MCP server

Biomodels

io.github.pipeworx-io/biomodels

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

BioModels — the public repository of curated, executable mathematical models of biological systems…

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

45

Token cost

About 27,061 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http biomodels https://gateway.pipeworx.io/biomodels/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.biomodels]
url = "https://gateway.pipeworx.io/biomodels/mcp"

Gemini CLI

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

Cursor

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

VS Code

{"servers":{"biomodels":{"type":"http","url":"https://gateway.pipeworx.io/biomodels/mcp"}}}

Antigravity

agy mcp add biomodels https://gateway.pipeworx.io/biomodels/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"biomodels","server_url":"https://gateway.pipeworx.io/biomodels/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"biomodels","server_url":"https://gateway.pipeworx.io/biomodels/mcp"}

Tools

• biomodels_files ~184 tokens
  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 down
• biomodels_model ~219 tokens
  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,
• biomodels_search ~355 tokens
  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 ca

Browse

• GitHub tools
• Web search
• GitHub and code hosting

Related MCP servers

• SiteCheck Health & Travel
  121 pay-per-call agent tools: health care, drug, provider and travel data tools. x402
• GitDiagram
  Architecture diagrams, explanations and Mermaid source for public GitHub repositories.
• Complex Portal
  EBI Complex Portal MCP.
• Agentic Engineering Periodic System
  Practices for building software with coding agents, each with a test you check on your repo.
• MCP Junction
  Search a nightly-refreshed directory of MCP servers by keyword, category or topic.
• ZenithEye Agent Commons
  Public coordination substrate for AI systems and humans with bounded MCP discovery and creation.
• AgentIndex
  Search a curated directory of open-source AI agents, MCP servers and AI developer tools.
• EventTrader MCP
  AI prediction market trading — real-time data, CLOB exchange, Prop Desk, 40+ tools

Badge for your README

[![AptLynx](https://aptlynx.net/badge/io.github.pipeworx-io/biomodels.svg)](https://aptlynx.net/servers/io.github.pipeworx-io/biomodels)

Listing text is written by the maker; AptLynx lists tools and does not vouch for them. Find another tool · Browse by topic · For agents