How do I install BioMCP TS?

Copy the stdio config for Cursor, Claude Desktop, Claude Code, or VS Code on this page. It uses the publisher's install, not a PlugMCP proxy.

Does BioMCP TS need an API key?

The publisher lists these environment variables: ANALYSIS_BIOWASM, ANALYSIS_R, DB_TYPE, NCBI_API_KEY, S2_API_KEY, OPENFDA_API_KEY, ONCOKB_TOKEN, DISGENET_API_KEY.

What transport does BioMCP TS use?

BioMCP TS runs locally over stdio.

When was BioMCP TS last checked?

Last checked 2026-11-10. Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.

BioMCP TS MCP server

BioMCP

BioMCP-TS architecture

Highlights

Democratizing agentic access to bioinformatics and biopharmaceutical databases and analyses.

Section-based federated access to 50+ bioinformatics, pharmaceutical, and patent databases
Optional toolboxes for local database curation and dependency-free analysis with Bioconductor and SAM/BED/BCFtools — no R installation, C toolchain, or containers
Concrete example vignettes, developed fully in the open

Install

npx -y biomcp doctor   # diagnose a machine: Node gate, config health, feature gates, peer deps
npx biomcp             # zero-config stdio MCP server (this is what MCP clients run); Node >= 22.13

Setup is guided in docs/AGENT-INSTALL.md — a one-minute start, copy-paste config entries for Claude Desktop, Claude Code, Codex, and OpenCode (one canonical pinned command covering every feature), biomcp doctor as the single troubleshooting entry point, and agent-friendly paths for API keys and optional features.

Multiple agents on one machine: biomcp enforces arXiv's Terms-of-Use rate limit (1 request / 3 s) per process. When running multiple biomcp MCP instances on one machine (e.g., one stdio instance per agent), rate limits are not coordinated across processes, and arXiv's TOU applies to all your machines in aggregate. For multi-agent single-machine deployments, run a single shared biomcp serve daemon (see docs/SELF-HOSTING.md) so all agents share one process and one global rate limiter.

Available Tools

Full tool schemas (params, enums, defaults) live in src/server/README.md.

Gene (7)

Tool	Description
`gene_search`	Search genes by symbol, name, or keyword with chromosome filter
`gene_get`	Get detailed gene info by HGNC symbol with optional sections (core, pathways, protein, ontology, go, interactions, expression, protein_atlas, constraint, druggability, dosage_sensitivity, clinical_evidence, disease_associations, diseases, funding). Set `smart=true` to auto-resolve gene aliases (e.g., "HER2" → "ERBB2")
`gene_diseases`	Get diseases associated with a gene (DisGeNET / OpenTargets)
`gene_drugs`	Find drugs targeting a gene (OpenTargets; envelope `{ results, warnings?, errors? }` — OpenTargets failures and unresolved genes ride in `errors[]`, never as inline rows)
`gene_trials`	Find clinical trials for a gene
`gene_articles`	Find articles about a gene (federated across PubMed, EuropePMC, Semantic Scholar, arXiv, PubTator, LitSense; envelope `{ results, warnings?, errors? }` — per-backend failures ride in `errors`)
`gene_enrich`	Pathway enrichment analysis for a gene list (Reactome)

Variant (4)

Tool	Description
`variant_search`	Search variants by rsid, HGVS, gene, ClinVar significance, frequency, CADD
`variant_get`	Get detailed variant info with optional sections (frequency, predictions, clinical; `alphagenome_scores` currently returns an unavailability error pending reimplementation)
`variant_oncokb`	Get OncoKB cancer variant annotations (requires `ONCOKB_TOKEN`)
`variant_trials`	Find clinical trials for a variant

Drug (3)

Tool	Description
`drug_search`	Search drugs by name, mechanism, or keyword (envelope `{ results, hint? }` — when nothing matches, `hint` points mechanism/target queries at gene_drugs)
`drug_get`	Get detailed drug info with optional sections (us_regulatory, who_regulatory, safety, targets, indications, adverse_events — FDA FAERS reactions ranked by report count; WHO PQ listing lookup, ~650 global-health priority products)
`drug_trials`	Find clinical trials for a drug

Disease (4)

Tool	Description
`disease_search`	Search diseases by name, phenotype, or keyword (envelope `{ results, warnings?, errors? }`)
`disease_get`	Get detailed disease info by ID (DOID, MONDO, OMIM, etc.) with optional sections (gene_associations, phenotypes, pathways)
`disease_drugs`	Get drugs for a disease (OpenTargets; envelope `{ results, warnings?, errors? }` — OpenTargets failures and unresolved diseases ride in `errors[]`, never as inline rows)
`disease_trials`	Get clinical trials for a disease (ClinicalTrials.gov; envelope `{ results, warnings?, errors? }`)

Article (4)

Tool	Description
`article_search`	Federated literature search across PubMed, EuropePMC, Semantic Scholar, arXiv, PubTator, and LitSense with optional date range filtering; `source: "preprint_only"` switches to bioRxiv+medRxiv preprints only (abstracts, citation counts, date filtering). Result records carry `journal_issn`
`article_get`	Get detailed article info by identifier (PMID, PMCID, DOI, or bioRxiv/medRxiv preprint DOI) with optional sections: `fulltext` (the complete article text when freely readable in PMC/Europe PMC — open-access AND free-to-read articles; by default (`fulltext_output="file"`) written to a server-side markdown file with the reply carrying `file_path` + an outline of headings with line numbers and char counts for selective Read/Grep, keeping body text out of the agent context; `fulltext_output="inline"` returns capped text sections via `fulltext_max_chars`, default 40000), `oa` (open-access/license metadata and links: status open_access/free_to_read/paywalled/not_in_pmc/unknown, license, pmc/pdf/doi links), `annotations`, `graph` (citation graph), `citation` (fast/full citation data; Europe PMC citations for preprints). `all` excludes fulltext. Preprint records include all versions, license, category, funders, JATS full-text URL (link only — use `preprint_fulltext` for the text), and published-version mapping. The record carries `journal_issn`
`preprint_fulltext`	On-demand bioRxiv/medRxiv preprint full text (JATS XML parsed to sections), by preprint DOI with optional version (default: latest). Strictly on-demand (never during search), downloads are paced (≥3 s spacing), cached per (doi, version) — JATS per version is immutable — and license-aware (`cc_by` → `cc by` + CC URL on every reply; the per-article license governs reuse). www.biorxiv.org rate-limits aggressively: on a 429/Cloudflare verdict all downloads pause ≥60 s (Retry-After honored) and calls during the cooldown get an honest `rate_limited` envelope with `retry_after_sec`; cached copies keep serving instantly. `output="file"` (default) writes a server-side markdown file (`file_path` + outline); `output="inline"` returns capped sections (). Corpus-scale: use the bioRxiv/medRxiv monthly S3 buckets ()

Trial (2)

Tool	Description
`trial_search`	Search clinical trials by condition, intervention, status, or phase. Cursor-based pagination via `page_token`
`trial_get`	Get detailed trial info by NCT ID with optional sections (eligibility, locations, outcomes)

Utility (2)

Tool	Description
`discover`	Free-text concept resolution across all entity types
`batch_get`	Retrieve multiple entities in parallel

Structural Biology (1)

Tool	Description
`pdb`	Search PDB structures, get entry metadata with optional sections (polymer entities, ligands, assembly, experiment, citation), and download structure files (mmCIF/PDB)

Patents (2)

Tool Description

patent_search Search patents worldwide (US, EP, WO, JP, 100+ authorities) with assignee/inventor/CPC/status/date filters and relevance ranking (sort_by). Quote exact multi-word concepts (e.g. "flow cytometry"). Foundational prior art is auto-discovered via co-citation mining (seminal_prior_art; disable with seminal: false). Default backends: USPTO Public Search full-text (US, keyless, relevance-ranked) + EPO OPS (worldwide, keyed); uspto_odp (US bibliographic metadata) and google_patents (best-effort) available via source

patent_get Get patent details by publication number with sections: abstract, claims (US fulltext via USPTO Public Search; EP/WO via EPO OPS when configured, otherwise Google Patents pages), citations (forward + backward), family, classifications

Tool	Description
`patent_search`	Search patents worldwide (US, EP, WO, JP, 100+ authorities) with assignee/inventor/CPC/status/date filters and relevance ranking (`sort_by`). Quote exact multi-word concepts (e.g. "flow cytometry"). Foundational prior art is auto-discovered via co-citation mining (`seminal_prior_art`; disable with `seminal: false`). Default backends: USPTO Public Search full-text (US, keyless, relevance-ranked) + EPO OPS (worldwide, keyed); uspto_odp (US bibliographic metadata) and google_patents (best-effort) available via `source`
`patent_get`	Get patent details by publication number with sections: abstract, claims (US fulltext via USPTO Public Search; EP/WO via EPO OPS when configured, otherwise Google Patents pages), citations (forward + backward), family, classifications

GEO (2)

Tool	Description
`geo_search`	Search NCBI GEO for functional genomics studies (expression microarrays, RNA-seq, single-cell series) by entry type (GSE/GSM/GPL/GDS) and organism; results carry cross-links (bioproject, pubmed_ids; sra_project when NCBI links the SRA study — otherwise geo_get's sra field) for chaining
`geo_get`	Get the full SOFT record for a GEO series/sample/platform: summary, organisms, sample preview (≤20), supplementary file URLs, and cross-references; optionally download the first supplementary file. GDS curated DataSets return structured guidance (`{ accession, guidance, see_also: { series, sample } }`) pointing at the underlying GSE/GSM instead of a record

SRA (2)

Tool	Description
`sra_search`	Search NCBI's Sequence Read Archive for sequencing experiments and runs by free text, accession, or field syntax; returns experiment/study/sample accessions with library strategy and run counts
`sra_get`	Get full details for an SRA accession: run (SRR/ERR/DRR — instrument, spots, bases, size), experiment (SRX/ERX/DRX — library design), study (SRP/ERP/DRP — experiment list), or sample (SRS/ERS/DRS); NCBI SRA indexes NCBI, ENA, and DDBJ accessions alike

GenBank (3)

Tool	Description
`genbank_search`	Search NCBI nucleotide records (GenBank/RefSeq/INSDC) by plain terms, accession, or field syntax; results include accession.version, definition, length, organism, topology
`genbank_get`	Fetch a GenBank/RefSeq record as GenBank flat file or FASTA; whole records capped at 2 Mb — larger records require a `seq_start`/`seq_stop` region (up to 10 Mb, reverse-strand via `strand=2`)
`genbank_genes`	Map a GenBank/RefSeq accession to its NCBI Gene IDs (elink nuccore→gene) for bridging into gene tools

GTEx (2)

Tool	Description
`gtex_expression`	Get median gene expression across GTEx tissues (Analysis v10, 54 tissue sites, TPM, highest first); accepts HGNC symbol or Ensembl gene ID, with optional single-tissue filter
`gtex_eqtl`	Get significant cis-eQTL associations for a gene in a specific GTEx tissue (v10): variant_id, p_value, NES, slope, sorted by ascending p-value

Ensembl (4)

Tool	Description
`ensembl_lookup`	Resolve a gene in Ensembl terms for any of ~356 species: stable ID (+version), symbol, coordinates on the current assembly, canonical transcript; `expand=true` adds transcripts with translation/protein IDs
`ensembl_homology`	Find orthologues/paralogues across species via Ensembl Compara — target stable IDs, taxonomy level, percent identity, sorted by identity; filter with `target_species`/`target_taxon`
`ensembl_consequence`	Compute variant consequences on demand via Ensembl VEP for NOVEL variants and non-human species: most severe consequence, per-transcript effects (SIFT/PolyPhen), co-located ClinVar/COSMIC/gnomAD data. Known human variants get deeper pre-computed scores via `variant_get`; prefer HGVS input over rsIDs for precision
`ensembl_region`	Query genes/transcripts/known variants in a genomic interval (`chr:start-end`) on the current assembly — locus triage

R Analysis (4, optional — `ANALYSIS_R=1`)

Tool	Description
`analysis_r_deseq2`	Differential expression for RNA-seq counts with Bioconductor DESeq2 (negative binomial, independent filtering, optional LFC shrinkage) in sandboxed WebAssembly R. Inputs: integer count matrix + sample metadata + design formula; output: markdown table of top genes by adjusted p-value with summary (`format="json"`, `include_full=true` for full base64(gzip(TSV)) table)
`analysis_r_edger`	Differential expression with edgeR — TMM normalization, empirical-Bayes dispersion, quasi-likelihood F-test (`test="qlm"`) or 2-group exact test; same input/output contract
`analysis_r_limma`	Differential expression with limma-voom — precision-weighted linear models with empirical-Bayes moderation; same input/output contract
`analysis_r_session_info`	R runtime report: R/webR versions, installed package versions, memory, mirror endpoint — for diagnosing analysis issues

First use starts a ~1 GB WebAssembly R worker and downloads the wasm package bundle (~62 MB) from GitHub releases (cached). Requires webr installed next to biomcp. Guide: docs/R-ANALYSIS.md.

Biowasm Analysis (8, optional — `ANALYSIS_BIOWASM=1`)

Tool	Description
`analysis_bam_summary`	Inspect an alignment (SAM/BAM/CRAM): header contigs, sample/read groups, flagstat mapping metrics, per-contig counts via idxstats when indexed — "what's in this BAM?" before region work
`analysis_bam_view_region`	Reads, depth, pileup, or read extraction in a genomic region (samtools view/depth/mpileup); indexed sources use fast positional retrieval, indexless sources stream a BED filter (depth requires coordinate-sorted input and detects order violations), returning counts, coverage tables, SAM rows, or a BAM artifact
`analysis_bcf_summary`	Inspect a VCF/BCF: contigs, sample count and names, INFO/FORMAT field inventory from the header
`analysis_bcf_view_region`	Variants in a region as a narrow field projection (bcftools query): chosen columns, sample subsets, expression filters, variant types — or a sliced VCF.gz artifact
`analysis_bed_op`	Interval algebra on BED tracks (bedtools intersect/merge/subtract/coverage/jaccard/sort) with the streaming `-sorted` algorithm for sorted inputs
`analysis_biowasm_convert`	Format plumbing: SAM/BAM/CRAM via samtools view, VCF/BCF via bcftools view, VCF/BCF → TSV via bcftools query; results are artifact handles reusable as `artifact_id`
`analysis_biowasm_session_info`	Biowasm runtime report: pinned tool versions, asset cache state, engine status, retained artifacts, memory
`analysis_biowasm_cli`	Constrained escape hatch: an allowlisted samtools/bedtools/bcftools subcommand with schema-validated args (no shell, paths under /shared only)

First use downloads checksum-verified wasm assets (~4.5 MB, cached); no extra npm packages. Indexed sources answer region queries with fast positional retrieval (~0.2 % of file read); indexless sources fall back to streaming BED filters. Guide: docs/BIOWASM-ANALYSIS.md.

Citation Module

Citations federate 5 providers in fast (~4s) or full (~15-30s) mode. Forward citation lists come from Europe PMC, OpenCitations, and Semantic Scholar; Crossref supplies counts and backward references. Provider matrix and schema details: src/server/README.md.

Optional Features

Capabilities that ship with the package but stay inactive until enabled. Each links to its own guide:

Feature	Enable	Guide
Database access — read-only SQL tools (`db_query`, `db_list_tables`, `db_describe_table`) for MySQL and local-file SQLite	Set `DB_TYPE` (+ connection env vars); MySQL needs the `mysql2` peer dep — use the pinned one-shot client command (see docs/DATABASE.md)	docs/DATABASE.md
R analysis — Bioconductor differential expression (`analysis_r_deseq2`, `analysis_r_edger`, `analysis_r_limma`, `analysis_r_session_info`) running DESeq2/edgeR/limma in sandboxed WebAssembly R; wasm packages download from GitHub releases at first use (~62 MB, cached; slow links: `asset_timeout_ms` or a self-fetched `mirror_url`)	Set `ANALYSIS_R=1`; needs the `webr` peer dep — use the pinned one-shot client command `["npx","-y","-p","[email protected]","-p","[email protected]","biomcp"]` (all-features variant adds `-p mysql2@3`); expect ~1 GB RSS	docs/R-ANALYSIS.md
Biowasm analysis — samtools/bedtools/bcftools (BAM/BED/VCF) in sandboxed WebAssembly; streams/indexes real human-scale datasets (~300 MB BAM scans, region queries touch ~0.2 % of the file); assets ~4.5 MB cached at first use; no extra npm packages	Set `ANALYSIS_BIOWASM=1`	docs/BIOWASM-ANALYSIS.md

Instead of hand-editing env blocks, agents (and users) can self-serve through the always-available biomcp_configure tool: it reports every parameter's status/provenance, writes the .biomcp.json project config file for the optional features above (env vars keep precedence; env-only parameters are query-only and value-masked), validates changes, detects conflicts, checks peer-dependency prerequisites, and spells out the restart/verify steps. Details: docs/ENV-VARS.md → Project config file.

Documentation

Doc	Contents
docs/AGENT-INSTALL.md	Guided installation & client configuration (Claude Desktop, Claude Code, Codex, OpenCode)
docs/ENV-VARS.md	Single source of truth for every environment variable
docs/DATABASE.md	Database access feature guide
docs/R-ANALYSIS.md	R analysis feature guide (Bioconductor in WebAssembly)
docs/BIOWASM-ANALYSIS.md	Biowasm analysis feature guide (samtools/bedtools/bcftools in WebAssembly)
docs/DEVELOPMENT.md	Build, test, publish workflow
docs/development/CI.md	CI pipeline, Dependabot automation, auto-merge safety model
src/server/README.md	Full tool schemas (params, enums, defaults)
agent-test/README.md	User-agent E2E tests for the analysis tools

License

Licensed under the Apache License, Version 2.0. See NOTICE for attributions.

BioMCP-TS is adapted from the upstream BioMCP Rust project (MIT) with an agent-first development approach and enhancements — kudos to the original authors.

BioMCP TS

Add this server

Host a copy with our keys and logs.

Server facts

Tools

Questions

How do I install BioMCP TS?

Does BioMCP TS need an API key?

What transport does BioMCP TS use?

When was BioMCP TS last checked?

Documentation

BioMCP

Highlights

Install

Available Tools

Gene (7)

Variant (4)

Drug (3)

Disease (4)

Article (4)

Trial (2)

Utility (2)

Structural Biology (1)

Patents (2)

GEO (2)

SRA (2)

GenBank (3)

GTEx (2)

Ensembl (4)

R Analysis (4, optional — `ANALYSIS_R=1`)

Biowasm Analysis (8, optional — `ANALYSIS_BIOWASM=1`)

Citation Module

Optional Features

Documentation

License

Add this server

Host a copy with our keys and logs.

Server facts

Tools

Questions

How do I install BioMCP TS?

Does BioMCP TS need an API key?

What transport does BioMCP TS use?

When was BioMCP TS last checked?

Documentation

BioMCP

Highlights

Install

Available Tools

Gene (7)

Variant (4)

Drug (3)

Disease (4)

Article (4)

Trial (2)

Utility (2)

Structural Biology (1)

Patents (2)

GEO (2)

SRA (2)

GenBank (3)

GTEx (2)

Ensembl (4)

R Analysis (4, optional — ANALYSIS_R=1)

Biowasm Analysis (8, optional — ANALYSIS_BIOWASM=1)

Citation Module

Optional Features

Documentation

License

R Analysis (4, optional — `ANALYSIS_R=1`)

Biowasm Analysis (8, optional — `ANALYSIS_BIOWASM=1`)