Cytoscape Desktop MCP

Connect Runs on your machine

claude mcp add cytoscape-desktop-mcp-bridge -e CYREST_PORT=<CYREST_PORT> -- https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb

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

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

{
  "servers": {
    "cytoscape-desktop-mcp-bridge": {
      "type": "stdio",
      "command": "https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb",
      "args": [],
      "env": {
        "CYREST_PORT": "<CYREST_PORT>"
      }
    }
  }
}

Replace the values in angle brackets with your own. Keys stay on your machine; we never see them.

Tools

This server runs locally, so its tools are listed by your MCP client once it starts.

Environment variables

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