PhysiCell Configuration Builder — Claude Code MCP server
This MCP server lets an agent create, inspect, and export PhysiCell and PhysiBoSS model configuration files when those files need to be prepared or checked.
claude mcp add physicell -- uvx mcp-biomodelling-serversWhat PhysiCell Configuration Builder does
PhysiCell Configuration Builder exposes configuration work through MCP over stdio. An agent can use it to create settings for PhysiCell and PhysiBoSS, examine existing configuration content, and produce exported files for the model workflow.
It is shipped inside mcp-biomodelling-servers. Installing the package with pip or uvx also installs its modelling dependencies and the MCP Python SDK 2.x. The supported Python range is 3.10–3.15.
A uv installation is required when the server is started through uvx. The server can be connected to Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, or Gemini CLI.
What it helps with
- create a PhysiCell model configuration
- inspect PhysiBoSS settings
- export a completed configuration file
- prepare model parameters for an agent workflow
Example prompts for the agent
- Create a PhysiCell configuration for this model.
- Inspect the PhysiBoSS settings and point out configuration problems.
- Export the completed PhysiCell configuration.
How to install PhysiCell Configuration Builder
Platform CLI
claude mcp add physicell -- 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 physicell -- 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": {
"physicell": {
"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": {
"physicell": {
"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 physicell 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 PhysiCell Configuration Builder
How do I install PhysiCell Configuration Builder in Claude Code?
Run claude mcp add physicell -- uvx mcp-biomodelling-servers.
What does PhysiCell Configuration Builder do?
It gives an MCP client tools for creating, inspecting, and exporting PhysiCell and PhysiBoSS configuration files.
Which Python versions does the server support?
It supports Python 3.10–3.15. The package installs its modelling dependencies during setup.
