# MaBoSS Boolean Network Simulator

Runs stochastic Boolean network simulations and attractor analysis directly through your agent. Useful for systems biologists testing mechanistic models without standalone tool setups.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 20
- Author: marcorusc
- License: GPL-3.0 · policy=link-only · description only; the file stays with the author
- Source: https://github.com/marcorusc/mcp-biomodelling-servers/tree/HEAD/maboss
- Updated: 2026-10-22
- HTML: https://affpapa.org/en/nevibecode/mcp/maboss-boolean-network-simulator

## What it does

This tool manages and simulates stochastic Boolean networks by connecting biological queries to `pyMaBoSS`. It communicates over stdio as part of the `mcp-biomodelling-servers` suite. No external MaBoSS binary is required.

The server runs via the `mcp-maboss-server` entry point. Computation relies on the bundled C++ engine `cmaboss`, distributed directly inside wheels. Prebuilt wheels cover major operating systems without manual compilation.

Python 3.10 to 3.15 is required. If your dependency manager strictly rejects pre-releases, installation will fail because `cmaboss` is currently distributed as `1.0.0b*` builds. The initial run via `uvx` downloads roughly 1 GB of cached packages.

## Requirements
- Needs: Python and uv (commands run via uvx)

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add maboss -- uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Codex

**Platform CLI**
```bash
codex mcp add maboss -- uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "maboss": {
            "command": "uvx",
            "args": [
                "mcp-biomodelling-servers"
            ]
        }
    }
}
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "maboss": {
            "type": "stdio",
            "command": "uvx",
            "args": [
                "mcp-biomodelling-servers"
            ]
        }
    }
}
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add maboss uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

## When to use it
- simulate stochastic Boolean biological models
- compute attractors and final phenotype probabilities
- test regulatory network transitions without complex terminal commands

## Example prompts
- Run a stochastic simulation on `cell_cycle.bnd` and list the terminal state probabilities.
- Analyze the attractors of this signaling model and check if apoptosis is reachable.

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From the same set: [marcorusc/mcp-biomodelling-servers](https://affpapa.org/en/nevibecode/by/marcorusc/mcp-biomodelling-servers.md) — 4 cards

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