Gephi MCP

Gephi AI

AI-powered network analysis through Gephi and the Model Context Protocol (MCP). Build, analyze, style, and export publication-ready network visualizations by talking to your AI assistant.

Built for researchers working across network science and AI.

Status: public beta. APIs may change between minor versions.

What you get

Your AI assistant drives Gephi. Say what you want in plain language and the assistant builds, analyzes, styles, and exports publication-ready network maps.

It's a conversation, not a command line. The assistant explains what it's doing, checks its own maps before showing them, and teaches you to read what you're seeing. You can point back: select nodes in the Gephi window and ask "what did I select?"

Any data, any MCP client. Network files import directly; spreadsheets and other data become networks conversationally. Works with Claude Code, Claude Desktop, or any MCP-compatible assistant.

Architecture

Three components connect your AI assistant to Gephi Desktop:

Claude / AI Assistant
        │
   MCP Protocol (stdio)
        │
   MCP Server (Python)          ← Translates MCP tool calls to HTTP
        │
   HTTP API (localhost:8080)
        │
   Gephi Plugin (Java)          ← Runs inside Gephi Desktop
        │
   Gephi Desktop                ← Must be running first

Install the Gephi plugin plus your AI client's connection — the Claude Code plugin bundles the MCP server, so most users install just two things. Gephi Desktop must be running before using any tools.

Security note: the plugin's HTTP API binds to 127.0.0.1 only, validates the request Host header (DNS-rebinding defense), and sends no CORS headers — it is reachable only by local processes such as the MCP server, never by a web page. It is not authenticated, so do not expose port 8080 beyond localhost.

macOS note: older plugin versions could wedge Gephi during sustained writes against a large rendered graph (calls hang; only gephi_health_check answers). Plugin 1.2.0 fixes the two causes on our side: writes now pause the renderer via Gephi's own viz-engine API, and a read-lock leak in the query endpoints (the main culprit) is closed. All lock waits are bounded, so a genuinely wedged Gephi returns an immediate "fully quit and reopen Gephi" error instead of hanging, and gephi_health_check exposes lock probes (graph_lock, graph_lock_stats) that detect the condition. If you ever see persistent "Graph is busy" errors, restart Gephi — and make sure you are on plugin 1.2.2 or newer.

Setup

Prerequisites

• Gephi Desktop 0.11.1+
• uv (runs the MCP server; one-line install, manages Python for you)
• Claude Code or Claude Desktop (for AI interaction)

Step 1: Install the Gephi plugin

This adds the HTTP API server inside Gephi Desktop. No build tools needed — download the pre-built plugin:

1. Download gephi-mcp-1.2.15.nbm from the Releases page (also available at the root of this repository).
2. In Gephi: Tools → Plugins → Downloaded → Add Plugins — select the .nbm file, then click Install.
3. Restart Gephi. The plugin starts automatically and listens on http://127.0.0.1:8080.

Verify: Open a browser to http://127.0.0.1:8080/health — you should see {"success": true}.

Step 2: Connect your AI assistant

Claude Desktop (fastest start)

Download gephi-ai-<version>.mcpb from the Releases page and double-click it — Claude Desktop installs the server with all dependencies bundled. No terminal, no config file. (Requires Python 3.10+ on your system, which modern macOS provides.)

Use ONE connection method per app. If you previously added gephi-mcp to claude_desktop_config.json by hand, remove that entry before installing the bundle — otherwise Claude Desktop runs two copies of the server and every tool appears twice.

{
  "mcpServers": {
    "gephi-mcp": {
      "command": "uvx",
      "args": ["gephi-mcp"]
    }
  }
}

Claude Code (most capable)

claude plugin marketplace add MattArtzAnthro/gephi-ai
claude plugin install gephi-network-analysis@gephi-ai

(Or run the same two commands as /plugin marketplace add … and /plugin install … inside a Claude Code session.)

The plugin bundles and runs the MCP server itself (via uv), and adds the slash commands, the network analyst agent, and the skills that teach Claude network science best practices. If you use Claude Code, this is the recommended setup.

claude mcp add gephi-mcp -- uvx gephi-mcp

Other MCP clients

Point your client at uvx gephi-mcp using stdio transport. uvx fetches the gephi-mcp package from PyPI on first run and caches it. For a persistent named command, pipx install gephi-mcp also works.

Step 3: Verify

First confirm the MCP server actually connected. In Claude Code, run /mcp — gephi-mcp should be listed as connected. (In Claude Desktop, check that the tools appear in the tools menu.) If it shows a failure like "Executable not found in $PATH", the launcher (uv/uvx or gephi-mcp) isn't on the global PATH — see the notes in Step 2.

Then, with Gephi running, ask your assistant:

"Check if Gephi is running"

It should call gephi_health_check and confirm the connection. In Claude Code, try:

/gephi-network-analysis:import-and-explore path/to/your/graph.gexf

Updating

gephi-ai improves often, so keep it current. Most fixes and new tools arrive through updates. The health check tells you once per session when your install is behind the latest release and shows the matching update step, but that notice only appears on recent versions, so if you installed a while ago (or an older command like /teach is missing), run the update below once to catch up. Updating is safe to do anytime.

• Claude Code: claude plugin update gephi-network-analysis@gephi-ai, then start a new session.
• Claude Desktop (one-click bundle): download the newest .mcpb from Releases and double-click it again.
• Claude Desktop (config file): nothing to do — the uvx entry fetches the latest release each time you fully quit and reopen Claude Desktop.
• Switching connection methods: remove the old one first (bundle: uninstall in Settings > Extensions; config file: delete the gephi-mcp block). Two methods at once means two servers and duplicated tools.
• Cowork: Cowork keeps its own copy of plugins, separate from Claude Code — updating one does not update the other. If Cowork's commands look older than this README (for example, no /teach), ask Cowork itself to update the gephi-network-analysis plugin, then fully quit and reopen the app.
• Gephi plugin: install the newest .nbm from Releases via Tools > Plugins > Downloaded and restart Gephi.

gephi_health_check reports both the Gephi plugin version and the MCP server version, and says whether they are up to date, so you can see at a glance what you are running.

What the Claude Code plugin adds

The plugin (claude-plugin/) goes beyond raw MCP tools:

Tools (104)

Example workflows

Community detection

1. gephi_create_project
2. gephi_import_file                  (your GEXF, GraphML, or CSV)
3. gephi_compute_degree
4. gephi_compute_modularity           (resolution: 1.0)
5. gephi_color_by_partition           (column: modularity_class)
6. gephi_size_by_ranking              (column: degree)
7. gephi_run_layout                   (ForceAtlas 2, 1000 iterations)
8. gephi_export_png                   (3840x2160 for publication)

Centrality analysis

1. Import or build graph
2. gephi_compute_betweenness
3. gephi_compute_pagerank
4. gephi_run_layout                   (ForceAtlas 2)
5. gephi_color_by_ranking             (column: betweenesscentrality)
6. gephi_size_by_ranking              (column: pageranks)
7. gephi_query_nodes                  (find top-ranked nodes)

Documentation

Reference guides are in claude-plugin/skills/gephi/:

• SKILL.md — Workflow patterns, best practices, and critical gotchas
• references/tool-reference.md — Complete API reference for all 104 tools
• references/layout-guide.md — Layout algorithm selection and parameter tuning
• references/statistics-guide.md — Statistics interpretation guide

Tech stack

• Gephi Plugin: Java 11, NetBeans Platform, NanoHTTPD, Gson
• MCP Server: Python 3.10+, MCP SDK (FastMCP), httpx, Pydantic, defusedxml; vendored sigma.js + graphology for the in-chat viewer
• Target: Gephi 0.11.1, NetBeans RELEASE290

Development

Building the Gephi plugin from source requires JDK 11+ and Maven:

cd gephi-mcp-plugin
mvn clean package    # output: target/gephi-mcp-<version>.nbm

The MCP server is a standard Python package under mcp-server/ (pytest for tests, ruff for linting).

Attribution

If you use or adapt this project in your work, please credit:

Built with gephi-ai (Matt Artz, 2025–2026) — https://github.com/MattArtzAnthro/gephi-ai

Citation

If you use this toolkit in your academic research, please cite:

Artz, Matt. 2025. Gephi AI. Software. Zenodo. https://doi.org/10.5281/zenodo.18673386

License

Apache License 2.0 — see LICENSE.

Author

Matt Artz — mattartz.me | ORCID