BioModels MCP

The BioModels MCP server enables AI agents to search and retrieve curated, executable mathematical models of biological systems from the BioModels repository. It provides tools to search models by pathway, disease, organism, gene, or author; fetch full model details including SBML notes and curation status; and list attached files such as SBML, CellML, BioPAX, and auto-generated conversions like MATLAB or SciLab scripts.

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Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Community listingLocal stdioSource reviewed; not executedPublished by Pipeworx

Vendor documentation

What you can do with it

Search for published mathematical models of biological systems by pathway or disease
Fetch full details of a specific BioModels entry by its model ID
List all attached files for a model, including SBML and auto-generated conversions

Source and maintenance

Community listingRegistry 0.2.1

mcp-registry: io.github.pipeworx-io/biomodels@0.2.1 Source repository Project website

Maintenance checked: Oct 31, 2026, 10:27 PM UTC

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@pipeworx/mcp-biomodels 0.2.1

npm

@pipeworx/mcp-biomodels package definition

{
  "version": "0.2.1",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-biomodels",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.

Cursor configuration

{
  "mcpServers": {
    "biomodels-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-biomodels@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.

Cline configuration

{
  "mcpServers": {
    "biomodels-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-biomodels@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.

VS Code configuration

{
  "servers": {
    "biomodels-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-biomodels@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.

Claude Desktop configuration

{
  "mcpServers": {
    "biomodels-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-biomodels@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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