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8 clients · secrets stay placeholders

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{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/[email protected]"
      ],
      "env": {
        "CYREST_PORT": "1234"
      }
    }
  }
}

claude mcp add cytoscape-desktop-mcp-bridge -e "CYREST_PORT=1234" -- npx -y @cytoscape/[email protected]

[mcp_servers.cytoscape-desktop-mcp-bridge]
command = "npx"
args = ["-y", "@cytoscape/[email protected]"]
env = { "CYREST_PORT" = "1234" }

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "cytoscape-desktop-mcp-bridge": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@cytoscape/[email protected]"
      ],
      "enabled": true,
      "environment": {
        "CYREST_PORT": "1234"
      }
    }
  }
}

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/[email protected]"
      ],
      "env": {
        "CYREST_PORT": "1234"
      }
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=cytoscape-desktop-mcp-bridge&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeXRvc2NhcGUvY3l0b3NjYXBlLWRlc2t0b3AtbWNwLWJyaWRnZUAxLjAuMyJdLCJlbnYiOnsiQ1lSRVNUX1BPUlQiOiIxMjM0In19"
}

{
  "servers": {
    "cytoscape-desktop-mcp-bridge": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/[email protected]"
      ],
      "env": {
        "CYREST_PORT": "1234"
      }
    }
  }
}

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/[email protected]"
      ],
      "env": {
        "CYREST_PORT": "1234"
      }
    }
  }
}

extensions:
  "cytoscape-desktop-mcp-bridge":
    enabled: true
    name: "cytoscape-desktop-mcp-bridge"
    type: stdio
    cmd: "npx"
    args:
      - "-y"
      - "@cytoscape/[email protected]"
    envs:
      "CYREST_PORT": "1234"
    timeout: 300

This is a local package: the command runs on your machine.

Quality – / 100not scored

Not scored: fewer than three checks apply, usually because no remote answered a credential-free probe or the server is a local package.

protocoln/a · weight 25

n/a
protocol.modern, protocol.stateless, protocol.transport, protocol.list_ttlno remote answered a protocol handshake (not probed yet, unreachable, or local-only)

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygienen/a · weight 30

n/a
tools.descriptions, tools.description_length, tools.schemas, tools.annotations, tools.directory_hints, tools.token_cost, tools.api_dumptool list unknown (behind auth, not probed, or empty)

stabilityn/a · weight 15

n/a
stability.changes, stability.rug_pulltool list unknown

dependencies100 · weight 15

pass
deps.known_vulnsno known advisory in 1 resolved packages
n/a
deps.mcp_sdk_versionthe official MCP SDK is not in the dependency graph
pass
deps.resolvable@cytoscape/[email protected] resolved: 1 packages

Tool list unknown · checked 2026-10-19 10:52 UTC

Tool changes

No tool definition changes recorded. A server's first observation is its baseline; later probes record what changes.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 90 / 100

provenance90

livenessn/a

freshness85

hygiene95

+repository +namespace-matches-repo +website ~liveness-unmeasured ~updated-69d-ago -unpinned-packages(1)

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Dependencies

@cytoscape/[email protected] npm0 dependencies, resolved · advisories checked 2026-10-19

No known advisory affects this dependency graph.

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

package	registry	version	runtime	secrets
`https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb`	mcpb	unpinned	–
`@cytoscape/cytoscape-desktop-mcp-bridge`	npm	1.0.3	–

Tools (0)

No tools observed. Local packages are never executed by the registry.

Schemas: list_tools.

Similar MCP servers

Official server.json

{
  "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."
}