MaBoSS Boolean Network Simulator — Claude Code MCP server: setup
Runs stochastic Boolean network simulations and attractor analysis directly through your agent. Useful for systems biologists testing mechanistic models without standalone tool setups.
claude mcp add maboss -- uvx mcp-biomodelling-serversWhat MaBoSS Boolean Network Simulator 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.
What it helps with
- simulate stochastic Boolean biological models
- compute attractors and final phenotype probabilities
- test regulatory network transitions without complex terminal commands
Example prompts for the agent
- Run a stochastic simulation on
cell_cycle.bndand list the terminal state probabilities. - Analyze the attractors of this signaling model and check if apoptosis is reachable.
How to install MaBoSS Boolean Network Simulator
Platform CLI
claude mcp add maboss -- uvx mcp-biomodelling-serversuvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>
Platform CLI
codex mcp add maboss -- uvx mcp-biomodelling-serversuvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>
Config file
{
"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>
Config file
{
"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>
Platform CLI
gemini mcp add maboss uvx mcp-biomodelling-serversuvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about MaBoSS Boolean Network Simulator
How to install MaBoSS Boolean Network Simulator in Claude Code?
Run the command claude mcp add maboss -- uvx mcp-biomodelling-servers in your terminal.
What does MaBoSS Boolean Network Simulator do?
It gives the model context to configure, simulate, and analyze stochastic Boolean regulatory networks using pyMaBoSS.
Do I need to compile standalone MaBoSS beforehand?
No, the required cmaboss simulation engine is bundled into Python wheels and installs automatically.
