Cytoscape Desktop MCP Server

Cytoscape Desktop MCP is an MCP integration. Drive a running Cytoscape Desktop to load, lay out, and style biological networks.

Packages and local setup

The published mcpb package is https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb. Its declared MCP transport is stdio.

The package declares CYREST_PORT: Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API).

The published npm package is @cytoscape/cytoscape-desktop-mcp-bridge, version 1.0.3. Its declared MCP transport is stdio.

Before connecting

Check the maintainer’s instructions for account access, authentication and the supported client configuration. Once connected, inspect the tools your client receives and try a small task that matches the server’s stated purpose. The registry description does not include a verified, complete tool list.

Project and source

View the publisher’s registry entry · Project repository · Project website. This profile uses version 1.0.3 from the registry. Registration identifies the publisher namespace; it does not establish that this is a first-party integration for every service it connects.

Browse related developer tools MCP servers for tools that cover the same kind of work.