Cytoscape Desktop MCP

Cytoscape Desktop MCP runs locally from an MCP Bundle: a single downloadable archive holding a local server and a manifest that describes it: https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb. It speaks MCP over stdio, so the client starts it as a program and talks to it through standard input and output. It needs a client that installs MCP Bundles; the file is opened in, or added to, that client. It reads the environment variable CYREST_PORT; set it in the client's configuration for this server.

Cytoscape Desktop MCP runs locally from a Node.js package published to the npm registry: @cytoscape/cytoscape-desktop-mcp-bridge version 1.0.3. It speaks MCP over stdio, so the client starts it as a program and talks to it through standard input and output. It needs Node.js; clients usually start it with npx — the usual command is npx -y @cytoscape/cytoscape-desktop-mcp-bridge@1.0.3. It reads the environment variable CYREST_PORT; set it in the client's configuration for this server.

In the mcpServers JSON format that many desktop and editor MCP clients read, the entry looks like this (placeholders in angle brackets):

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge@1.0.3"
      ],
      "env": {
        "CYREST_PORT": "<value>"
      }
    }
  }
}

Derived from the registry entry, not tested here. What the server does, and on what terms, is set by its publisher; check its repository or website before giving it access to your accounts or files. How to add an MCP server to an assistant · Before you connect