PDF. You can download our copy of the glyphs [here]({{< relref "visual-glyphs" >}}). +Glyphs are available as PNG, SVG, and PDF; download them from the [glyph library]({{< relref "visual-glyphs" >}}). If you plan on creating your own glyphs, we recommend following the guidelines in the [SBOL Visual Specification]({{< relref "visual-specification" >}}) to ensure they will work well as part of an SBOL Visual diagram. -### Proposing a New Feature to the SBOL Data Model +### Proposing a New Feature to SBOL Visual To propose a new feature to SBOL visual, a standard procedure must be followed. 1. Submit a [new issue](https://github.com/SynBioDex/SBOL-visual/issues) on the SBOL-visual Github repository. 2. Create a SBOL Enhancement Proposal (SEP) - * A detailed description about what is an SEP, how to create an SEP, and how to submit an SEP can be found [here](https://github.com/SynBioDex/SEPs/issues/1). - * A template of what a general SEP should look like can be found [here](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). + * Read [what an SEP is and how to submit one](https://github.com/SynBioDex/SEPs/issues/1). + * Start from the [SEP template](https://raw.githubusercontent.com/SynBioDex/SEPs/master/sep_002_template.md). * For further assistance, please contact the [SBOL Editors](mailto:sbol-editors@googlegroups.com). 3. The community will discuss on the proposed SEP through the GitHub issue created for the corresponding SEP. 4. When the community has reached a consensus for the proposed SEP, voting will then be initiated to determine if the SEP will get accepted into the new release of SBOL Visual. diff --git a/content/visual-examples/_index.md b/content/visual-examples/_index.md index 007edf0e0..d0ec14074 100644 --- a/content/visual-examples/_index.md +++ b/content/visual-examples/_index.md @@ -12,6 +12,10 @@ view: 3 header: caption: "" image: "" +subtitle: "Publications and example diagrams that show SBOL Visual in use." +layout: sbol-page +subnav: visual +summary: "Publications and example diagrams that show SBOL Visual in use." --- ## 2020 (Visual Examples) diff --git a/content/visual-gallery/_index.md b/content/visual-gallery/_index.md index af28a4b7a..c7bc4122e 100644 --- a/content/visual-gallery/_index.md +++ b/content/visual-gallery/_index.md @@ -2,4 +2,9 @@ title: SBOL Visual Gallery subtitle: A showcase of beautiful SBOL Visual diagrams from published manuscripts. Click any image to view it in full and explore the original publication. submit_url: "https://forms.gle/JVf211WTvj46vLRt8" +subnav: visual +hero_buttons: + - text: "Recommend an image" + url: "https://forms.gle/JVf211WTvj46vLRt8" +summary: A showcase of beautiful SBOL Visual diagrams from published manuscripts. Click any image to view it in full and explore the original publication. --- diff --git a/content/visual-glyphs/index.md b/content/visual-glyphs/index.md index fd2c42bd8..b9b85f460 100644 --- a/content/visual-glyphs/index.md +++ b/content/visual-glyphs/index.md @@ -2,6 +2,9 @@ title: SBOL Visual Glyphs type: visual-glyphs layout: single +subtitle: "Every glyph in the current SBOL Visual release, grouped by category. Click a glyph to download it." +subnav: visual +summary: "Every glyph in the current SBOL Visual release, grouped by category. Click a glyph to download it." --- SBOL Visual is built off of the latest [specification release]({{< relref "visual-specification" >}}). diff --git a/content/visual-spec-examples/_index.md b/content/visual-spec-examples/_index.md index 7c0a37b26..dd678d258 100644 --- a/content/visual-spec-examples/_index.md +++ b/content/visual-spec-examples/_index.md @@ -1,19 +1,22 @@ --- - title: SBOL Visual Examples from Specification - - # View. - # 1 = List - # 2 = Compact - # 3 = Card - # 4 = Citation - view: 3 - - # Optional header image (relative to `static/img/` folder). - header: - caption: "" - image: "" +title: "SBOL Visual specification examples" + +# View. +# 1 = List +# 2 = Compact +# 3 = Card +# 4 = Citation +view: 3 + +# Optional header image (relative to `static/img/` folder). +header: + caption: "" + image: "" +subtitle: "The diagram examples from the specification appendix, with their captions." +layout: sbol-page +subnav: visual +summary: "The diagram examples from the specification appendix, with their captions." --- - {{< figure library="true" src="SBOLVisualSpecExamples/apdx-exa1.png" title="DNA sequence for a functional unit in which the pTet promoter and an anonymous ribosome entry site regulate expression of a coding sequence for GFP, ended by a terminator." lightbox="true" width="470" >}} {{< figure library="true" src="SBOLVisualSpecExamples/apdx-exa2.png" title="The same functional unit as in \ref{f:apdx:exa1}, with additional assembly-focused information: there is a 5' overhang before the promoter, a 3' overhand after the terminator, and an assembly scar between the promoter and the ribosome entry site left over from a prior step of assembly." lightbox="true" width="470" >}} diff --git a/content/visual-specification/_index.md b/content/visual-specification/_index.md index 46d490100..e73731a76 100644 --- a/content/visual-specification/_index.md +++ b/content/visual-specification/_index.md @@ -1,5 +1,8 @@ --- title: SBOL Visual Specification +subtitle: "The standard set of glyphs and diagram rules for depicting genetic designs, grounded in the SBOL data model." +subnav: visual +issues_url: https://github.com/SynBioDex/SBOL-visual/issues # View. # 1 = List @@ -12,17 +15,10 @@ view: 3 header: caption: "" image: "" +cascade: + share: false + profile: false +summary: "The standard set of glyphs and diagram rules for depicting genetic designs, grounded in the SBOL data model." --- -[Report an Issue with the Current SBOL Visual Specification](https://github.com/SynBioDex/SBOL-visual/issues) - -___ - -[Glyphs]({{< relref "visual-glyphs" >}}) - - \ No newline at end of file + diff --git a/data/subnav.yaml b/data/subnav.yaml new file mode 100644 index 000000000..0f9fe4a7a --- /dev/null +++ b/data/subnav.yaml @@ -0,0 +1,18 @@ +# Section sub-navigation rendered by partials/sbol/hero.html when a page sets `subnav: `. +datamodel: + section: SBOL Data Model + items: + - { name: About, url: /datamodel/ } + - { name: Specification, url: /datamodel-specification/ } + - { name: Ontology, url: /ontology/ } + - { name: Examples, url: /datamodel-examples/ } +visual: + section: SBOL Visual + items: + - { name: About, url: /visual/ } + - { name: Specification, url: /visual-specification/ } + - { name: Glyphs, url: /visual-glyphs/ } + - { name: Ontology, url: /sbol-visual-ontology/ } + - { name: Gallery, url: /visual-gallery/ } + - { name: Examples, url: /visual-examples/ } + - { name: 10 Years, url: /sbolv-10-years/ } diff --git a/layouts/404.html b/layouts/404.html new file mode 100644 index 000000000..2e34c5c99 --- /dev/null +++ b/layouts/404.html @@ -0,0 +1,15 @@ +{{- define "main" -}} +{{/* Site 404: shared hero, then the same destination cards the navigation panels use. */}} +{{ $ctx := dict "Title" "Page not found" "Params" (dict "subtitle" "That page has moved or never existed. Here is where most people are heading." "hero_buttons" (slice (dict "text" "Go to the homepage" "url" "/"))) "RelPermalink" "/404.html" }} +{{ partial "sbol/hero.html" $ctx }} +
+
+ SBOL Data ModelThe standard and its specification + SBOL VisualGlyphs and diagram rules + LibrariesImplementations for your language + ApplicationsTools that support SBOL + PublicationsPapers behind the standard + Join the communityMeetings, Slack and how to contribute +
+
+{{- end -}} diff --git a/layouts/DataModel-Specification/list.html b/layouts/DataModel-Specification/list.html index 66a964b24..8ce0800c5 100644 --- a/layouts/DataModel-Specification/list.html +++ b/layouts/DataModel-Specification/list.html @@ -1,39 +1,4 @@ {{ define "main" }} - - {{ partial "page_header.html" . }} - -
- - - {{.Content}} - - - - - - - - - - - - {{ range .Pages }} - - - - - - {{ if isset .Params "citation"}} - - {{ else }} - - {{ end }} - -
VersionSummarySpecificationCitation
- {{.Params.Version}} - {{.Summary}} Specification Cite - {{ end }} -
-
- +{{ partial "sbol/hero.html" . }} +{{ partial "sbol/spec-list.html" . }} {{ end }} diff --git a/layouts/_default/list.html b/layouts/_default/list.html new file mode 100644 index 000000000..e5bd74db6 --- /dev/null +++ b/layouts/_default/list.html @@ -0,0 +1,8 @@ +{{- define "main" -}} +{{/* Fallback list (taxonomy terms: tags, categories, publication types): shared hero + card list. */}} +{{ partial "sbol/hero.html" . }} +{{ with .Content }}
{{ . }}
{{ end }} +{{ $paginator := .Paginate .Data.Pages }} +{{ partial "sbol/card-list.html" (dict "pages" $paginator.Pages "empty" "Nothing tagged here yet.") }} +
{{ partial "pagination.html" . }}
+{{- end -}} diff --git a/layouts/_default/redirect.html b/layouts/_default/redirect.html new file mode 100644 index 000000000..110ab8c78 --- /dev/null +++ b/layouts/_default/redirect.html @@ -0,0 +1,3 @@ +{{ define "main" }} +{{ partial "sbol/redirect.html" . }} +{{ end }} diff --git a/layouts/_default/sbol-page.html b/layouts/_default/sbol-page.html new file mode 100644 index 000000000..c7bdcc721 --- /dev/null +++ b/layouts/_default/sbol-page.html @@ -0,0 +1,11 @@ +{{ define "main" }} +{{ partial "sbol/hero.html" . }} +
+ {{ if .Params.toc }} + + {{ end }} +
+ {{ .Content }} +
+
+{{ end }} diff --git a/layouts/_default/single.html b/layouts/_default/single.html new file mode 100644 index 000000000..6150afd33 --- /dev/null +++ b/layouts/_default/single.html @@ -0,0 +1,12 @@ +{{- define "main" -}} +{{/* Site override: the article gets a section class so tool, library and GenAI pages can constrain their logo and hide the date. */}} +
+ {{ partial "page_header" . }} +
+
+ {{ .Content }} +
+ {{ partial "page_footer" . }} +
+
+{{- end -}} diff --git a/layouts/applications/list.html b/layouts/applications/list.html index 8678c5146..26649afa1 100644 --- a/layouts/applications/list.html +++ b/layouts/applications/list.html @@ -1,157 +1,87 @@ {{ define "main" }} - -{{/* ── Collect pages ── */}} {{ $active := where .Pages "Params.active" "!=" false }} {{ $deprecated := where .Pages "Params.active" false }} - -{{/* ── Unique tag set from all pages ── */}} {{ $tags := slice }} -{{ range .Pages }} -{{ range .Params.tags }} -{{ $tags = $tags | append . }} -{{ end }} -{{ end }} +{{ range .Pages }}{{ range .Params.tags }}{{ $tags = $tags | append . }}{{ end }}{{ end }} {{ $tags = $tags | uniq | sort }} - -{{/* ── Submit URL from section front matter ── */}} {{ $submitURL := .Params.submit_url | default "" }} - -{{/* ── Hero ── */}} -
-
- -

{{ .Title }}

-

{{ .Params.subtitle }}

-
-
- -
- - {{/* ── Filter bar ── */}} -
- +{{ partial "sbol/hero.html" . }} +
+
+ {{ range $tags }} - {{ $t := . }} - {{ $count := 0 }} - {{ range $active }} - {{ if in .Params.tags $t }}{{ $count = add $count 1 }}{{ end }} - {{ end }} - + {{ $t := . }}{{ $count := 0 }} + {{ range $active }}{{ if in .Params.tags $t }}{{ $count = add $count 1 }}{{ end }}{{ end }} + {{ end }}
- {{/* ── Card grid ── */}} -
- +
{{ range $active }} - {{ $url := "" }} - {{ with .Params.links }}{{ $url = (index . 0).url }}{{ end }} - {{ if not $url }}{{ $url = .Params.external_link }}{{ end }} - -
-
- {{ .Title }} - {{ with $url }} - - - - - - - - {{ end }} -
-

{{ .Summary | plainify | truncate 130 "…" }}

-
- {{ range .Params.tags }} - {{ . }} - {{ end }} + {{ $url := "" }}{{ with .Params.links }}{{ $url = (index . 0).url }}{{ end }}{{ if not $url }}{{ $url = .Params.external_link }}{{ end }} +
+
+

{{ .Title }}

+ {{ with $url }}{{ end }}
+

{{ .Summary | plainify | htmlUnescape | truncate 130 "…" }}

+ {{ with .Params.meta }}

{{ delimit (slice .language .platform .license | complement (slice nil "")) " · " }}

{{ end }} +
{{ range .Params.tags }}{{ . }}{{ end }}
{{ end }} - - {{/* ── Submit a Tool CTA card ── */}} {{ with $submitURL }} -
-
- - - - - -
-

Submit a Tool

-

Built something that supports SBOL? Let the community know.

- Submit +
+ +

Submit a tool

+

Built something that supports SBOL? Let the community know.

+
Submit
{{ end }} +
-
{{/* /app-grid */}} - - {{/* ── Deprecated section ── */}} {{ with $deprecated }} -
-

Legacy Tools

-

Preserved here for reference - these tools supported SBOL at the time of listing. -

- -
+
+

Legacy tools

+

Preserved for reference: these tools supported SBOL at the time of listing.

+
{{ range . }} - {{ $url := "" }} - {{ with .Params.links }}{{ $url = (index . 0).url }}{{ end }} - {{ if not $url }}{{ $url = .Params.external_link }}{{ end }} -
- - {{ .Title }} - - Legacy -

{{ .Summary | plainify | truncate 100 "…" }}

-
- {{ range .Params.tags }} - {{ . }} - {{ end }} -
+
+
Legacy
+

{{ .Title }}

+

{{ .Summary | plainify | htmlUnescape | truncate 100 "…" }}

+ {{ with .Params.meta }}

{{ delimit (slice .language .platform .license | complement (slice nil "")) " · " }}

{{ end }} +
{{ range .Params.tags }}{{ . }}{{ end }}
{{ end }}
-
+
{{ end }} - -
{{/* /universal-wrapper */}} - +
- -{{ end }} \ No newline at end of file +{{ end }} diff --git a/layouts/authors/list.html b/layouts/authors/list.html new file mode 100644 index 000000000..a1b25301d --- /dev/null +++ b/layouts/authors/list.html @@ -0,0 +1,13 @@ +{{- define "main" -}} +{{/* Author page: shared hero (name, role and affiliation as subtitle), then their pages as cards. */}} +{{ $pages := where .Pages ".IsNode" false }} +{{ $bits := slice }} +{{ with .Params.role }}{{ $bits = $bits | append . }}{{ end }} +{{ range .Params.organizations }}{{ with .name }}{{ $bits = $bits | append . }}{{ end }}{{ end }} +{{ $ctx := dict "Title" .Title "Params" (dict "subtitle" (delimit $bits " · ")) "RelPermalink" .RelPermalink }} +{{ partial "sbol/hero.html" $ctx }} +{{ with $pages }} +

Publications and posts

+{{ end }} +{{ partial "sbol/card-list.html" (dict "pages" $pages "empty" "No publications or posts yet.") }} +{{- end -}} diff --git a/layouts/biologist/list.html b/layouts/biologist/list.html index 6a537dc1a..3289c3c79 100644 --- a/layouts/biologist/list.html +++ b/layouts/biologist/list.html @@ -1,240 +1,58 @@ {{ define "main" }} - {{ $p := .Params }} - -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ $p.subtitle }}

-
-
- -
- - {{/* ── Benefits ── */}} +{{ partial "sbol/hero.html" . }} +
{{ with $p.benefits }} -
+
{{ range . }} -
-
-

{{ .title }}

-

{{ .description }}

+
+
+

{{ .title }}

+

{{ .description }}

{{ end }}
{{ end }} - {{/* ── Tools ── */}} {{ range $p.tools }} {{ $img := $.Resources.GetMatch .image }} -
-
- {{ with $img }} - - {{ end }} + {{ $name := .name }} +
+
+ {{ with $img }}Screenshot of {{ $name }}{{ end }}
-
-

{{ .name }}

-

{{ .description }}

-
    - {{ range .bullets }}
  • {{ . }}
    • {{ end }} -
- {{ .cta_text }} +
+

{{ .name }}

+

{{ .description }}

+
    {{ range .bullets }}
  • {{ . }}
    • {{ end }}
+ {{ .cta_text }}
{{ end }} -
{{/* /universal-wrapper */}} - -{{/* ── Visual Language ── */}} -{{ with $p.glyphs_title }} -
-
-

{{ . }}

-

{{ $p.glyphs_description }}

-
- {{ with $p.glyphs_url }} - - - Browse the Glyphs - Full glyph library - - {{ end }} - {{ with $p.glyphs_gallery_url }} - - - View the Gallery - Diagrams from published papers - - {{ end }} - {{ with $p.glyphs_history_url }} - - - 10 Years of SBOL Visual - How the standard evolved - - {{ end }} + {{ with $p.genai_title }} +
+
+
+

{{ . }}

+

{{ $p.genai_description }}

+ {{ with $p.genai_url }}Explore AI tools{{ end }}
+ {{ end }}
-{{ end }} -{{/* ── GenAI tools ── */}} -{{ with $p.genai_title }} -
-
-
-
-

{{ . }}

-

{{ $p.genai_description }}

+{{ with $p.glyphs_title }} +
+
+

{{ . }}

+

{{ $p.glyphs_description }}

+
+ {{ with $p.glyphs_url }}Browse the glyphsFull glyph library{{ end }} + {{ with $p.glyphs_gallery_url }}View the galleryDiagrams from published papers{{ end }} + {{ with $p.glyphs_history_url }}10 years of SBOL VisualHow the standard evolved{{ end }}
- {{ with $p.genai_url }} - Explore AI Tools - {{ end }}
{{ end }} - - - {{ end }} diff --git a/layouts/blog/list.html b/layouts/blog/list.html index 3a12f2030..a69072508 100644 --- a/layouts/blog/list.html +++ b/layouts/blog/list.html @@ -1,66 +1,4 @@ {{ define "main" }} - -{{/* ── Hero header ── */}} -
-
-

SBOL Blog

-

Insights, tutorials, and perspectives from the synthetic biology community.

-
-
- -
- - {{ $pages := .Pages }} - {{ $top := first 1 $pages }} - {{ $rest := after 1 $pages }} - - {{/* ── Featured / lead post ── */}} - {{ range $top }} - {{ $resource := (.Resources.ByType "image").GetMatch "*featured*" }} - - {{ if $resource }} - {{ $img := $resource.Fill "900x520 Smart" }} -
- {{ .Title }} -
- {{ end }} -
- {{ with .Params.tags }} -
{{ range first 3 . }}{{ . }}{{ end }}
- {{ end }} -

{{ .Title }}

-

{{ .Date.Format "January 2, 2006" }}

- {{ with .Params.summary }}

{{ . }}

{{ end }} - Read article → -
- - {{ end }} - - {{/* ── Card grid ── */}} - {{ if $rest }} -
- {{ range $rest }} - {{ $resource := (.Resources.ByType "image").GetMatch "*featured*" }} - - {{ if $resource }} - {{ $img := $resource.Fill "600x360 Smart" }} -
- {{ .Title }} -
- {{ end }} -
- {{ with .Params.tags }} -
{{ range first 2 . }}{{ . }}{{ end }}
- {{ end }} -

{{ .Title }}

-

{{ .Date.Format "Jan 2, 2006" }}

- {{ with .Params.summary }}

{{ . | plainify | truncate 130 "…" }}

{{ end }} - Read more → -
- - {{ end }} -
- {{ end }} - -
+{{ partial "sbol/hero.html" . }} +{{ partial "sbol/post-list.html" . }} {{ end }} diff --git a/layouts/community-meetings/list.html b/layouts/community-meetings/list.html index a51090f02..ebd9944e9 100644 --- a/layouts/community-meetings/list.html +++ b/layouts/community-meetings/list.html @@ -1,427 +1,101 @@ {{ define "main" }} - {{ $now := now }} {{ $meetings := .Params.meetings | default slice }} {{ $outreach := .Params.outreach | default slice }} {{ $connectLinks := .Params.connect_links | default slice }} {{ $connectText := .Params.connect_text | default "" }} -{{ $heroBtnText := .Params.hero_btn_text | default "Join the Community" }} -{{ $heroBtnIcon := .Params.hero_btn_icon | default "" }} -{{ $heroBtnUrl := .Params.hero_btn_url | default "" }} - -{{/* ── Split meetings: upcoming vs archive ── */}} -{{ $upcoming := slice }} -{{ $past := slice }} -{{ range $meetings }} - {{ $d := "" }} - {{ with .date }}{{ $d = time . }}{{ end }} - {{ if and $d (ge $d $now) }} - {{ $upcoming = $upcoming | append . }} - {{ else }} - {{ $past = $past | append . }} - {{ end }} -{{ end }} - -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ .Params.subtitle }}

- {{ with $heroBtnUrl }} - - {{ with $heroBtnIcon }}{{ end }}{{ $heroBtnText }} - - {{ end }} -
-
- -
- - {{/* ── Workshops & Conferences ── */}} -
-

Workshops & Conferences

- -
- - -
- -
- {{ if $upcoming }} - - - - {{ range $upcoming }} - - - - - - - {{ end }} - -
EventDateLocationResources
- {{ .type }} - {{ if .url }}{{ .name }} - {{ else }}{{ .name }}{{ end }} - {{ .date_display }}{{ .location }}{{ with .slides_url }}Slides{{ end }}
- {{ else }} -

No upcoming events scheduled — check back soon.

- {{ end }} +{{ $upcoming := slice }}{{ $past := slice }} +{{ range $meetings }}{{ $d := "" }}{{ with .date }}{{ $d = time . }}{{ end }}{{ if and $d (ge $d $now) }}{{ $upcoming = $upcoming | append . }}{{ else }}{{ $past = $past | append . }}{{ end }}{{ end }} +{{ $outreachUpcoming := slice }}{{ $outreachPast := slice }} +{{ range $outreach }}{{ $d := "" }}{{ with .date }}{{ $d = time . }}{{ end }}{{ if and $d (ge $d $now) }}{{ $outreachUpcoming = $outreachUpcoming | append . }}{{ else }}{{ $outreachPast = $outreachPast | append . }}{{ end }}{{ end }} +{{ partial "sbol/hero.html" . }} +
+
+

Workshops & conferences

+
+ +
- -
- {{ if $past }} - + {{ range $i, $set := (slice (dict "id" "panel-upcoming" "rows" $upcoming "empty" "No upcoming events scheduled. Check back soon.") (dict "id" "panel-archive" "rows" $past "empty" "")) }} +
+ {{ if $set.rows }} +
+
- {{ range $past }} + {{ range $set.rows }} - - - - + + + + {{ end }}
EventDateLocationResources
- {{ .type }} - {{ if .url }}{{ .name }} - {{ else }}{{ .name }}{{ end }} - {{ .date_display }}{{ .location }}{{ with .slides_url }}Slides{{ end }}{{ .type }} {{ if .url }}{{ .name }}{{ else }}{{ .name }}{{ end }}{{ .date_display }}{{ .location }}{{ with .slides_url }}Slides{{ end }}
- {{ end }} +
+ {{ else if $set.empty }}

{{ $set.empty }}

{{ end }}
-
- - {{/* ── Outreach & Education ── */}} - {{ $outreachUpcoming := slice }} - {{ $outreachPast := slice }} - {{ range $outreach }} - {{ $d := "" }} - {{ with .date }}{{ $d = time . }}{{ end }} - {{ if and $d (ge $d $now) }} - {{ $outreachUpcoming = $outreachUpcoming | append . }} - {{ else }} - {{ $outreachPast = $outreachPast | append . }} {{ end }} - {{ end }} - -
-

Outreach & Education

+
-
- - +
+

Outreach & education

+
+ +
- -
- {{ if $outreachUpcoming }} -
- {{ range $outreachUpcoming }} -
- {{ .type }} - {{ if .url }} - {{ .name }} - {{ else }} - {{ .name }} - {{ end }} - {{ .date_display }}{{ with .location }} · {{ . }}{{ end }} + {{ range $i, $set := (slice (dict "id" "panel-outreach-upcoming" "rows" $outreachUpcoming "empty" "No upcoming outreach events scheduled. Check back soon.") (dict "id" "panel-outreach-archive" "rows" $outreachPast "empty" "")) }} +
+ {{ if $set.rows }} +
+ {{ range $set.rows }} +
+
{{ .type }}
+ {{ if .url }}{{ .name }}{{ else }}{{ .name }}{{ end }} + {{ .date_display }}{{ with .location }} · {{ . }}{{ end }}
{{ end }}
- {{ else }} -

No upcoming outreach events scheduled — check back soon.

- {{ end }} -
- -
- {{ if $outreachPast }} -
- {{ range $outreachPast }} -
- {{ .type }} - {{ if .url }} - {{ .name }} - {{ else }} - {{ .name }} - {{ end }} - {{ .date_display }}{{ with .location }} · {{ . }}{{ end }} -
- {{ end }} -
- {{ end }} + {{ else if $set.empty }}

{{ $set.empty }}

{{ end }}
+ {{ end }}
+
-
{{/* /universal-wrapper */}} - -{{/* ── Stay Connected ── */}} {{ if $connectLinks }} -
-
-

Stay Connected

- {{ with $connectText }}

{{ . }}

{{ end }} -
+
+
+

Stay connected

+ {{ with $connectText }}

{{ . }}

{{ end }} +
{{ range $connectLinks }} - - {{ with .icon }} {{ end }}{{ .name }} - {{ .description }} + + {{ with .icon }}{{ end }} + {{ .name }} + {{ .description }} {{ end }}
{{ end }} - - - - {{ end }} diff --git a/layouts/developer/list.html b/layouts/developer/list.html index 1d2a75cce..fc0a79773 100644 --- a/layouts/developer/list.html +++ b/layouts/developer/list.html @@ -1,231 +1,86 @@ {{ define "main" }} - {{ $p := .Params }} - -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ $p.subtitle }}

-
-
- -
- - {{/* ── Benefits ── */}} +{{ partial "sbol/hero.html" . }} +
{{ with $p.benefits }} -
+
{{ range . }} -
-
-

{{ .title }}

-

{{ .description }}

+
+
+

{{ .title }}

+

{{ .description }}

{{ end }}
{{ end }} - {{/* ── Libraries ── */}} {{ with $p.libraries_title }} -
-
-

{{ . }}

-

{{ $p.libraries_description }}

- Browse All Libraries -
+
+

{{ . }}

+

{{ $p.libraries_description }}

+ Browse all libraries
{{ end }} - {{/* ── Specification ── */}} {{ with $p.spec_title }} -
-

{{ . }}

-

{{ $p.spec_description }}

-
+
+

{{ . }}

+

{{ $p.spec_description }}

+
{{ range $p.spec_links }} - - - {{ .label }} - {{ .description }} + + + {{ .label }} + {{ .description }} {{ end }}
{{ end }} - {{/* ── Toolchain ── */}} {{ with $p.toolchain_title }} -
-

{{ . }}

-

{{ $p.toolchain_description }}

-
+
+

{{ . }}

+

{{ $p.toolchain_description }}

+
{{ range $p.toolchain_links }} - - - {{ .label }} - {{ .description }} + + + {{ .label }} + {{ .description }} {{ end }}
{{ end }} -
{{/* /universal-wrapper */}} - -{{/* ── GenAI ── */}} -{{ with $p.genai_title }} -
-
-
-
-

{{ . }}

-

{{ $p.genai_description }}

+ {{ with $p.genai_title }} +
+
+
+

{{ . }}

+

{{ $p.genai_description }}

- {{ with $p.genai_url }} - Explore AI Tools - {{ end }} + {{ with $p.genai_url }}Explore AI tools{{ end }}
+ {{ end }}
-{{ end }} -{{/* ── Contribute ── */}} {{ with $p.contribute_title }} -
-
-

{{ . }}

-

{{ $p.contribute_description }}

-
+
+
+

{{ . }}

+

{{ $p.contribute_description }}

+
{{ range $p.contribute_links }} - - - {{ .label }} - {{ .description }} + + + {{ .label }} + {{ .description }} {{ end }}
{{ end }} - - - {{ end }} diff --git a/layouts/genai-tools/list.html b/layouts/genai-tools/list.html index 79cb426cc..509176648 100644 --- a/layouts/genai-tools/list.html +++ b/layouts/genai-tools/list.html @@ -1,118 +1,19 @@ {{ define "main" }} - -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ .Params.subtitle }}

-
-
- -
-
+{{ partial "sbol/hero.html" . }} +
+
{{ range .Pages }} - {{ $url := .Params.external_url | default .Permalink }} - {{ $platform := .Params.platform | default "" }} - {{ $version := .Params.sbol_version | default "" }} - -
- {{ with $platform }} - {{ . }} - {{ end }} - {{ with $version }} - SBOL {{ . }} - {{ end }} + {{ $url := .Params.external_url | default .Permalink }} + +
+ {{ with .Params.platform }}{{ . }}{{ end }} + {{ with .Params.sbol_version }}SBOL {{ . }}{{ end }}
-

{{ .Title }}

-

{{ .Params.summary }}

- Try it → +

{{ .Title }}

+

{{ .Params.summary }}

+ Try it → {{ end }}
- - - {{ end }} diff --git a/layouts/join/list.html b/layouts/join/list.html index 42086e8c3..0f2e3d2d2 100644 --- a/layouts/join/list.html +++ b/layouts/join/list.html @@ -1,266 +1,79 @@ {{ define "main" }} - {{ $p := .Params }} - -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ $p.subtitle }}

-
-
- -
- - {{/* ── Reasons ── */}} +{{ partial "sbol/hero.html" . }} +
{{ with $p.reasons }} -
+
{{ range . }} -
-
-

{{ .title }}

-

{{ .description }}

+
+
+

{{ .title }}

+

{{ .description }}

{{ end }}
{{ end }} - {{/* ── Stats ── */}} {{ with $p.stats }} -
-
- {{ range . }} -
- {{ .number }} - {{ .label }} -
- {{ end }} -
- {{ with $p.stats_note }} -

{{ . }}

+
+ {{ range . }} +
{{ .number }}{{ .label }}
{{ end }} + {{ with $p.stats_note }}

{{ . }}

{{ end }}
{{ end }} - {{/* ── Connect ── */}} {{ with $p.connect_title }} -
-

{{ . }}

-
+
+

{{ . }}

+ {{ with $p.connect_description }}

{{ . }}

{{ end }} +
{{ range $p.connect_links }} - - - {{ .label }} - {{ .description }} + + + {{ .label }} + {{ .description }} {{ end }}
{{ end }} - {{/* ── Meetings ── */}} {{ with $p.meetings_title }} -
-
-

{{ . }}

-

{{ $p.meetings_description }}

- {{ with $p.meetings_url }} - View Meetings & Outreach - {{ end }} +
+
+
+

{{ . }}

+

{{ $p.meetings_description }}

-
+ {{ with $p.meetings_url }}View meetings & outreach{{ end }} +
{{ end }} - {{/* ── Structure ── */}} {{ with $p.structure_title }} -
-

{{ . }}

-

{{ $p.structure_description }}

-
+
+

{{ . }}

+

{{ $p.structure_description }}

+
{{ range $p.structure_links }} - - - {{ .label }} - {{ .description }} + + + {{ .label }} + {{ .description }} {{ end }}
{{ end }} +
-
{{/* /universal-wrapper */}} - -{{/* ── CTA ── */}} {{ with $p.cta_title }} -
-
-

{{ . }}

-

{{ $p.cta_description }}

- {{ with $p.cta_btn_url }} - {{ $p.cta_btn_text }} - {{ end }} +
+
+

{{ . }}

+

{{ $p.cta_description }}

+ {{ with $p.cta_btn_url }}{{ $p.cta_btn_text }}{{ end }}
{{ end }} - - - {{ end }} diff --git a/layouts/libraries/list.html b/layouts/libraries/list.html index d1165fda3..f96e4419c 100644 --- a/layouts/libraries/list.html +++ b/layouts/libraries/list.html @@ -1,199 +1,83 @@ {{ define "main" }} - -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ .Params.subtitle }}

- -
-
- -{{/* ── Tab bar ── */}} -
-
+{{ partial "sbol/hero.html" . }} +
+
{{ range $i, $tab := .Params.tabs }} - + {{ end }}
-
- -
{{ range $i, $tab := $.Params.tabs }} {{ $tabID := $tab.id }} - - {{/* Filter pages for this version */}} {{ $tabPages := slice }} - {{ range $.Pages }} - {{ if in .Params.sbol_versions $tabID }} - {{ $tabPages = $tabPages | append . }} - {{ end }} - {{ end }} - + {{ range $.Pages }}{{ if in .Params.sbol_versions $tabID }}{{ $tabPages = $tabPages | append . }}{{ end }}{{ end }} {{ $primary := where $tabPages "Params.lib_category" "primary" }} {{ $libraries := where $tabPages "Params.lib_category" "library" }} {{ $resources := where $tabPages "Params.lib_category" "resource" }} - -
- - {{/* ── Primary Libraries ── */}} - {{ with $primary }} -
-
-

Primary Libraries

-

Actively maintained core implementations.

+
+ {{ range $group := (slice (dict "title" "Primary libraries" "sub" "Actively maintained core implementations." "pages" $primary "badge" (cond (eq $tabID "3") "Active development" "")) (dict "title" "Other libraries" "sub" "Additional language implementations." "pages" $libraries "badge" "")) }} + {{ with $group.pages }} +
+
+

{{ $group.title }}

{{ $group.sub }}

+ {{ with $group.badge }}{{ . }}{{ end }}
- {{ if eq $tabID "3" }}Active Development{{ end }} -
-
- {{ range . }} - {{ $github := "" }} - {{ $docs := "" }} - {{ range .Params.links }} - {{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }} - {{ if or (in .name "Documentation") (in .name "API") (eq .icon "edge") }}{{ $docs = .url }}{{ end }} - {{ end }} -
-
- {{ .Title }} - {{ with $github }} - - - - - - - - {{ end }} -
-

{{ .Summary | plainify }}

-
- {{ with $docs }} - Documentation - {{ end }} - {{ with $github }} - GitHub - {{ end }} - More Info +
+ {{ range . }} + {{ $github := "" }}{{ $docs := "" }} + {{ range .Params.links }} + {{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }} + {{ if or (in .name "Documentation") (in .name "API") (eq .icon "edge") }}{{ $docs = .url }}{{ end }} + {{ end }} +
+
+

{{ .Title }}

+ {{ with $github }}{{ end }} +
+

{{ .Summary | plainify | htmlUnescape }}

+
{{ range .Params.sbol_versions }}SBOL {{ . }}{{ end }}{{ with .Params.meta }}{{ with .license }}{{ . }}{{ end }}{{ end }}
+
+ {{ with $docs }}Documentation{{ end }} + {{ with $github }}GitHub{{ end }} + More info +
+ {{ end }}
- {{ end }} -
+
{{ end }} - - {{/* ── Other Libraries ── */}} - {{ with $libraries }} -
-
-

Other Libraries

-

Additional language implementations.

-
-
-
- {{ range . }} - {{ $github := "" }} - {{ $docs := "" }} - {{ range .Params.links }} - {{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }} - {{ if or (in .name "Documentation") (in .name "API") (eq .icon "edge") }}{{ $docs = .url }}{{ end }} - {{ end }} -
-
- {{ .Title }} - {{ with $github }} - - - - - - - - {{ end }} -
-

{{ .Summary | plainify }}

-
- {{ with $docs }} - Documentation - {{ end }} - {{ with $github }} - GitHub - {{ end }} - More Info -
-
- {{ end }} -
{{ end }} - {{/* ── Developer Resources ── */}} {{ with $resources }} -
-
-
-

Developer Resources

-

Tools and notebooks to accelerate your work with SBOL.

-
-
-
+
+

Developer resources

+

Tools and notebooks to accelerate your work with SBOL.

+
{{ range . }} - {{ $github := "" }} - {{ range .Params.links }} - {{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }} - {{ end }} -
-

{{ .Title }}

-

{{ .Summary | plainify }}

- {{ with $github }} - Explore on GitHub → - {{ end }} + {{ $github := "" }}{{ range .Params.links }}{{ if or (eq .name "Github") (eq .icon "github") }}{{ $github = .url }}{{ end }}{{ end }} +
+

{{ .Title }}

+

{{ .Summary | plainify | htmlUnescape }}

+ {{ with $github }}
Explore on GitHub →
{{ end }}
{{ end }}
-
+
{{ end }} - -
{{/* /lib-panel */}} - {{ end }}{{/* /range tabs */}} - -
{{/* /universal-wrapper */}} - +
+ {{ end }} +
- -{{ end }} \ No newline at end of file +{{ end }} diff --git a/layouts/partials/custom_js.html b/layouts/partials/custom_js.html new file mode 100644 index 000000000..7d5399bdc --- /dev/null +++ b/layouts/partials/custom_js.html @@ -0,0 +1,28 @@ + diff --git a/layouts/partials/jsonld/main.html b/layouts/partials/jsonld/main.html new file mode 100644 index 000000000..eb6a16bcc --- /dev/null +++ b/layouts/partials/jsonld/main.html @@ -0,0 +1,23 @@ +{{ $page := .page }} +{{ $summary := .summary }} +{{ $site_type := site.Params.site_type | default "Person" }} + +{{- if $page.IsHome -}} + + {{ partialCached "jsonld/website.html" $page }} + + {{ if ne $site_type "Person" }} + {{ partial "jsonld/business.html" $page }} + {{ end }} + +{{- else if $page.IsPage -}} + + {{ if (eq $page.Type "post") | or (eq $page.Type "blog") | or (eq $page.Type "publication") | or (eq $page.Type "project") }} + {{ partial "jsonld/article.html" (dict "page" $page "summary" $summary) }} + {{ end }} + + {{ if eq $page.Type "event" }} + {{ partial "jsonld/event.html" (dict "page" $page "summary" $summary) }} + {{ end }} + +{{- end }} diff --git a/layouts/partials/li_card.html b/layouts/partials/li_card.html index fb419627e..9e698f243 100644 --- a/layouts/partials/li_card.html +++ b/layouts/partials/li_card.html @@ -1,70 +1,27 @@ +{{/* Publication / talk card on the shared card component. Used by the theme's list templates (view 3). */}} {{ $item := . }} - - -{{/* Dynamic view adjusts to content type. */}} -{{ $show_buttons := false }} -{{ if eq $item.Type "talk" }} - {{ $show_buttons = true }} -{{ else if eq $item.Type "publication" }} - {{ $show_buttons = true }} -{{ end }} - -{{/* Get summary. */}} +{{ $show_buttons := or (eq $item.Type "talk") (eq $item.Type "publication") }} {{ $summary := "" }} -{{ if $item.Params.summary }} - {{ $summary = $item.Params.summary | markdownify | emojify }} -{{ else if .Params.abstract }} - {{ $summary = .Params.abstract | markdownify | emojify }} -{{ else if $item.Summary }} - {{ $summary = $item.Summary }} -{{ end }} - -
- - {{ if eq $item.Type "talk" }} -
- {{ if $item.Params.authors }} -
- {{ partial "page_metadata_authors" $item }} -
- {{ end }} - - {{ partial "functions/get_event_dates" $item }} - - {{ with $item.Params.location }} - - {{ . }} - {{ end }} -
- {{ else }} - {{ partial "page_metadata" (dict "page" $item "is_list" 1) }} - {{ end }} - - {{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} - {{ $anchor := $item.Params.image.focal_point | default "Smart" }} +{{ if $item.Params.summary }}{{ $summary = $item.Params.summary | plainify | htmlUnescape }} +{{ else if $item.Params.abstract }}{{ $summary = $item.Params.abstract | plainify | htmlUnescape | truncate 320 "…" }} +{{ else if $item.Summary }}{{ $summary = $item.Summary | plainify | htmlUnescape }}{{ end }} +{{ $resource := ($item.Resources.ByType "image").GetMatch "*featured*" }} +
{{ with $resource }} - {{ $image := $resource.Fit "600x400" }} - - {{ $item.Title }} - - {{end}} - -

- {{ $item.Title }} -

- - {{ with $summary }} - -
-

{{.}}

-
- + {{ $image := .Fit "900x600" }} + {{ end }} - - {{ if $show_buttons }} -
- {{ partial "page_links" (dict "page" $item "is_list" 1) }} +
+
+ {{ if eq $item.Type "talk" }} + {{ if $item.Params.authors }}{{ partial "page_metadata_authors" $item }} {{ end }} + {{ partial "functions/get_event_dates" $item }}{{ with $item.Params.location }} {{ . }}{{ end }} + {{ else }} + {{ partial "page_metadata" (dict "page" $item "is_list" 1) }} + {{ end }} +
+

{{ $item.Title }}

+ {{ with $summary }}

{{ . }}

{{ end }} + {{ if $show_buttons }}
{{ partial "page_links" (dict "page" $item "is_list" 1) }}
{{ end }}
- {{ end }} -
diff --git a/layouts/partials/li_list.html b/layouts/partials/li_list.html new file mode 100644 index 000000000..48f79dba5 --- /dev/null +++ b/layouts/partials/li_list.html @@ -0,0 +1,22 @@ +{{/* Compact list item (view 1) on the shared card component: icon, title, metadata, page links. */}} +{{ $item := . }} +{{ $icon_pack := "far" }}{{ $icon := "fa-file-alt" }} +{{ $show_authors := false }}{{ $show_buttons := false }} +{{ $link := $item.RelPermalink }}{{ $target := "" }} +{{ with $item.Params.external_link }}{{ $link = . }}{{ $target = "target=\"_blank\" rel=\"noopener\"" }}{{ end }} +{{ if eq $item.Type "post" }}{{ $icon = "fa-newspaper" }} +{{ else if eq $item.Type "talk" }}{{ $icon = "fa-calendar-alt" }} +{{ else if eq $item.Type "publication" }}{{ $show_authors = true }}{{ $show_buttons = true }} +{{ else if eq $item.Type "project" }}{{ $icon_pack = "fas" }}{{ $icon = "fa-project-diagram" }}{{ $show_authors = true }}{{ $show_buttons = true }}{{ end }} +
+ +
+

{{ $item.Title }}

+
+ {{/* page_metadata already prints authors; only talks need them separately */}} + {{ if eq $item.Type "talk" }}{{ if $show_authors }}
{{ partial "page_metadata_authors" $item }}
{{ end }}{{ partial "functions/get_event_dates" $item }}{{ with $item.Params.location }} {{ . }}{{ end }} + {{ else }}{{ partial "page_metadata" (dict "page" $item "is_list" 1) }}{{ end }} +
+ {{ if $show_buttons }}
{{ partial "page_links" (dict "page" $item "is_list" 1) }}
{{ end }} +
+
diff --git a/layouts/partials/navbar.html b/layouts/partials/navbar.html new file mode 100644 index 000000000..70934aba8 --- /dev/null +++ b/layouts/partials/navbar.html @@ -0,0 +1,215 @@ +{{ $show_navbar := site.Params.main_menu.enable | default true }} +{{ if $show_navbar }} + +{{ $current_page := . }} +{{ $highlight_active_link := site.Params.main_menu.highlight_active_link | default true }} +{{ $show_current_language := site.Params.main_menu.show_language | default false }} + +{{/* Get site logo. */}} +{{ $show_logo := site.Params.main_menu.show_logo | default true }} +{{ $has_logo := fileExists "assets/images/logo.png" | or (fileExists "assets/images/logo.svg") }} +{{ $logo := "" }} +{{ if $has_logo }} + {{ $logo = (partial "functions/get_logo" (dict "constraint" "max_height" "size" 70)) }} +{{ end }} + + +{{end}}{{/* End show navbar. */}} diff --git a/layouts/partials/page_metadata.html b/layouts/partials/page_metadata.html new file mode 100644 index 000000000..96cdf1c61 --- /dev/null +++ b/layouts/partials/page_metadata.html @@ -0,0 +1,65 @@ +{{ $is_list := .is_list }} +{{ $page := .page }} + +
+ + {{/* If `authors` is set and is not empty. */}} + {{ if $page.Params.authors }} + {{ $authorLen := len $page.Params.authors }} + {{ if gt $authorLen 0 }} +
+ {{ partial "page_metadata_authors" $page }} +
+ {{ end }} + {{ end }} + + {{ if not (in (slice "event" "page") $page.Type) }} + + {{ $date := $page.Lastmod.Format site.Params.date_format }} + {{ if eq $page.Type "publication" }} + {{ $date = $page.Date.Format (site.Params.publications.date_format | default "January, 2006") }} + {{ else }} + {{ if ne $page.Params.Lastmod $page.Params.Date }} + {{ i18n "last_updated" }} + {{ end }} + {{ end }} + {{ $date }} + + {{ end }} + + {{/* Site override: print the venue separator only when there is a venue, so cards never end in a stray divider. */}} + {{ $venue := $page.Params.publication_short | default $page.Params.publication }} + {{ if and (eq $is_list 1) (eq $page.Type "publication") $venue }} + + {{ $venue | markdownify }} + {{ end }} + + {{ if and (eq $page.Type "post") (not (or (eq site.Params.reading_time false) (eq $page.Params.reading_time false))) }} + + + {{ $page.ReadingTime }} {{ i18n "minute_read" }} + + {{ end }} + + {{/* Show Disqus comment count if enabled. */}} + {{ $commentable_map := site.Params.comments.commentable | default dict }} + {{ $commentable_bool := index $commentable_map $page.Type | default false }} + {{ $disqus_enabled := eq site.Params.comments.engine 1 | and $commentable_bool | and (ne $page.Params.commentable false) | or $page.Params.commentable }} + {{ if and $disqus_enabled (site.Params.comments.disqus.show_count | default true) }} + + + {{ end}} + + {{ $taxonomy := "categories" }} + {{ if $page.Param $taxonomy }} + + + + {{- range $index, $value := ($page.GetTerms $taxonomy) -}} + {{- if gt $index 0 }}, {{ end -}} + {{ .LinkTitle }} + {{- end -}} + + {{ end }} + +
diff --git a/layouts/partials/sbol/card-list.html b/layouts/partials/sbol/card-list.html new file mode 100644 index 000000000..3407e83fa --- /dev/null +++ b/layouts/partials/sbol/card-list.html @@ -0,0 +1,11 @@ +{{/* A list of pages rendered with the shared card component. Params: pages, empty (message). */}} +{{ $pages := .pages }} +
+ {{ if $pages }} +
+ {{ range $pages }}{{ partial "li_card" . }}{{ end }} +
+ {{ else }} +

{{ .empty | default "Nothing here yet." }}

+ {{ end }} +
diff --git a/layouts/partials/sbol/hero.html b/layouts/partials/sbol/hero.html new file mode 100644 index 000000000..15cb39714 --- /dev/null +++ b/layouts/partials/sbol/hero.html @@ -0,0 +1,31 @@ +{{/* Section hero. Front matter: subtitle, hero_eyebrow, hero_meta, hero_buttons [{text,url,icon,style}], subnav (key in data/subnav.yaml). */}} +{{ $p := .Params }} +{{ $subnav := dict }} +{{ with $p.subnav }}{{ $subnav = index site.Data.subnav . | default dict }}{{ end }} +{{ $title := .Title }} +{{ if not $title }}{{ with $subnav.section }}{{ $title = . }}{{ end }}{{ end }} +{{ $current := strings.TrimSuffix "/" .RelPermalink }} +
+
+ {{ with $p.hero_eyebrow }}{{ . }}{{ end }} +

{{ $title }}

+ {{ with $p.subtitle }}

{{ . | markdownify }}

{{ end }} + {{ with $p.hero_meta }}

{{ . | markdownify }}

{{ end }} + {{ with $p.hero_buttons }} +
+ {{ range . }} + {{ with .icon }}{{ end }}{{ .text }} + {{ end }} +
+ {{ end }} +
+ {{ with $subnav.items }} + + {{ end }} +
diff --git a/layouts/partials/sbol/post-list.html b/layouts/partials/sbol/post-list.html new file mode 100644 index 000000000..7db57c762 --- /dev/null +++ b/layouts/partials/sbol/post-list.html @@ -0,0 +1,47 @@ +{{/* Post list: lead card for the newest item, card grid for the rest. Used by /blog/ and /post/. */}} +{{ $pages := .Pages }} +{{ $top := first 1 $pages }} +{{ $rest := after 1 $pages }} +{{ $kind := .Params.list_badge | default "" }} +
+ {{ range $top }} + {{ $resource := (.Resources.ByType "image").GetMatch "*featured*" }} + + {{ if $resource }}{{ $img := $resource.Fill "900x520 Smart" }} +
+ {{ end }} +
+
+ {{ with $kind }}{{ . }}{{ end }} + {{ with .Params.tags }}{{ range first 3 . }}{{ . }}{{ end }}{{ end }} +
+

{{ .Title }}

+

{{ .Date.Format "January 2, 2006" }}

+ {{ with .Params.summary }}

{{ . }}

{{ end }} + Read article → +
+ + {{ end }} + {{ if $rest }} +
+ {{ range $rest }} + {{ $resource := (.Resources.ByType "image").GetMatch "*featured*" }} + + {{ if $resource }}{{ $img := $resource.Fill "600x360 Smart" }} +
+ {{ end }} +
+
+ {{ with $kind }}{{ . }}{{ end }} + {{ with .Params.tags }}{{ range first 2 . }}{{ . }}{{ end }}{{ end }} +
+

{{ .Title }}

+

{{ .Date.Format "Jan 2, 2006" }}

+ {{ with .Params.summary }}

{{ . | plainify | htmlUnescape | truncate 130 "…" }}

{{ end }} + Read more → +
+ + {{ end }} +
+ {{ end }} +
diff --git a/layouts/partials/sbol/redirect.html b/layouts/partials/sbol/redirect.html new file mode 100644 index 000000000..a1e7e83bc --- /dev/null +++ b/layouts/partials/sbol/redirect.html @@ -0,0 +1,8 @@ +{{ $to := .Params.redirect_to | default "/" }} + +
+
+

{{ .Title }}

+

This page has moved to {{ $to }}.

+
+
diff --git a/layouts/partials/sbol/spec-list.html b/layouts/partials/sbol/spec-list.html new file mode 100644 index 000000000..43aa812e9 --- /dev/null +++ b/layouts/partials/sbol/spec-list.html @@ -0,0 +1,44 @@ +{{/* Specification landing: current-version card, then a table of every version. Version pages provide version, date, specification, citation. */}} +{{ $versions := .Pages.ByDate.Reverse }} +{{ $current := index $versions 0 }} +{{ $issues := .Params.issues_url }} +
+ {{ with $current }} +
+
+ Current version + Published {{ .Date.Format "January 2, 2006" }} +
+

{{ .Title }}

+

{{ .Summary | plainify | htmlUnescape | truncate 260 "…" }}

+
+ {{ with .Params.specification }}Specification (PDF){{ end }} + {{ with .Params.citation }}Cite{{ end }} + What changed + {{ with $issues }}Report an issue{{ end }} +
+
+ {{ end }} + +
+

All versions

+
+ + + + {{ range $i, $v := $versions }} + + + + + + + + + {{ end }} + +
VersionDateStatusSummarySpecificationCitation
{{ .Params.version }}{{ .Date.Format "Jan 2, 2006" }}{{ if eq $i 0 }}Current{{ else }}Superseded{{ end }}{{ .Summary | plainify | htmlUnescape | truncate 110 "…" }} More{{ with .Params.specification }}PDF{{ end }}{{ with .Params.citation }}Cite{{ end }}
+
+
+ {{ with .Content }}
{{ . }}
{{ end }} +
diff --git a/layouts/partials/search.html b/layouts/partials/search.html new file mode 100644 index 000000000..fda36780d --- /dev/null +++ b/layouts/partials/search.html @@ -0,0 +1,48 @@ +{{/* Partial for built-in search and Algolia search. */}} +{{ if eq site.Params.search.engine 1 | or (eq site.Params.search.engine 2) }} + +{{end}} diff --git a/layouts/partials/site_footer.html b/layouts/partials/site_footer.html index 1e2aea19b..378110bb2 100644 --- a/layouts/partials/site_footer.html +++ b/layouts/partials/site_footer.html @@ -1,12 +1,21 @@ -
- {{ if site.Menus.footer }} -

- {{ range site.Menus.footer }} - {{ .Name }} - {{ end }} -

- {{ end }} -

© 2026 SBOL. This webpage is under license CC BY NC ND - 4.0

-
\ No newline at end of file + diff --git a/layouts/partials/widgets/people.html b/layouts/partials/widgets/people.html new file mode 100644 index 000000000..7db79d2e8 --- /dev/null +++ b/layouts/partials/widgets/people.html @@ -0,0 +1,69 @@ +{{/* People Widget */}} + +{{/* Initialise */}} +{{ $ := .root }} +{{ $page := .page }} +{{ $show_social := $page.Params.design.show_social | default false }} +{{ $show_interests := $page.Params.design.show_interests | default true }} +{{ $show_organizations := $page.Params.design.show_organizations | default false }} +{{ $show_role := $page.Params.design.show_role | default true }} + +
+ {{ with $page.Title }} +
+

{{ . | markdownify | emojify }}

+ {{ if $page.Params.subtitle }}

{{ $page.Params.subtitle | markdownify | emojify }}

{{ end }} +
+ {{ end }} + + {{ with $page.Content }} +
+ {{ . }} +
+ {{ end }} + + {{ range $page.Params.content.user_groups }} + {{ $query := where (where site.Pages "Section" "authors") ".Params.user_groups" "intersect" (slice .) }} + + {{if $query}} +
+

{{ . | markdownify }}

+
+ {{end}} + + {{ range $query }} + {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} + {{/* Get link to user's profile page. */}} + {{ $link := "" }} + {{ with site.GetPage (printf "/authors/%s" (path.Base (path.Split .Path).Dir)) }} + {{ $link = .RelPermalink }} + {{ end }} +
+ {{ $src := "" }} + {{ if site.Params.avatar.gravatar }} + {{ $src = printf "https://s.gravatar.com/avatar/%s?s=150" (md5 .Params.email) }} + {{ else if $avatar }} + {{ $avatar_image := $avatar.Fill "270x270 Center" }} + {{ $src = $avatar_image.RelPermalink }} + {{ end }} + {{ if $src }} + {{ $avatar_shape := site.Params.avatar.shape | default "circle" }} + {{with $link}}{{end}}Portrait of {{ .Title }}{{if $link}}{{end}} + {{ else }} + {{/* No photo on file: initials on a green tint. Adding avatar.jpg to the author folder replaces it. */}} + {{ $initials := "" }} + {{ range first 2 (split .Title " ") }}{{ $initials = printf "%s%s" $initials (substr . 0 1) }}{{ end }} + {{with $link}}{{end}}{{if $link}}{{end}} + {{ end }} + +
+

{{with $link}}{{end}}{{ .Title }}{{if $link}}{{end}}

+ {{ if and $show_organizations .Params.organizations }}{{ range .Params.organizations }}

{{ .name }}

{{ end }}{{ end }} + {{ if and $show_role .Params.role }}

{{ .Params.role | markdownify | emojify }}

{{ end }} + {{ if $show_social }}{{ partial "social_links" . }}{{ end }} + {{ if and $show_interests .Params.interests }}

{{ delimit .Params.interests ", " | markdownify | emojify }}

{{ end }} +
+
+ {{ end }} + {{ end }} +
diff --git a/layouts/post/list.html b/layouts/post/list.html new file mode 100644 index 000000000..a69072508 --- /dev/null +++ b/layouts/post/list.html @@ -0,0 +1,4 @@ +{{ define "main" }} +{{ partial "sbol/hero.html" . }} +{{ partial "sbol/post-list.html" . }} +{{ end }} diff --git a/layouts/section/publication.html b/layouts/section/publication.html new file mode 100644 index 000000000..34a9111c8 --- /dev/null +++ b/layouts/section/publication.html @@ -0,0 +1,79 @@ +{{- define "main" -}} + +{{/* Site override: shared hero instead of the theme header; the rest of the theme template is unchanged. */}} +{{ partial "sbol/hero.html" . }} + +
+
+
+ + {{ with .Content }} +
{{ . }}
+ {{ end }} + + {{/* Array of distinct years. */}} + {{ range .Pages.ByDate.Reverse }} + {{ $year := print (.Date.Format "2006") }} + {{ $.Scratch.SetInMap "years" $year $year }} + {{ end }} + +
+
+ +
+
+ +
+
+ +
+
+ +
+ {{ range .Pages.ByDate.Reverse }} + + {{ if .Params.publication_types }} + {{ $.Scratch.Set "pubtype" (index .Params.publication_types 0) }} + {{ else }} + {{ $.Scratch.Set "pubtype" 0 }} + {{ end }} + +
+ {{ if eq $.Params.view 1 }} + {{ partial "li_list" . }} + {{ else if eq $.Params.view 3 }} + {{ partial "li_card" . }} + {{ else if eq $.Params.view 4 }} + {{ partial "li_citation" . }} + {{ else }} + {{ partial "li_compact" . }} + {{ end }} +
+ + {{ end }} +
+ +
+
+
+ +{{- end -}} diff --git a/layouts/shortcodes/card.html b/layouts/shortcodes/card.html index 1a4f2b2a6..a90f01217 100644 --- a/layouts/shortcodes/card.html +++ b/layouts/shortcodes/card.html @@ -2,9 +2,9 @@ {{- $image := .Get "image" -}} {{- $link := .Get "link" -}} - -
- {{ $title }} + +
+ {{ $title }}
-
{{ $title }}
+
{{ $title }}
 diff --git a/layouts/shortcodes/hero-feed.html b/layouts/shortcodes/hero-feed.html index 40ce9e2a9..028f064b9 100644 --- a/layouts/shortcodes/hero-feed.html +++ b/layouts/shortcodes/hero-feed.html @@ -9,7 +9,6 @@ btn2_text — secondary button label btn2_link — secondary button URL - Note: Contains an embedded
@@ -145,10 +31,10 @@

{{ $title }}

{{ $subtitle }}

{{ with $btn1_text }} - {{ . }} + {{ . }} {{ end }} {{ with $btn2_text }} - {{ with $btn2_icon }}{{ end }}{{ . }} + {{ with $btn2_icon }}{{ end }}{{ . }} {{ end }}
@@ -165,22 +51,20 @@

{{ $title }}

{{ if $recent }} {{ range $recent }} -
-
+ +
{{ if eq .Section "blog" }} - Blog + Blog {{ else }} - Announcement + Announcement {{ end }} {{ .Date.Format "Jan 2, 2006" }}
-
- {{ .Title }} -
+
{{ .Title }}
{{ with .Summary }} -
{{ . | plainify | truncate 120 "…" }}
+
{{ . | plainify | htmlUnescape | truncate 120 "…" }}
{{ end }} -
+ {{ end }} {{ else }}

No posts yet — check back soon.

diff --git a/layouts/shortcodes/journey-cards.html b/layouts/shortcodes/journey-cards.html index fd08adcca..b3bb21f27 100644 --- a/layouts/shortcodes/journey-cards.html +++ b/layouts/shortcodes/journey-cards.html @@ -1,64 +1,4 @@ -{{- /* - journey-cards: Responsive 3-column card grid container. - Use with nested {{< card >}} shortcodes. - Embed once per page — the - +{{- /* journey-cards: responsive card row; use with nested {{< card >}} shortcodes. Styles live in assets/scss/sbol/_pages.scss. */ -}}
{{ .Inner }}
diff --git a/layouts/shortcodes/sbol-people.html b/layouts/shortcodes/sbol-people.html new file mode 100644 index 000000000..68f8d0a76 --- /dev/null +++ b/layouts/shortcodes/sbol-people.html @@ -0,0 +1,27 @@ +{{- /* Roster of authors in a user group. Params: group (required), role (show role line, default true), social (default false), sort (weight|name). */ -}} +{{ $group := .Get "group" }} +{{ $showRole := ne (.Get "role") "false" }} +{{ $showSocial := eq (.Get "social") "true" }} +{{ $people := where (where site.Pages "Section" "authors") ".Params.user_groups" "intersect" (slice $group) }} +{{ if eq (.Get "sort") "name" }}{{ $people = sort $people ".Title" }}{{ else }}{{ $people = sort $people ".Params.weight" }}{{ end }} +
+ {{ range $people }} + {{ $avatar := (.Resources.ByType "image").GetMatch "*avatar*" }} + {{ $link := "" }}{{ with site.GetPage (printf "/authors/%s" (path.Base (path.Split .Path).Dir)) }}{{ $link = .RelPermalink }}{{ end }} +
+ {{ if $avatar }} + {{ $img := $avatar.Fill "220x220 Center" }} + Portrait of {{ .Title }} + {{ else }} + {{ $initials := "" }}{{ range first 2 (split .Title " ") }}{{ $initials = printf "%s%s" $initials (substr . 0 1) }}{{ end }} + + {{ end }} +
+ {{ .Title }} + {{ with .Params.organizations }}{{ range . }}{{ .name }}{{ end }}{{ end }} + {{ if and $showRole .Params.role }}{{ .Params.role | markdownify }}{{ end }} + {{ if $showSocial }}{{ end }} +
+
+ {{ end }} +
diff --git a/layouts/sitemap.xml b/layouts/sitemap.xml new file mode 100644 index 000000000..6765a30c7 --- /dev/null +++ b/layouts/sitemap.xml @@ -0,0 +1,16 @@ +{{ printf "" | safeHTML }} + + {{ range .Data.Pages }} + {{/* Tag and category pages are thin duplicates; keep author pages, which carry publication lists. */}} + {{ if and (or (eq .Kind "taxonomy") (eq .Kind "term")) (in (slice "tags" "categories" "publication_types") .Data.Plural) }}{{ continue }}{{ end }} + {{ if or .Params.private .Params.redirect_to }}{{ continue }}{{ end }} + + {{ .Permalink }}{{ if not .Lastmod.IsZero }} + {{ safeHTML ( .Lastmod.Format "2006-01-02T15:04:05-07:00" ) }}{{ end }}{{ with .Sitemap.ChangeFreq }} + {{ . }}{{ end }}{{ if ge .Sitemap.Priority 0.0 }} + {{ .Sitemap.Priority }}{{ end }}{{ if .IsTranslated }}{{ range .Translations }} + {{ end }} + {{ end }} + + {{ end }} + diff --git a/layouts/sponsor-sbol/list.html b/layouts/sponsor-sbol/list.html index 444462016..a03d66680 100644 --- a/layouts/sponsor-sbol/list.html +++ b/layouts/sponsor-sbol/list.html @@ -1,337 +1,55 @@ {{ define "main" }} - {{ $benefits := .Params.benefits | default slice }} {{ $pastSponsors := .Params.past_sponsors | default slice }} {{ $bdacURL := .Params.bdac_url | default "https://bio-design-automation.org" }} - -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ .Params.subtitle }}

- - Support via BDAC - -
-
- -
- - {{/* ── About SBOL ── */}} -
-

SBOL is open and community-powered

-
-
- -

An international standard

-

SBOL is the globally recognized data standard for synthetic biology, used by researchers and engineers across academia and industry to share and exchange biological designs.

-
-
- -

Volunteer-driven

-

The SBOL community is a volunteer organization. There are no membership fees and participation is open to all. The standard remains free and open by design.

-
-
- -

Staying visible takes effort

-

Keeping SBOL present at conferences, active in publications, and relevant to tool developers requires sustained organizational support from the broader community.

-
+{{ partial "sbol/hero.html" . }} +
+
+

SBOL is open and community-powered

+
+

An international standard

SBOL is the globally recognized data standard for synthetic biology, used by researchers and engineers across academia and industry to share and exchange biological designs.

+

Volunteer-driven

The SBOL community is a volunteer organization. There are no membership fees and participation is open to all. The standard remains free and open by design.

+

Staying visible takes effort

Keeping SBOL present at conferences, active in publications, and relevant to tool developers requires sustained organizational support from the broader community.

- {{/* ── How it works ── */}} -
-

How sponsorship works

-

Sponsorship for SBOL flows through the Bio-Design Automation Consortium (BDAC). BDAC is the umbrella organization for the biodesign automation community, and supporting BDAC is supporting SBOL.

-
-
-
1
-
-

Contact BDAC

-

Reach out to the Bio-Design Automation Consortium to discuss supporting the community.

-
-
- -
-
2
-
-

Fund the consortium

-

Your contribution supports the BDAC community, including SBOL standards development, tooling, and outreach.

-
-
- -
-
3
-
-

SBOL recognizes your support

-

BDAC sponsors receive acknowledgment across SBOL's presentations, website, and community communications.

-
-
+
+

How sponsorship works

+

Sponsorship for SBOL flows through the Bio-Design Automation Consortium (BDAC). BDAC is the umbrella organization for the biodesign automation community, and supporting BDAC is supporting SBOL.

+
+
1

Contact BDAC

Reach out to the Bio-Design Automation Consortium to discuss supporting the community.

+
2

Fund the consortium

Your contribution supports the BDAC community, including SBOL standards development, tooling, and outreach.

+
3

SBOL recognizes your support

BDAC sponsors receive acknowledgment across SBOL's presentations, website, and community communications.

- {{/* ── Benefits ── */}} {{ with $benefits }} -
-

What your support means for SBOL

-
+
+

What your support means for SBOL

+
{{ range . }} -
-
-

{{ .title }}

-

{{ .body }}

-
+

{{ .title }}

{{ .body }}

{{ end }}
{{ end }} - {{/* ── Past Sponsors ── */}} {{ with $pastSponsors }} -
-

Organizations that have supported SBOL

-

These organizations previously supported SBOL through the SBOL Industrial Consortium. We are grateful for their contributions to the community.

-
- {{ range . }} -
- {{ .name }} -
- {{ end }} +
+

Organizations that have supported SBOL

+

These organizations previously supported SBOL through the SBOL Industrial Consortium. We are grateful for their contributions to the community.

+
+ {{ range . }}
{{ .name }}
{{ end }}
{{ end }} +
-
{{/* /universal-wrapper */}} - -{{/* ── CTA ── */}} -
-
-

Interested in supporting SBOL?

-

Get in touch with BDAC to learn how your organization can help sustain the synthetic biology open language standard.

- - Visit BDAC   - +
+
+

Interested in supporting SBOL?

+

Get in touch with BDAC to learn how your organization can help sustain the Synthetic Biology Open Language standard.

+ Visit BDAC
- - - {{ end }} diff --git a/layouts/talk/redirect.html b/layouts/talk/redirect.html new file mode 100644 index 000000000..110ab8c78 --- /dev/null +++ b/layouts/talk/redirect.html @@ -0,0 +1,3 @@ +{{ define "main" }} +{{ partial "sbol/redirect.html" . }} +{{ end }} diff --git a/layouts/visual-gallery/list.html b/layouts/visual-gallery/list.html index 1ebe7a3f4..749c8210a 100644 --- a/layouts/visual-gallery/list.html +++ b/layouts/visual-gallery/list.html @@ -2,20 +2,8 @@ {{ $submitURL := .Params.submit_url | default "" }} -{{/* ── Hero ── */}} -
-
-

{{ .Title }}

-

{{ .Params.subtitle }}

- {{ with $submitURL }} - - Recommend an Image - - {{ end }} -
-
- -
+{{ partial "sbol/hero.html" . }} +
{{/* ── Image grid ── */}}
@@ -39,7 +27,7 @@

{{ .Title }}

{{ if $bibRaw }} {{ range (split $bibRaw "\n") }} {{ if findRE `(?i)author\s*=\s*\{` . }} - {{ $credit = . | replaceRE `(?i).*author\s*=\s*\{(.+)\}.*` "$1" | replaceRE ` and others$` "" }} + {{ $credit = . | replaceRE `(?i).*author\s*=\s*\{(.+)\}.*` "$1" | replaceRE ` and others$` "" | replaceRE ` and ` ", " }} {{ end }} {{ if findRE `(?i)\byear\s*=\s*\{` . }} {{ $year = . | replaceRE `(?i).*\byear\s*=\s*\{(\d{4})\}.*` "$1" }} @@ -57,7 +45,7 @@

{{ .Title }}

{{ with $img }}