Cytoscape Desktop MCP

io.github.cytoscape/cytoscape-desktop-mcp-bridge

Drive a running Cytoscape Desktop to load, lay out, and style biological networks.

View repository →Homepage →

Connect this server

Add this to your MCP client config — claude_desktop_config.json (Claude Desktop) or .cursor/mcp.json (Cursor).Suits: Claude Desktop · Cursor.

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge@1.0.3"
      ],
      "env": {
        "CYREST_PORT": "1234"
      }
    }
  }
}
Environment variables
  • CYREST_PORTPort Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)

A starting point — check the repository for exact arguments and setup. Restart your client after editing the config.

Category
Developer Tools
Version
1.0.3
Registry
active
Published
8/11/2026

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