Cytoscape Desktop MCP

Overview

Cytoscape Desktop MCP is a Model Context Protocol server that lets you drive a running Cytoscape Desktop instance to load, lay out, and style biological networks. It exposes Cytoscape's network visualization and analysis capabilities as tools that AI assistants can invoke directly, making it easy to automate network manipulation and exploration.

The server runs locally on your machine via the npm package @cytoscape/cytoscape-desktop-mcp-bridge, communicating over stdio with no authentication required. Install it with npx -y @cytoscape/cytoscape-desktop-mcp-bridge. The latest release is v1.0.3, published under the BSD-3-Clause license with source code available at cytoscape/cytoscape-desktop-mcp on GitHub.

Cytoscape Desktop MCP is listed in the Development category on mcp.site and works with MCP clients including Claude Desktop, Claude Code, Cursor, VS Code, Windsurf, and Zed. If you maintain this server, claim your listing to earn the Verified badge and keep information up to date.

Installation

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