marcorusc/mcp-biomodelling-servers
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A repository that stores all the MCP servers for creating biological mechanistic models. It includes server for NeKo, MaBoSS, PhysiCell/PhysiBoSS.
Обзор
This package provides four stateful Model Context Protocol servers for mechanistic and systems-biology modelling: All four servers use MCP over stdio and are distributed together as mcp-biomodelling-servers. For more details, please check the related article: Marco Ruscone, Miguel Vazquez & Alfonso Valencia, npj Systems Biology and Applications (2026) https://doi.org/10.1038/s41540-026-00767-3 - Python 3.10–3.14. - MCP Python SDK 2.x, installed automatically with this package. - The modelling-package dependencies declared in pyproject.toml, installed automatically by pip or uvx. - The Graphviz system runtime for NeKo history diagrams. The Python graphviz package is not a replacement for the external dot renderer. Check whether Graphviz is available with: If this command is missing, install Graphviz using your operating system or environment package manager. See the Graphviz installation guide for platform-specific instructions. NeKo (nekomata) 1.10.1 or newer (below 2.
README
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MCP Bio-Modelling Servers
This package provides four stateful Model Context Protocol servers for mechanistic and systems-biology modelling:
| Server | Modelling role | Upstream project | MCP Registry name |
|---|---|---|---|
| MaBoSS | Configure, simulate, and analyze stochastic Boolean models | pyMaBoSS | io.github.marcorusc/MaBoSS |
| NeKo | Build and analyze signalling networks from interaction databases | NeKo | io.github.marcorusc/NeKo |
| BioMASS | Construct, visualize, and simulate evidence-backed ODE models | BioMASS | io.github.marcorusc/BioMASS |
| PhysiCell | Build, inspect, and export PhysiCell and PhysiBoSS configuration files | PhysiCell-settings | io.github.marcorusc/PhysiCell |
All four servers use MCP over stdio and are distributed together as
mcp-biomodelling-servers.
Publication
For more details, please check the related article:
“Intelligent tool orchestration for rapid mechanistic model prototyping: MCP servers as AI-biology interfaces” Marco Ruscone, Miguel Vazquez & Alfonso Valencia, npj Systems Biology and Applications (2026) https://doi.org/10.1038/s41540-026-00767-3
Requirements
- Python 3.10–3.15.
- MCP Python SDK 2.x, installed automatically with this package.
- The modelling-package dependencies declared in
pyproject.toml, installed automatically bypiporuvx.
No system software is needed. MaBoSS simulations use the compiled cmaboss
engine that ships with pyMaBoSS, so the separate MaBoSS executable is not
required. NeKo history diagrams and BioMASS graphs render with PyGraphviz,
whose wheels bundle Graphviz, so the external dot program is not required
either. Prebuilt wheels cover Linux, macOS and Windows.
Installation
Install with pip
python -m pip install mcp-biomodelling-servers
This installs every server’s modelling dependencies, including NeKo
(nekomata 1.10.2 or newer, below 2.0), PhysiCell-settings 0.6.3 or newer
(below 0.7), the bundled MaBoSS engine and PyGraphviz. To reproduce a specific
release, pin it, for example mcp-biomodelling-servers==2.5.2.
The MaBoSS engine package, cmaboss, has no stable release yet: every build
on PyPI is a 1.0.0b* pre-release. The dependency cmaboss>=1.0.0b32,<2 names
Установка
uvx --from mcp-biomodelling-servers mcp-neko-server