Install Cytoscape Desktop MCP for Claude Desktop

Claude Desktop reads mcpServers from claude_desktop_config.json. Restart the app after saving.

Open ~/Library/Application Support/Claude/claude_desktop_config.json on macOS, %APPDATA%\Claude\claude_desktop_config.json on Windows, or ~/.config/Claude/claude_desktop_config.json on Linux.
Paste the JSON config below.
Replace placeholder secrets, then restart the client if it does not reload on its own.

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "cytoscape-cytoscape-desktop-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb"
      ],
      "env": {
        "CYREST_PORT": "1234"
      }
    }
  }
}

Official Claude Desktop docs

Install Cytoscape Desktop MCP for Claude Desktop | MCPpedia