LocalFree

Cytoscape Desktop MCP server

cytoscape/cytoscape-desktop-mcp

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

8 GitHub stars4 forks
Source code

Install Cytoscape Desktop in Claude Code

MCP Bundle (.mcpb)

Claude Code
curl -LO https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb
mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)
Download cytoscape-mcp.mcpb and double-click it to install in Claude Desktop.

MCP Bundles install in one click in Claude Desktop. Download the file, then open it.

npm

Claude Code
claude mcp add cytoscape-desktop -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge
mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)
{
  "mcpServers": {
    "cytoscape-desktop": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ]
    }
  }
}

Frequently asked questions

What does the Cytoscape Desktop MCP server do?

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

Is the Cytoscape Desktop MCP server free?

Yes, most likely. Open source and no paid account or API key is mentioned in the listing. Check the provider for current pricing.

Does Cytoscape Desktop run locally or remotely?

Local. Runs on your machine (stdio). You install it with npx, uvx, Docker or from source.

How do I add Cytoscape Desktop to Claude Code?

Run: curl -LO https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb

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