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    Repositories list

    109 repositories

    • coPI.science

      Public
      Python
      •0•4•14•1•Updated Oct 21, 2026Oct 21, 2026

    • sulab.org

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •9•0•0•1•Updated Oct 18, 2026Oct 18, 2026

    • DrugMechDB-agentic

      Public
      Agent-assisted curation of DrugMechDB drug–disease mechanism paths, with per-edge evidence.
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•1•43•1•Updated Sep 15, 2026Sep 15, 2026

    • ECAA-workflow

      Public
      Rust
      •
      Apache License 2.0
      •0•3•2•0•Updated Aug 5, 2026Aug 5, 2026

    • OKN-WOBD

      Public
      Python
      •2•2•4•0•Updated Jul 21, 2026Jul 21, 2026

    • lotz-ivd

      Public
      IVD single-cell atlas: cell types and states in the human intervertebral disc across aging and degeneration
      Jupyter Notebook
      •0•1•0•0•Updated Jun 23, 2026Jun 23, 2026

    • claude-ro-crate-skill

      Public
      Claude Code skill to create RO-Crate packages for recording workflows, execution, and provenance
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 23, 2026Jun 23, 2026

    • DrugMechDB

      Public
      A database of paths that represent the mechanism of action from a drug to a disease in an indication.
      ncats-translator
      ncats-translator
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •24•79•9•3•Updated Jun 3, 2026Jun 3, 2026

    • TSRI-CBB

      Public
      This is the Github repository for The Scripps Research Institute Computational Biology and Bioinformatics (CBB) community and affiliated core track for graduate…
      HTML
      •1•9•1•0•Updated May 25, 2026May 25, 2026

    • agentic-bte

      Public
      Biomedical research platform combining LLMs with BioThings Explorer knowledge graphs. Features MCP Server and LangGraph multi-agent workflows for drug discovery…
      Python
      •
      MIT License
      •1•1•0•0•Updated Jan 30, 2026Jan 30, 2026

    • DBR-X

      Public
      DBR-X: Drug-Based Reasoning Explainer
      Jupyter Notebook
      •0•3•0•0•Updated Jan 14, 2026Jan 14, 2026

    • Applied-Bioinformatics-2025

      Public
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 4, 2025Mar 4, 2025

    • KnowledgeGraphEmbedding

      Public
      Jupyter Notebook
      •
      MIT License
      •270•2•0•0•Updated Aug 9, 2024Aug 9, 2024

    • CBRonMRN

      Public
      Python
      •0•0•0•0•Updated Feb 21, 2024Feb 21, 2024

    • WikidataIntegrator

      Public
      A Wikidata Python module integrating the MediaWiki API and the Wikidata SPARQL endpoint
      Python
      •
      MIT License
      •47•261•11•3•Updated Nov 14, 2023Nov 14, 2023

    • DMDB_Analysis

      Public
      Jupyter Notebook
      •2•0•0•2•Updated Apr 20, 2023Apr 20, 2023

    • DrugMechDB-1

      Public
      A database of paths that represent the mechanism of action from a drug to a disease in an indication.
      Jupyter Notebook
      •
      MIT License
      •24•0•0•0•Updated Apr 13, 2023Apr 13, 2023

    • path_plots

      Public
      A simple repo to quickly plot paths in a newtorkx graph
      Python
      •3•0•0•0•Updated Mar 23, 2023Mar 23, 2023

    • scheduled-bots

      Public
      GeneWiki Scheduled Bots
      Jupyter Notebook
      •
      MIT License
      •15•9•15•2•Updated Feb 17, 2023Feb 17, 2023

    • GeneWikiCentral

      Public
      GeneWiki Organization
      JavaScript
      •
      MIT License
      •2•5•74•9•Updated Feb 2, 2023Feb 2, 2023

    • mark2cure

      Public
      Mark2Cure allows anyone that can read English, regardless of background, to help in the process of biomedical discovery.
      Python
      •8•14•35•50•Updated Jan 11, 2023Jan 11, 2023

    • Lit2Hybrid

      Public
      Vue
      •0•0•0•26•Updated Jan 6, 2023Jan 6, 2023

    • genewikiworld

      Public
      Generate a network of all items we care about, and some we don't....
      Jupyter Notebook
      •
      Apache License 2.0
      •2•6•2•6•Updated Dec 8, 2022Dec 8, 2022

    • Wikidata-phenomizer

      Public
      Incorporate wikidata statements into phenomizer
      Jupyter Notebook
      •
      MIT License
      •1•3•0•22•Updated Dec 8, 2022Dec 8, 2022

    • wikidata-translate

      Public
      Python
      •2•0•0•6•Updated Dec 8, 2022Dec 8, 2022

    • Krusty

      Public
      neo4j <-> wikibase import/export tool
      neo4jwikibaseimport-export
      neo4jwikibaseimport-export
      Python
      •2•2•9•4•Updated Dec 8, 2022Dec 8, 2022

    • garbanzo

      Public
      Wikidata Semantic Query API
      Python
      •6•2•1•7•Updated Dec 7, 2022Dec 7, 2022

    • bioshovel

      Public
      Biological text mining tool.
      Python
      •1•3•0•1•Updated Oct 20, 2022Oct 20, 2022

    • Applied-Bioinformatics

      Public
      Student course material for the Applied Bioinformatics course at Scripps Research
      Jupyter Notebook
      •31•39•2•0•Updated Oct 11, 2022Oct 11, 2022

    • dataset-repository-selector

      Public
      A tool to help biologists make their datasets more findable, accessible, and schema.org-compliant
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Sep 21, 2022Sep 21, 2022
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