Repositories list

• biorouter

  Public
  Foundational AI Platform for Biomedical Research Allowing Agents built by the Community

  Rust

  •

  Apache License 2.0

  •00 forks•88 stars•22 issues•00 pull requests•Updated Jun 11, 2026Jun 11, 2026

• biorouter-landing

  Public
  The Landing Page of UCSF BioRouter

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 11, 2026Jun 11, 2026

• biorouter-skills

  Public
  BioRouter skills collection

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 10, 2026Jun 10, 2026

• PlaywrightAgent

  Public
  BioRouter extension (.brxt) wrapping Microsoft's @playwright/mcp browser-automation MCP server.

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 13, 2026May 13, 2026

• SPOKEAgent

  Public
  MCP server for SPOKE biomedical knowledge graph

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 13, 2026May 13, 2026

• UCSFOMOPAgent

  Public
  MCP server for UCSF OMOP clinical database

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 6, 2026May 6, 2026

• CDWAgent

  Public
  MCP server for a de-identified Epic Caboodle Clinical Data Warehouse (SQL Server, read-only). BioRouter extension, sibling of UCSFOMOPAgent.

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 6, 2026May 6, 2026

• baranzinilab.github.io

  Public
  Redirects to the Baranzini Lab UCSF main website

  CSS

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• tkoi

  Public
  Transcriptomic Knowledge-Graph Omics Integration for Human Pathway Analysis

  R

  •

  Other

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• spoke-cli

  Public
  A command-line interface for querying the SPOKE biomedical knowledge graph via Neo4j/Cypher.

  Rust

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• ucsfomop-cli

  Public
  UCSF OMOP CLI

  Rust

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 7, 2026Apr 7, 2026

• tKOIAgent

  Public
  Transcriptomic Knowledge Graph Integration Agent - Contextualize RNAseq studies using biomedical knowledge graphs

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• spoke_genelab

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •66 forks•99 stars•00 issues•00 pull requests•Updated Mar 20, 2026Mar 20, 2026

• ML3DgenomeHeight

  Public
  Machine learning reveals 3D regulatory mechanisms for height-associated haplotypes

  Jupyter Notebook

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 6, 2026Mar 6, 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

  •00 forks•33 stars•11 issue•00 pull requests•Updated Feb 24, 2026Feb 24, 2026

• fMedCP

  Public
  Functional interface with MedCP, using the Claude API key and the MedCP MCP tools

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 2, 2026Feb 2, 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

  •66 forks•00 stars•00 issues•00 pull requests•Updated Jan 6, 2026Jan 6, 2026

• MSConsole

  Public
  An AI-powered console for accessing UCSF MSBase database

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 5, 2026Jan 5, 2026

• ssdr

  Public
  Statistical Software Development in R (SSDR)

  Batchfile

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 10, 2025Nov 10, 2025

• iMSMS_study

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 24, 2025Oct 24, 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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 27, 2025Mar 27, 2025

• translator_summarization

  Public
  Python

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 16, 2024Nov 16, 2024

• versa_kg_rag_documentation

  Public
  Jupyter Notebook

  •11 fork•77 stars•00 issues•00 pull requests•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-graph+ 17

  bioinformaticsbiomedical-informaticsknowledge-graphllamagptknowledge-basecontext-awarebioinformatics-algorithmsbiomedical-applicationsrag+ 10

  Jupyter Notebook

  •

  Apache License 2.0

  •112112 forks•939939 stars•66 issues•22 pull requests•Updated Nov 9, 2024Nov 9, 2024

• Ocrelizumab_vs_rituximab

  Public
  Repo for LLM

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 29, 2024Oct 29, 2024

• Biothings4SPOKE

  Public
  Batchfile

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 9, 2024Oct 9, 2024

• SpokeSigv2

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Sep 23, 2024Sep 23, 2024

• iMSMS_metabolomics

  Public
  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 27, 2024Aug 27, 2024

• app_patient_profile_imsms

  Public
  Python

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 24, 2024Mar 24, 2024

• metapath_dwpc_analysis

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 22, 2024Mar 22, 2024