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:

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.