Biomodels MCP server

@pipeworx/biomodels

BioModels (EMBL-EBI) — the public repository of curated, executable mathematical models of biological systems (SBML, CellML, BioPAX and more), searchable by pathway, disease, organism, gene or author, with the model files themselves and the paper each model came from.

Part of Pipeworx — an MCP gateway connecting AI agents to 1679+ live data sources.

Tools

process, disease, organism, gene or author, with facet counts by curation status, modelling approach and cross-referenced ontology terms.

• biomodels_search(query, limit?, offset?) — find published models by pathway,

modelling approach (with its MAMO term), the source publication, contributors and version history.

• biomodelsmodel(modelid) — one entry in full: SBML notes, curation status,

MD5/SHA-256 and a direct download URL: the primary SBML plus auto-generated BioPAX, Octave/MATLAB, VCML and SciLab conversions.

• biomodelsfiles(modelid) — every attached file with MIME type, size,

Auth

Keyless. No registration step.

Data sources

• — faceted model search.
• — one model's metadata.
• — file listing.
• — file bytes.

Not the same service as biostudies

BioStudies is EMBL-EBI's general repository for the data supporting a publication (any assay, any format); BioModels is specifically executable models. Neither is a search surface for the other, and BioModels ids (BIOMD…, MODEL…) are not BioStudies accessions (S-…).

Things that cost time to rediscover (measured 2026-09-17)

answers 301 to biomodels.org, which redirects again to www.biomodels.org. This pack calls the final host directly rather than depending on two hops being followed with the query string intact.

• The host in every old doc is a redirect. https://www.ebi.ac.uk/biomodels/…

or 3 returns 10 rows; asking for 25 returns 25. A caller that trusted the parameter would report 10 results as "the top 3". This pack truncates the list itself and always requests at least the floor so offset paging stays aligned.

• format=json is required — without it you get HTML with a 200.
• numResults has a floor of 10 and does not clamp downward. Asking for 2

MAMO term), not a bare string; publication.accession is the PubMed ID when publication.type says "PubMed ID".

• offset is row-based and does work — page with offset += limit.
• facetStats is a JSON string containing JSON, not an object.
• modellingApproach is an object ({accession, name, resource} over a

within one minute, so the default 25s fetch bound reports an up service as down. The search path uses 45s; by-id endpoints are sub-second.

• A model's description is an SBML XHTML blob, not prose.
• Search latency is spiky — the same query measured 0.6s, 5.5s and >25s

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "biomodels": {
      "url": "https://gateway.pipeworx.io/biomodels/mcp"
    }
  }
}

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/biomodels/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — askpipeworx, discovertools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

Shortened. The full README is on GitHub.