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    45 repositories

    • BioRouter

      Public
      Foundational AI Platform for Biomedical Research Allowing Agents built by the Community
      Rust
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • biorouter-landing

      Public
      The Landing Page of UCSF BioRouter
      HTML
      •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • CDW_MedCP

      Public
      MCP server connecting LLMs to a de-identified Epic Caboodle Clinical Data Warehouse via SQL Server
      mcpclinical-dataepic-caboodle
      Python
      •0•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • MedCP

      Public
      An MCP server that integrates electronic health record databases and a large-scale heterogeneous knowledge graph for rapid clinical record query and fast biomed…
      Python
      •
      MIT License
      •0•1•1•0•Updated Feb 24, 2026Feb 24, 2026

    • MSBaseAgent

      Public
      MCP server for UCSF BioRouter to query the MSBase database
      Python
      •0•0•0•0•Updated Feb 14, 2026Feb 14, 2026

    • SPOKEAgent

      Public
      MCP server for SPOKE biomedical knowledge graph
      Python
      •0•1•0•0•Updated Feb 14, 2026Feb 14, 2026

    • UCSFOMOPAgent

      Public
      MCP server for UCSF OMOP clinical database
      Python
      •0•0•0•0•Updated Feb 14, 2026Feb 14, 2026

    • fMedCP

      Public
      Functional interface with MedCP, using the Claude API key and the MedCP MCP tools
      Python
      •0•0•0•0•Updated Feb 2, 2026Feb 2, 2026

    • spoke_genelab

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•7•0•0•Updated Jan 30, 2026Jan 30, 2026

    • baranzinilab.github.io

      Public
      Redirects to the Baranzini Lab UCSF main website
      HTML
      •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • mcp-proto-okn

      Public
      A Model Context Protocol (MCP) server that provides tools for querying SPARQL endpoints, with specialized support for NSF-funded Proto-OKN (Prototype Open Knowl…
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•0•0•0•Updated Jan 6, 2026Jan 6, 2026

    • MSConsole

      Public
      An AI-powered console for accessing UCSF MSBase database
      Python
      •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

    • ssdr

      Public
      Statistical Software Development in R (SSDR)
      Batchfile
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

    • tkoi

      Public
      Transcriptomic Knowledge-Graph Omics Integration for Human Pathway Analysis
      R
      •
      Other
      •0•1•0•0•Updated Oct 25, 2025Oct 25, 2025

    • iMSMS_study

      Public
      HTML
      •0•0•0•0•Updated Oct 24, 2025Oct 24, 2025

    • ML3DgenomeHeight

      Public
      Machine learning reveals 3D regulatory mechanisms for height-associated haplotypes
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Sep 10, 2025Sep 10, 2025

    • MS_note_concept_ML

      Public
      This repository contains code for predicting Multiple Sclerosis (MS) diagnosis using clinical concepts extracted from electronic health records (EHR) notes and …
      Jupyter Notebook
      •0•0•0•0•Updated Mar 27, 2025Mar 27, 2025

    • translator_summarization

      Public
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Nov 16, 2024Nov 16, 2024

    • versa_kg_rag_documentation

      Public
      Jupyter Notebook
      •0•6•0•0•Updated Nov 13, 2024Nov 13, 2024

    • KG_RAG

      Public
      Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
      bioinformaticsbiomedical-informaticsknowledge-graphllamagptknowledge-basecontext-awarebioinformatics-algorithmsbiomedical-applicationsrag
      Jupyter Notebook
      •
      Apache License 2.0
      •111•934•5•1•Updated Nov 9, 2024Nov 9, 2024

    • Ocrelizumab_vs_rituximab

      Public
      Repo for LLM
      Python
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • Biothings4SPOKE

      Public
      Batchfile
      •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • SpokeSigv2

      Public
      Python
      •0•1•0•0•Updated Sep 23, 2024Sep 23, 2024

    • iMSMS_metabolomics

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Aug 27, 2024Aug 27, 2024

    • app_patient_profile_imsms

      Public
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Mar 24, 2024Mar 24, 2024

    • metapath_dwpc_analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • spoke_api_demo

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •1•1•0•0•Updated Mar 21, 2024Mar 21, 2024

    • IMSGC_federated

      Public
      CLI python scripts for federated analysis
      Python
      •0•0•0•0•Updated Jan 31, 2024Jan 31, 2024

    • spoke_35M

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 21, 2023Sep 21, 2023

    • EHR-Ranges

      Public
      ipynb for generating EHR lab ranges from patient data
      Jupyter Notebook
      •0•0•0•0•Updated Jun 28, 2023Jun 28, 2023