@pipeworx/biomodels

Connect: https://gateway.pipeworx.io/biomodels/mcp · Install: one-click buttons

No MCP client? Skip the connection: POST https://gateway.pipeworx.io/v1/tools/search_packs {"query":"..."} to find a tool below, GET /v1/tools/<name> for its schema, POST the same URL with arguments for the data — see For AI agents.

Tools: 3

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.

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.

Tools

• biomodels_search — Search BioModels for published, executable mathematical models of biological systems — metabolic pathways, signalling cascades, cell-cycle and circadian oscillators, whole-cell metabolic reconstructio
• biomodels_model — Fetch one BioModels entry in full by its model id (BIOMD… for curated models, MODEL… for non-curated) — name, the SBML notes describing what the model does, format, curation status, modelling approach
• biomodels_files — List every file attached to a BioModels entry — the primary SBML/CellML model plus auto-generated conversions (BioPAX levels 2 and 3, SBML-to-Octave/MATLAB, VCML, SciLab) and any supplementary figures