Cytoscape Desktop MCP

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

What does this entry provide?

Cytoscape Desktop MCP is an MCP server entry in ChatHome Skills, sourced from Official MCP Registry and scored 73/100. As a Model Context Protocol server, it exposes tools that MCP-compatible LLM clients such as Claude, Cursor, and Copilot can call directly, extending an agent's reach beyond its built-in capabilities. ChatHome Skills discovered this entry through its daily ingest of official registries and GitHub discovery queries, and re-verifies repository facts, freshness signals, and install metadata on every run. The quality score weighs official-registry presence, a working install command, license clarity, GitHub star trajectory, and repository freshness — the full formula is on the Sources page. The install command above is ready to copy. Review the last-pushed date and repository status before adding Cytoscape Desktop MCP to a production agent workflow; the snapshot facts below are point-in-time values from the most recent ingest.

Snapshot facts

Source: Official MCP Registry
Quality: 73/100
Install method: npm
Repo: cytoscape/cytoscape-desktop-mcp
Repo updated: Aug 11, 2026

Install command

npx -y @cytoscape/cytoscape-desktop-mcp-bridge@1.0.3

Install method: npm

Review the upstream source before running this command.

GitHub project

Quality

Repo stars

Repo updated

Aug 11, 2026

How is this score calculated?

Weighted across six dimensions, scored 0-100.
Provenance (25): listed in an official or curated registry.
Installability (25): a runnable install command beats a declared transport, which beats a source checkout.
Maintenance (20): recency of the last push; archived entries score zero here.
Adoption (20): repository stars on a log curve.

MCP manifest

{
  "_meta": {
    "io.modelcontextprotocol.registry/official": {
      "status": "active",
      "isLatest": true,
      "updatedAt": "2026-08-11T20:08:17.855626Z",
      "publishedAt": "2026-08-11T20:08:17.855626Z",
      "statusChangedAt": "2026-08-11T20:08:17.855626Z"
    }
  },
  "server": {
    "name": "io.github.cytoscape/cytoscape-desktop-mcp-bridge",
    "title": "Cytoscape Desktop MCP",
    "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
    "version": "1.0.3",
    "packages": [
      {
        "transport": {
          "type": "stdio"
        },
        "fileSha256": "587db028294397065f071af1b0d2130daaf26be14fd936c9d540dc1cacf00d3c",
        "identifier": "https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb",
        "registryType": "mcpb",
        "environmentVariables": [
          {
            "name": "CYREST_PORT",
            "default": "1234",
            "description": "Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)"
          }
        ]
      },
      {
        "version": "1.0.3",
        "transport": {
          "type": "stdio"
        },
        "identifier": "@cytoscape/cytoscape-desktop-mcp-bridge",
        "registryType": "npm",
        "environmentVariables": [
          {
            "name": "CYREST_PORT",
            "default": "1234",
            "description": "Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)"
          }
        ]
      }
    ],
    "repository": {
      "url": "https://github.com/cytoscape/cytoscape-desktop-mcp",
      "source": "github"
    },
    "websiteUrl": "https://github.com/cytoscape/cytoscape-desktop-mcp",
    "description": "Drive a running Cytoscape Desktop to load, lay out, and style biological networks."
  }
}

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