MCPLow riskUnclaimed

Cytoscape Desktop MCP

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

cytoscapecytoscape/cytoscape-desktop-mcp-bridge★ 7Updated Aug 11, 2026

server.json

{
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "name": "io.github.cytoscape/cytoscape-desktop-mcp-bridge",
  "description": "Drive a running Cytoscape Desktop to load, lay out, and style biological networks.",
  "title": "Cytoscape Desktop MCP",
  "repository": {
    "url": "https://github.com/cytoscape/cytoscape-desktop-mcp",
    "source": "github"
  },
  "version": "1.0.3",
  "websiteUrl": "https://github.com/cytoscape/cytoscape-desktop-mcp",
  "packages": [
    {
      "registryType": "mcpb",
      "identifier": "https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb",
      "fileSha256": "587db028294397065f071af1b0d2130daaf26be14fd936c9d540dc1cacf00d3c",
      "transport": {
        "type": "stdio"
      },
      "environmentVariables": [
        {
          "description": "Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)",
          "default": "1234",
          "name": "CYREST_PORT"
        }
      ]
    },
    {
      "registryType": "npm",
      "identifier": "@cytoscape/cytoscape-desktop-mcp-bridge",
      "version": "1.0.3",
      "transport": {
        "type": "stdio"
      },
      "environmentVariables": [
        {
          "description": "Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)",
          "default": "1234",
          "name": "CYREST_PORT"
        }
      ]
    }
  ]
}

Permissions

DeclaredDetected
Runs code—bundlenode
Installs—mcpb:https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpbnpm:@cytoscape/cytoscape-desktop-mcp-bridge@1.0.3
Runs install scripts—None
NetworkNoneNone
Needs credentialsNoneNone
Outside the workspace—None
Agent tools—None

Checks

Low risk · Nothing worth a warning was found.

Not reviewed by a person · Checked by rules; the model review is not switched on yet.

Versions

  1. #11.0.3latestOct 7, 2026