BioMASS ODE Model Builder — Claude Code MCP server
This MCP server builds, displays, and simulates ODE models tied to supporting evidence. Use it for systems-biology modelling tasks.
claude mcp add biomass -- uvx mcp-biomodelling-serversWhat BioMASS ODE Model Builder does
BioMASS ODE Model Builder gives an agent tools to create ODE models, inspect their visual structure, and run simulations. The models are intended to be grounded in supporting evidence. It communicates over MCP via stdio and is shipped inside mcp-biomodelling-servers.
The package needs Python 3.10–3.15; its modelling dependencies are installed by pip or uvx. BioMASS graph rendering uses PyGraphviz wheels that include Graphviz, so a separate Graphviz installation is not needed. Plugin use requires uv, and the package environment is fetched on first launch.
The server entry point is mcp-biomass-server. A Claude Code connection exposes its MCP tools to the whole session. A package resolver configured to reject pre-release builds will fail on the cmaboss dependency bundled with the distribution.
What it helps with
- build an ODE model from biological data
- inspect a model before running calculations
- display model components and their connections
- simulate an ODE model
- compare simulations with supporting data
Example prompts for the agent
- Build an ODE model for the biological process described in this project and prepare it for simulation.
- Display the BioMASS model graph and explain how its components are connected.
- Run the model simulation, then compare the resulting trajectories with the source data.
How to install BioMASS ODE Model Builder
Platform CLI
claude mcp add biomass -- 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 biomass -- 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": {
"biomass": {
"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": {
"biomass": {
"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 biomass 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 BioMASS ODE Model Builder
How do I install BioMASS ODE Model Builder in Claude Code?
Run claude mcp add biomass -- uvx mcp-biomodelling-servers.
What does BioMASS ODE Model Builder do?
It lets an agent create, visualize, and simulate ODE models grounded in supporting evidence. The server connects to the client over MCP stdio.
What does BioMASS ODE Model Builder require?
It requires Python 3.10–3.15. Plugin launches also need uv; the modelling dependencies are installed automatically.
