From 0ba9e427cf4c0f44bfbaec5a57f13e78dba28226 Mon Sep 17 00:00:00 2001
From: Carolus Vitalis
Date: Tue, 18 Aug 2026 09:27:25 -0600
Subject: [PATCH 1/5] Design consistency
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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?
-
-
-
-
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?
-
-
-
-
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?
-
-
-
-
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
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----
-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
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----
-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
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--- a/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105329.md
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----
-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
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--- a/.history/hugo_themes/content/DataModel-Libraries/_index_20200921105649.md
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----
-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
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----
-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
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----
-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
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--- a/.history/hugo_themes/content/DataModel-Specification/_index_20201123170921.md
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----
-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?
-
-
-
-
\ 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
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--- a/.history/hugo_themes/content/sbol-industrial/_index_20201203130618.md
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----
-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
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--- a/.history/hugo_themes/content/sbol-visual-ontology/_index_20201211132740.md
+++ /dev/null
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----
-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 }}
-