# Simbiology Build Model

Build, modify, and diagram SimBiology models, API reference, helper functions, and...

- Repository: https://github.com/matlab/matlab-agentic-toolkit (1237 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-10-27
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add matlab/matlab-agentic-toolkit --skill simbiology-build-model -g -a claude-code -y`
Codex: `npx skills add matlab/matlab-agentic-toolkit --skill simbiology-build-model -g -a codex -y`
Cursor: `npx skills add matlab/matlab-agentic-toolkit --skill simbiology-build-model -g -a cursor -y`
Gemini CLI: `npx skills add matlab/matlab-agentic-toolkit --skill simbiology-build-model -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add matlab/matlab-agentic-toolkit`

## Description

Build, modify, and diagram SimBiology models, API reference, helper functions, and layout patterns. Use when constructing or editing models programmatically or visually.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# Build SimBiology Models

API reference, helper functions, and patterns for building, modifying, and
diagramming SimBiology models. Works in all MATLAB environments (desktop,
headless, batch, remote). Diagram/layout features require the Model Builder
app and are activated only when the user requests visual output.

## When to Use

- Building or modifying SimBiology models (compartments, species, reactions, parameters, rules, events, doses, observables, variants)
- Opening, saving, or loading models in the Model Builder / Analyzer apps
- Designing or adjusting diagram layouts
- Keywords: "build", "create", "modify", "add compartment/species/reaction", "diagram", "layout"

## When NOT to Use

- Simulation and analysis (use `simbiology-simulate-model`)
- Parameter fitting, population modeling, NCA (use `simbiology-fit-model`)

## Must-Follow Rules

### 1. Add helper scripts to the MATLAB path first

Run at the start of every session:
```matlab
addpath(fullfile('<WORKSPACE_ROOT>', '.claude', 'skills', 'simbiology-build-model', 'scripts'));
disp('Helper scripts added to path.')
```

### 2. Only open the Builder when needed

Do NOT open the Model Builder by default. Open it when:
- The user explicitly requests a diagram, layout, or visual
- The input is an `.sbproj` file, use `loadViaBuilder` to preserve
  diagram layout/styling (`sbioloadproject` loses this data)

A model is fully functional without a diagram, it can be simulated,
fitted, and analyzed using only the model object on `sbioroot`.

### 3. Model construction uses standard SimBiology API

Build models using `addcompartment`, `addspecies`, `addreaction`, etc.
directly. This works in all environments: desktop, headless, batch, remote.

The rest: https://github.com/matlab/matlab-agentic-toolkit/blob/HEAD/skills-catalog/computational-biology/simbiology-build-model/SKILL.md