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    53 repositories

    • biocypher

      Public
      A unifying framework for biomedical research knowledge graphs
      bioinformaticsframeworksql
      bioinformaticsframeworksqlneo4jrdfpostgresqlontologyknowledge-graphbiomedicalrdfs
      Python
      •
      Apache License 2.0
      •51•305•178•11•Updated May 20, 2026May 20, 2026

    • karenina

      Public
      Backend library for benchmarking LLMs through templates
      Python
      •3•6•18•0•Updated May 20, 2026May 20, 2026

    • biotope

      Public
      The repository for creating a command line integration for biocypher software components
      Python
      •
      MIT License
      •3•3•8•1•Updated May 19, 2026May 19, 2026

    • biochatter-paper

      Public
      The Manubot repository for writing the BioChatter paper
      HTML
      •
      Creative Commons Attribution 4.0 International
      •7•2•0•0•Updated May 19, 2026May 19, 2026

    • iggytop

      Public
      Pipeline for harmonising immunological receptor–epitope interactions
      knowledge-graphimmunologyt-cell-receptor
      knowledge-graphimmunologyt-cell-receptorb-cell-receptorbiocypherb-cell-epitopet-cell-epitope
      Python
      •
      MIT License
      •1•7•4•0•Updated May 7, 2026May 7, 2026

    • open-targets

      Public
      Python
      •
      MIT License
      •8•15•14•0•Updated Apr 29, 2026Apr 29, 2026

    • documentation

      Public
      This is the unified documentation of BioCypher ecosystem libraries
      2•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • karenina-gui

      Public
      GUI implementation of the karenina testing framework in React
      TypeScript
      •0•0•2•0•Updated Apr 16, 2026Apr 16, 2026

    • karenina-server

      Public
      FastAPI server for karenina integration into web apps
      Python
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • biochatter

      Public
      Backend library for conversational AI in biomedicine
      chatbotknowledge-graphvector-database
      chatbotknowledge-graphvector-databasellmretrieval-augmented-generationbiocypher
      Jupyter Notebook
      •
      Apache License 2.0
      •57•208•104•6•Updated Apr 15, 2026Apr 15, 2026

    • omnipath-secondary-adapter

      Public
      BioCypher adapter to retrieve data from Omnipath database (Networks, Intercell, Complexes, EnzymePTM and Annotations).
      neo4jknowledge-graphbiological-networks
      neo4jknowledge-graphbiological-networksbiocypherontoweaver
      Jupyter Notebook
      •
      MIT License
      •5•3•9•0•Updated Apr 10, 2026Apr 10, 2026

    • sys-bio-kgs

      Public
      Python
      •2•2•7•0•Updated Apr 7, 2026Apr 7, 2026

    • pole

      Public
      Demo data repository (crime statistics)
      Python
      •
      MIT License
      •4•4•2•0•Updated Mar 18, 2026Mar 18, 2026

    • collectri

      Public
      Python
      •
      MIT License
      •3•2•0•0•Updated Jan 28, 2026Jan 28, 2026

    • biochatter-light

      Public
      The light frontend for BioChatter, in pure Python
      Python
      •
      MIT License
      •14•54•19•1•Updated Jan 22, 2026Jan 22, 2026

    • schema-helper-web

      Public
      Aids in building biocypher schema
      JavaScript
      •0•0•2•0•Updated Jan 21, 2026Jan 21, 2026

    • project-template

      Public template
      Template for creating a BioCypher-driven knowledge graph
      Python
      •
      MIT License
      •12•13•2•1•Updated Jan 15, 2026Jan 15, 2026

    • karenina-mcp

      Public
      MCP tooling to interact with the Karenina evaluation framework (experimental)
      Python
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • .github

      Public
      0•0•0•0•Updated Dec 7, 2025Dec 7, 2025

    • biocypher-cookiecutter-template

      Public
      Cookiecutter template to set up a BioCypher project
      Python
      •0•0•1•0•Updated Nov 26, 2025Nov 26, 2025

    • igvf-catalog

      Public
      Catalog API for the IGVF project (fork from the original at IGVF-DACC)
      Python
      •
      MIT License
      •4•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • biocypher-mcp

      Public
      Python
      •1•2•1•0•Updated Nov 20, 2025Nov 20, 2025

    • alfredo

      Public
      Alfredo provides a LangGraph-based agentic scaffold that combines planning, execution, and verification into a cohesive agent framework. Built with extensibilit…
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 24, 2025Oct 24, 2025

    • biocage

      Public
      Fast, secure, and practical Python sandbox designed specifically for safely executing code generated by LLMs
      Python
      •
      MIT License
      •0•3•0•0•Updated Sep 18, 2025Sep 18, 2025

    • governance

      Public
      Shallow repository to organise biocypher governance, mainly by issues and discussions.
      0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • mcp-template

      Public template
      More minimal BioCypher pipeline template for use with the BioCypher MCP server
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

    • biogather

      Public
      Placeholder
      Python
      •
      MIT License
      •1•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • metalinks

      Public
      Python
      •
      GNU General Public License v3.0
      •2•8•5•0•Updated Feb 7, 2025Feb 7, 2025

    • DFG528753569

      Public
      Home of the software sustainability project under No. DFG 528753569
      0•0•25•0•Updated Jan 22, 2025Jan 22, 2025

    • biochatter-next

      Public
      The advanced implementation for BioChatter, using Next.js
      TypeScript
      •
      MIT License
      •9•18•10•1•Updated Jan 17, 2025Jan 17, 2025
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