MaBoSS Boolean Network Simulator MCP Server

The MaBoSS server exposes stochastic Boolean-model construction, configuration, simulation, analysis, and export through the Model Context Protocol (MCP). It uses pyMaBoSS as its simulation engine and can participate in a verified modelling pipeline from NeKo to MaBoSS to PhysiCell.

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

VERIFIED ACTIVE

LAST COMMIT 2026-08-19 · ★ 18 · #33 OF 151 MAINTAINED SCIENCE & HEALTH · VERIFIED 2026-08-25

Python servers · how we verify → /methodology

01 · Install MaBoSS Boolean Network Simulator

Claude Code

claude mcp add marcorusc-mcp-biomodelling-servers-mabos -- uvx mcp-biomodelling-servers

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "marcorusc-mcp-biomodelling-servers-mabos": {
      "command": "uvx",
      "args": [
        "mcp-biomodelling-servers"
      ]
    }
  }
}

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

license no standard license detected - usage rights unclear; check the repo before commercial use

pypi package mcp-biomodelling-servers - check the name against the project README before installing (PyPI has no namespace ownership)

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

03 · What MaBoSS Boolean Network Simulator can do

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

Latest releases

v2.2.0 · 2026-08-13

NeKo policy-semantics release. Updates the NeKo MCP interface to explicit path_policy and reuse_policy options, propagates those policies through session defaults and previews, adds concise strategy guidance, and…

v2.0.0 · 2026-08-03

Highlights · Upgrades the NeKo, MaBoSS, and PhysiCell servers to the stable MCP Python SDK 2.x and MCP 2026-07-28 protocol generation. · Adds explicit application session handles, per-session concurrency protection…

v1.0.0 · 2026-04-16

Three MCP servers for systems biology modelling, now available on PyPI and the MCP Registry. · Servers · NeKo (io.github.marcorusc/NeKo) - biological network construction from gene lists using pathway databases…

04 · Who maintains MaBoSS Boolean Network Simulator

MaBoSS Boolean Network Simulator is maintained by marcorusc. We track 3 MCP servers from marcorusc - 3 actively maintained, 18 combined GitHub stars, oldest repo from Aug 2025.

05 · Facts

repository: github.com/marcorusc/mcp-biomodelling-servers
category: science & health - ranked #33 of 151 actively-maintained science & health servers as of 2026-08-25.
release cadence: 2 releases in the last 90 days (latest 2026-08-13)
registry: io.github.marcorusc/MaBoSS (active, first published 2026-04-16 · 4 versions)
packages: pypi:mcp-biomodelling-servers

06 · MaBoSS Boolean Network Simulator FAQ

What is MaBoSS Boolean Network Simulator?

Is MaBoSS Boolean Network Simulator still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-19 and it shipped 2 releases in the last 90 days. We re-verify nightly.

How do I install MaBoSS Boolean Network Simulator?

Run `uvx mcp-biomodelling-servers`. You can also paste the ready-made client config above.

Does MaBoSS Boolean Network Simulator run locally?

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

07 · Alternatives to MaBoSS Boolean Network Simulator

Alternatives to MaBoSS Boolean Network Simulator

Maintained science & health servers if MaBoSS Boolean Network Simulator isn't the fit.

More science & health MCP servers · PhysiCell Configuration Builder · Oura Ring MCP · Scholar Sidekick · Molecare MCP · Data Aggregator

More Python MCP servers · NeKo Biological Network Builder · Server Spreadsheet · Apolo Cad · Publish MCP Server · see all