# Cytoscape MCP Server

> Cytoscape MCP Server — cytoscape-cytoscape-desktop-mcp. Use this tool when you need to remotely control and interact with Cytoscape Desktop, loading networks and setting active views over HTTP. It solves problems of automated network analysis and visualization, enabling AI agents to integrate with Cytoscape's functionality. The tool accepts HTTP requests as input and outputs controlled interactions with the Cytoscape Desktop application.

Canonical page: https://skillsregistry.net/skills/cytoscape-cytoscape-desktop-mcp  
JSON: https://api.skillsregistry.net/v1/skills/cytoscape-cytoscape-desktop-mcp

## Description

An embedded MCP server for Cytoscape Desktop that lets AI agents load networks, set active views, and control the desktop application over HTTP.

## Trust

- **Trust score (0–1):** 0.56
- **Verification tier:** scanned
- **Last scanned:** 2026-08-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** ai-ml
- **Updated:** 2026-08-28

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/u8veuyp5id)
- **Repository:** <https://github.com/cytoscape/cytoscape-desktop-mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "cytoscape-cytoscape-desktop-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/cytoscape-cytoscape-desktop-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/cytoscape-cytoscape-desktop-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt