bioinformatics mcp servers

tomtommyyuan/spmind

MCP server Claude CodeCodexCursor +2

MCP server "spmind" as configured in tomtommyyuan/spmind. Runs spmind.mcp_stdio with python.

AlterLab-IEU/AlterLab-Academic-Skills

MCP server Claude CodeCodexCursor +2

The fast, Pythonic way to build MCP servers and clients. Runs locally from the fastmcp Python package.

cafferychen777/ChatSpatial

MCP server Claude CodeCodexCursor +2

ChatSpatial: Natural language-driven spatial transcriptomics analysis via Model Context Protocol (MCP) integration. Runs locally from the chatspatial Python package.

ammawla/encode-toolkit

MCP server Claude CodeCodexCursor +2

20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines. Runs locally from the encode-toolkit npm package.

lynnlangit/precision-medicine-mcp

MCP server Claude CodeCodexCursor +2

MCP server "openimagedata" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-openimagedata Python package. Needs 3 environment variables to run.

lynnlangit/precision-medicine-mcp

MCP server Claude CodeCodexCursor +2

MCP server "patient-report" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-patient-report Python package. Needs 3 environment variables to run.

lynnlangit/precision-medicine-mcp

MCP server Claude CodeCodexCursor +2

MCP server "perturbation" as configured in lynnlangit/precision-medicine-mcp. Runs locally from the /Users/lynnlangit/Documents/GitHub/spatial-mcp/servers/mcp-perturbation Python package. Needs 3 environment variables to run.

pascalwhoop/medical-mcps

MCP server Claude CodeCodexCursor +2

MCP server "medical-mcps", hosted remotely at mcp.cloud.curiloo.com, as configured in pascalwhoop/medical-mcps.

pascalwhoop/medical-mcps

MCP server Claude CodeCodexCursor +2

MCP server "local-medical-mcp", hosted remotely at localhost, as configured in pascalwhoop/medical-mcps.

nickzren/opentargets-mcp

MCP server Claude CodeCodexCursor +2

MCP server for Open Targets Platform biomedical data access. Runs locally from the opentargets-mcp Python package.

cyanheads/pubchem-mcp-server

MCP server Claude CodeCodexCursor +2

Search PubChem compounds, properties, safety data, bioactivity, and cross-references. Runs locally from the @cyanheads/pubchem-mcp-server npm package. Needs 1 environment variable to run.

HERRY423/CellTypePilot

MCP server Claude CodeCodexCursor +2

MCP server "celltypepilot" as configured in HERRY423/CellTypePilot. Launched with celltypepilot-mcp.

HERRY423/CellTypePilot

MCP server Claude CodeCodexCursor +2

Anthropic's hosted PubMed server: lets the agent search biomedical literature and read abstracts and citations from PubMed. Remote server at pubmed.mcp.claude.com.

HERRY423/CellTypePilot

MCP server Claude CodeCodexCursor +2

One of Anthropic's hosted health and life-sciences servers (bioRxiv/medRxiv preprints, ClinicalTrials.gov, ChEMBL and others): lets the agent search and read that source directly. Remote server at hcls.mcp.claude.com.

cyanheads/protein-mcp-server

MCP server Claude CodeCodexCursor +2

MCP Server for 3D protein structural data retrieval & analysis from RCSB PDB, PDBe, and UniProt. Runs locally from the protein-mcp-server npm package. Needs 1 environment variable to run.

smaniches/alphafold-sovereign-mcp

MCP server Claude CodeCodexCursor +2

MCP server wrapping AlphaFold DB and 8 other biomedical data sources, with a local SQLite knowledge graph. Runs locally from the alphafold-sovereign-mcp Python package.

smaniches/alphafold-sovereign-mcp

MCP server Claude CodeCodexCursor +2

MCP server wrapping AlphaFold DB and 8 other biomedical data sources, with a local SQLite knowledge graph. Runs locally from the alphafold-sovereign-mcp Python package.

cyanheads/brapi-mcp-server

MCP server Claude CodeCodexCursor +2

Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more. Runs locally from the @cyanheads/brapi-mcp-server npm package. Needs 4 environment variables to run.

musharna/plant-genomics-mcp

MCP server Claude CodeCodexCursor +2

Plant genomics MCP — 50 tools across 23 live backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, Planteome, PlantCyc/PMN, g:Profiler, AlphaFold, PDBe, InterPro, JASPAR, ThaleMine, PANTHER, OrthoDB, AraGWAS, 1001 Genomes, BLAST, Gramene, KEGG, STRING, ATTED-II, BAR) for Claude Code. Runs locally from the…

musharna/plant-genomics-mcp

MCP server Claude CodeCodexCursor +2

Plant genomics MCP — 50 tools across 23 live backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, Planteome, PlantCyc/PMN, g:Profiler, AlphaFold, PDBe, InterPro, JASPAR, ThaleMine, PANTHER, OrthoDB, AraGWAS, 1001 Genomes, BLAST, Gramene, KEGG, STRING, ATTED-II, BAR) for Claude Code. Runs locally from the…

smaniches/uniprot-mcp

MCP server Claude CodeCodexCursor +2

Verifiable, release-aware protein evidence workflows over UniProt and linked scientific sources. Runs locally from the uniprot-mcp-server Python package.

smaniches/uniprot-mcp

MCP server Claude CodeCodexCursor +2

Verifiable, release-aware protein evidence workflows over UniProt and linked scientific sources. Runs locally from the uniprot-mcp-server Python package.

cyanheads/ensembl-mcp-server

MCP server Claude CodeCodexCursor +2

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST. Runs locally from the @cyanheads/ensembl-mcp-server npm package. Needs 2 environment variables to run.

berntpopp/genefoundry-router

MCP server Claude CodeCodexCursor +2

MCP gateway federating 21 biomedical MCP servers behind one endpoint: gnomAD, ClinVar, HPO, VEP. Remote server at genefoundry.org.