MCP server exposing 3 tools for biomodels.
This URL is a JSON-RPC 2.0 endpoint over HTTP. Issue POST requests with a JSON-RPC body. Browsers and search crawlers land here on GET.
POST https://gateway.pipeworx.io/biomodels/mcp
Content-Type: application/json
{"jsonrpc":"2.0","id":1,"method":"tools/list"}biomodels_search — Search BioModels for published, executable mathematical models of biological systems — metabolic pathways, signalling cascades, cell-cycle and circadian oscillators, whole-cell metabolic reconstructions, infectious-disease models. AUTHORITATIVE for "is there a published computational model of X I can actually run", which web search answers with papers rather than with loadable SBML. Returns model id, name, format, submitter and date, plus facet counts (curation status, modelling approach, and cross-referenced taxonomy/GO/UniProt/ChEBI terms) that show how the matching models break down. Search accepts pathway names, diseases, organisms, genes, proteins and author names.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 (ODE, constraint-based, Petri net, Markov chain…), the publication it was taken from, contributors, version history, and the annotations linking its species and reactions to UniProt, ChEBI, GO and taxonomy terms. Use after biomodels_search, or when a paper cites a BIOMD accession.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 or scripts the submitter added — with MIME type, byte size, MD5/SHA-256 checksums and a direct download URL for each. This is the step between finding a model and actually loading it into a simulator.Code samples (curl / TypeScript / one-click client install), schemas, and the live playground are on the pack page:
https://pipeworx.io/packs/biomodels/
Pipeworx is an open MCP gateway connecting AI agents to live data. pipeworx.io