Biomodelling

Set up a dedicated Conda environment that contains the runtime dependencies for all three servers: NeKo, MaBoSS, and PhysiCell. Note the Python interpreter path inside the environment (e.g. ~/miniforge3/envs/mcp_modelling/bin/python) as you will need it for configuration.

conda create -n mcp_modelling python=3.11
conda activate mcp_modelling

Install the package via pip inside the activated Conda environment. Alternatively, use uvx for a no-install execution if you prefer not to modify the environment.

pip install mcp-biomodelling-servers

After installation, three CLI entry points are available. Test each one to confirm they launch without errors before wiring them into your MCP client.

mcp-neko-server --help
mcp-maboss-server --help
mcp-physicell-server --help

Edit your VS Code MCP configuration file to register each server. Use the full path to the Python interpreter inside your Conda environment as the command.

// ~/.config/Code/User/mcp.json
{
  "servers": {
    "mcp-neko-server": {
      "type": "stdio",
      "command": "/home/you/miniforge3/envs/mcp_modelling/bin/python",
      "args": ["-m", "mcp_biomodelling_servers.neko"]
    },
    "mcp-maboss-server": {
      "type": "stdio",
      "command": "/home/you/miniforge3/envs/mcp_modelling/bin/python",
      "args": ["-m", "mcp_biomodelling_servers.maboss"]
    },
    "mcp-physicell-server": {
      "type": "stdio",
      "command": "/home/you/miniforge3/envs/mcp_modelling/bin/python",
      "args": ["-m", "mcp_biomodelling_servers.physicell"]
    }
  }
}

Open VS Code's Copilot Chat panel, type /tools, and verify that the NeKo, MaBoSS, and PhysiCell tools appear. Select the tools you want to enable for your session before sending modelling requests.