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@calacademy-research

California Academy of Sciences, Institute for Biodiversity Science & Sustainability

Public repositories for IBSS projects

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  1. minibar minibar Public

    Dual barcode and primer demultiplexing for MinION sequenced reads

    Python 42 7

  2. antcat antcat Public

    World Catalog of Ants

    Ruby 21 9

  3. antweb antweb Public

    AntWeb is the world's largest online database of images, specimen records, and natural history information on ants. It is community driven and open to contribution from anyone with specimen records…

    Java 9 5

  4. RAxML_Astral_trees RAxML_Astral_trees Public

    This project generates Astral-III species trees from gene trees generated from RAxML using UCE data generated by the Phyluce pipeline. Then runs an Astral III analysis.

    Shell 8 2

  5. BLATq BLATq Public

    blatq is a modified version of BLAT—The BLAST-Like Alignment Tool to allow direct use of fastq files

    C 5 1

  6. COMB COMB Public

    C O M B

    R 5 6

Repositories

Showing 10 of 67 repositories
  • cas_bot_georeference Public

    The python GeoReferencer which defines a BELS --> Geolocate --> GVS pipeline to assign lat/long coordinates + error radii.

    calacademy-research/cas_bot_georeference's past year of commit activity
    Python 1 0 0 0 Updated Oct 1, 2026
  • picturae_csv_parser Public

    stand alone program , used to QC csvs ready for specify import from picturae, nfn and digileap supplied data

    calacademy-research/picturae_csv_parser's past year of commit activity
    Python 2 0 0 0 Updated Oct 1, 2026
  • web-asset-importer Public

    Image client used in conjunction with web-asset-server to process images/data into image server, and specify databases.

    calacademy-research/web-asset-importer's past year of commit activity
    Python 1 2 1 3 Updated Sep 30, 2026
  • expedition-clustering Public

    Expedition Clustering groups California Academy of Sciences botany specimens into inferred expeditions using a reproducible spatiotemporal DBSCAN pipeline.

    calacademy-research/expedition-clustering's past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Sep 28, 2026
  • cas-web-asset-server Public Forked from specify/web-asset-server

    Sample attachment server implementation for Specify.

    calacademy-research/cas-web-asset-server's past year of commit activity
    Python 2 18 0 0 Updated Sep 26, 2026
  • specify7 Public Forked from specify/specify7

    An open-source platform for managing biological and geological collections.

    calacademy-research/specify7's past year of commit activity
    TypeScript 0 GPL-3.0 53 0 0 Updated Sep 23, 2026
  • awesome-specify Public Forked from specify/awesome-specify

    A list of awesome Specify integrations, software, and resources developed by the community.

    calacademy-research/awesome-specify's past year of commit activity
    0 4 0 0 Updated Sep 23, 2026
  • load_analyzer Public
    calacademy-research/load_analyzer's past year of commit activity
    Python 1 GPL-3.0 1 1 0 Updated Sep 23, 2026
  • LabelLlama_CAS Public Forked from rafelafrance/LabelLlama

    Extract information from labels on images of museum specimens. Custom modifications for the California Academy of Sciences..

    calacademy-research/LabelLlama_CAS's past year of commit activity
    Python 1 MIT 1 0 0 Updated Sep 14, 2026
  • galapagos_island_mapper Public
    calacademy-research/galapagos_island_mapper's past year of commit activity
    R 1 1 0 0 Updated Sep 11, 2026
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