Cytoscape Desktop MCP

[gradle]: https://gradle.org/ [java]: https://www.oracle.com/java/index.html [git]: https://git-scm.com/ [make]: https://www.gnu.org/software/make [cytoscape]: https://cytoscape.org/ [mcp]: https://modelcontextprotocol.io/ [ndex]: https://www.ndexbio.org/. It runs locally over stdio via the published package.

People connecting science & health tools to Claude, Cursor, VS Code, or another MCP client. The project is written in Java.

VERIFIED ACTIVE

LAST COMMIT 2026-08-11 · ★ 6 · #42 OF 60 MAINTAINED SCIENCE & HEALTH · VERIFIED 2026-08-25

BSD-3-Clause · Java · how we verify → /methodology

01 · Install Cytoscape Desktop MCP

Claude Code

claude mcp add cytoscape-cytoscape-desktop-mcp -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "cytoscape-cytoscape-desktop-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions · Claude Desktop extension (.mcpb bundle)

license BSD-3-Clause - declared in the repository

npm package @cytoscape/cytoscape-desktop-mcp-bridge - published under the repo owner's npm scope (@cytoscape)

registry namespace io.github.cytoscape is GitHub-verified and matches the repo owner

03 · What Cytoscape Desktop MCP can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

Latest releases

mcpb-v1.0.3 · 2026-08-11

[mcpb-v1.0.3] - 2026-08-06 · Added: · support for releasing and publishing the MCP bridge (MCPB) to the MCP Registry and npm, so the bridge can be picked up by agentic marketplaces and "Install Now" style wrappers.…

1.0.2 · 2026-05-24

fixed · Fix mcp app reload during restart of desktop to be consistent, it was susceptible to be skipped due to race conditions in osgi timing and as a result mcp service was not started. pull/8

1.0.1 · 2026-05-14

fixed · Fixed app init after installing app into a running instance of desktop. The app init routine wasn't getting triggered to render the toolbar icon for mcp and start the etl service, had to restart desktop. This…

04 · Who maintains Cytoscape Desktop MCP

Cytoscape Desktop MCP is maintained by cytoscape. It's the only MCP server we track from this author; the repo dates to Feb 2026.

05 · Facts

repository
github.com/cytoscape/cytoscape-desktop-mcp
website
https://github.com/cytoscape/cytoscape-desktop-mcp
category
science & health - ranked #42 of 60 actively-maintained science & health servers as of 2026-08-25.
release cadence
1 release in the last 90 days (latest 2026-08-11)
registry
io.github.cytoscape/cytoscape-desktop-mcp-bridge (active, first published 2026-08-11)
packages
mcpb:https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb · npm:@cytoscape/cytoscape-desktop-mcp-bridge

06 · Cytoscape Desktop MCP FAQ

What is Cytoscape Desktop MCP?

[gradle]: https://gradle.org/ [java]: https://www.oracle.com/java/index.html [git]: https://git-scm.com/ [make]: https://www.gnu.org/software/make [cytoscape]: https://cytoscape.org/ [mcp]: https://modelcontextprotocol.io/ [ndex]: https://www.ndexbio.org/. It runs locally over stdio via the published package.

Is Cytoscape Desktop MCP still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-11 and it shipped 1 release in the last 90 days. We re-verify nightly.

How do I install Cytoscape Desktop MCP?

Run `npx -y @cytoscape/cytoscape-desktop-mcp-bridge`. You can also paste the ready-made client config above.

Does Cytoscape Desktop MCP run locally?

Yes - it's a stdio server: it runs on your machine (via npx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Cytoscape Desktop MCP

Alternatives to Cytoscape Desktop MCP

Maintained science & health servers if Cytoscape Desktop MCP isn't the fit.

  1. Arxiv MCP Server (blazickjp) Search arXiv papers, download full text, semantic search, citation graphs, and alerts via MCP. ★ 3,071 · 2026-08-24
  2. Paper Banana Generate academic diagrams and statistical plots from text using multi-agent AI. ★ 2,279 · 2026-08-17
  3. Pyscn Python code analysis for AI agents: complexity, dead code, clones, coupling, and a health score. ★ 1,035 · 2026-08-25
  4. Pubmed MCP Server Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms. ★ 137 · 2026-08-21
  5. FHIR MCP Server MCP server providing seamless access to FHIR APIs for AI tools and healthcare applications ★ 132 · 2026-07-14
  6. Clinicaltrialsgov MCP Server Search ClinicalTrials.gov - find studies, retrieve results, match patients to eligible trials. ★ 90 · 2026-08-21

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