# BioMASS ODE Model Builder

This MCP server builds, displays, and simulates ODE models tied to supporting evidence. Use it for systems-biology modelling tasks.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 20
- Author: marcorusc
- License: GPL-3.0 · policy=link-only · description only; the file stays with the author
- Source: https://github.com/marcorusc/mcp-biomodelling-servers/tree/HEAD/biomass
- Updated: 2026-10-22
- HTML: https://affpapa.org/en/nevibecode/mcp/biomass-ode-model-builder

## What it 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.

## Requirements
- Needs: Python and uv (commands run via uvx)

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add biomass -- uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Codex

**Platform CLI**
```bash
codex mcp add biomass -- uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "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>

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "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>

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add biomass uvx mcp-biomodelling-servers
```
uvx runs the command named after the package; if the README names another one, use uvx --from mcp-biomodelling-servers <command>

## When to use it
- 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
- 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.

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From the same set: [marcorusc/mcp-biomodelling-servers](https://affpapa.org/en/nevibecode/by/marcorusc/mcp-biomodelling-servers.md) — 4 cards

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