FluxForge_MCP

The installable MCP server for FluxForge — a fail-closed Model Context Protocol server that fuses literature, regulatory/PPI networks, and genome-scale metabolic models to predict CRISPR gene dependencies and drug targets. 18 typed tools.

This is a lightweight distribution repo (server + ~1.5 MB runtime data only) so it clones and installs fast. The full research code — the benchmark engine, datasets, figures, and paper materials — lives in the main repo: https://github.com/ali-kishk/FluxForge.

Install

1. Install the package (pulls all Python dependencies — cobra, pandas, networkx, httpx, pydantic, mcp — and ships the ~1.5 MB runtime data bundled inside the wheel):

pip install fluxforge-mcp

Solver is GLPK (bundled with cobra; no CPLEX/MATLAB needed).

2a. Claude Code — plugin marketplace (simplest; runs python -m mcp_server.server, no PYTHONPATH or data-dir env vars needed once the package is installed):

/plugin marketplace add ali-kishk/FluxForge_MCP
/plugin install fluxforge@fluxforge

2b. Claude Code — direct:

claude mcp add fluxforge -- python -m mcp_server.server

2c. Claude Desktop — config (claude_desktop_config.json → mcpServers):

{
  "mcpServers": {
    "fluxforge": {
      "command": "python",
      "args": ["-m", "mcp_server.server"]
    }
  }
}

Use the full path to your interpreter (e.g. .../python.exe) if python isn't on the client's PATH, or if you installed fluxforge-mcp into a specific virtualenv.

Only literature.extract_claim needs an LLM backend (configure MCP_LLM_*); the other 17 tools run with no LLM.

Related MCP server: GenomeMCP

Verify

Ask the client to "list your fluxforge tools" → you should get 18, starting with session.init_artifacts. Or offline:

python -m mcp_server.server --selftest    # -> registered tools: 18

Data & output locations

The runtime data (Recon3D model, PPI table, regulatory map, CRISPR benchmark, comparators) ships inside the installed package and is found automatically — no configuration needed. Outputs (session dumps, viewers, negative-result reports) are written to ~/.fluxforge/outputs by default. Override either with MCP_INPUT_DIR / MCP_OUTPUT_DIR if you need a different location.

License & citation

Apache-2.0 (see LICENSE / NOTICE) — © 2026 Ali Kishk. Cite via CITATION.cff. For the benchmark methodology and results, cite the main FluxForge repo / preprint.