Biomodels

@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 1875+ live data sources. This is an independent, unofficial integration — not affiliated with, endorsed by, or published by the upstream provider.

Tools

• biomodels_search(query, limit?, offset?) — find published models by pathway, process, disease, organism, gene or author, with facet counts by curation status, modelling approach and cross-referenced ontology terms.
• biomodels_model(model_id) — one entry in full: SBML notes, curation status, modelling approach (with its MAMO term), the source publication, contributors and version history.
• biomodels_files(model_id) — every attached file with MIME type, size, MD5/SHA-256 and a direct download URL: the primary SBML plus auto-generated BioPAX, Octave/MATLAB, VCML and SciLab conversions.

Auth

Keyless. No registration step.

Data sources

• <https://www.biomodels.org/search?query=&format=json>; — faceted model search.
• https://www.biomodels.org/{modelId}?format=json — one model's metadata.
• https://www.biomodels.org/model/files/{modelId}?format=json — file listing.
• https://www.biomodels.org/model/download/{modelId}?filename= — 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)

• The host in every old doc is a redirect. https://www.ebi.ac.uk/biomodels/… 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.
• 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 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.
• 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 MAMO term), not a bare string; publication.accession is the PubMed ID when publication.type says "PubMed ID".
• A model's description is an SBML <notes> XHTML blob, not prose.
• Search latency is spiky — the same query measured 0.6s, 5.5s and >25s 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.

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 — ask_pipeworx, discover_tools, 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.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

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

Both URLs reach the same gateway and the same 1875+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/biomodels_search \
  -H 'Content-Type: application/json' \
  -d '{"query":"glycolysis","limit":3}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/biomodels_search. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "biomodels": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-biomodels"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-biomodels

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Biomodels data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT