C

Cytoscape Desktop MCP

MCP server · by cytoscape

Developer Tools mcpbnpm v1.0.3

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

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Install

Run one of the commands below, then add the client config underneath.

mcpbhttps://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb
npmnpx -y @cytoscape/cytoscape-desktop-mcp-bridge

Client configuration

Paste into Claude Desktop, Cursor (mcp.json), VS Code or any MCP client, then restart the client.

mcpServers{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ]
    }
  }
}

About this server

Cytoscape Desktop MCP is listed in the Developer Tools category of the MCPNav directory. It is distributed as mcpb, npm and can be loaded by any client that speaks the Model Context Protocol.

Typical uses include giving your assistant scoped access to the corresponding service so it can answer questions and take actions with real data instead of guessing. Always review what a server can access before you enable it — see our MCP security guide.

Frequently asked questions

What is the Cytoscape Desktop MCP MCP server?

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

How do I install Cytoscape Desktop MCP?

Install it with: https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb. Then add the JSON config to your client's MCP settings and restart the client.

Is Cytoscape Desktop MCP free to use?

The MCP server itself is free to install. The source is public on https://github.com/cytoscape/cytoscape-desktop-mcp. Any third-party API it calls (such as a search or maps API) may require its own key and billing.

Which clients support Cytoscape Desktop MCP?

Any MCP-compatible client can use it, including Claude Desktop, Cursor, VS Code, Windsurf and custom agents.