BioModels

liveBiologyScience

BioModels — 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.

3tools
0msauth
free tier50 calls/day

Tools

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

No parameters required.

▶Try it
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

No parameters required.

▶Try it

Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/biomodels/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/biomodels/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"biomodels_search","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("biomodels_search", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("biomodels — 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");