# Simbiology Simulate Model

Simulate SimBiology models, ODE, stochastic (SSA), scenarios, and sensitivity analysis.

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

## Description

Simulate SimBiology models, ODE, stochastic (SSA), scenarios, and sensitivity analysis. Use when asked to run, simulate, predict, explore what-if, or identify influential parameters.

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

# Simulate SimBiology Models

Run simulations of SimBiology models: deterministic ODE, stochastic SSA,
scenario exploration, and sensitivity analysis.

## When to Use

- "simulate", "run", "predict" model behavior
- "what if" / "what happens if" (implies simulation or scenarios)
- Time-course results from a model
- Dose-response studies, parameter sweeps, factorial designs
- Stochastic, SSA, Gillespie, noise, gene expression variability
- "which parameters matter most", sensitivity, Sobol, Morris
- Keywords: "simulate", "run", "predict", "what-if", "stochastic", "sensitivity"

## When NOT to Use

- Model construction or diagram layout (use `simbiology-build-model`)
- Parameter estimation from data (use `simbiology-fit-model`)
- NCA / AUC / Cmax from data (use `simbiology-fit-model`)

## Must-Follow Rules

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

Run at the start of every session:
```matlab
addpath(fullfile('<WORKSPACE_ROOT>', '.claude', 'skills', 'simbiology-simulate-model', 'scripts'));
```

### 1. Element-wise operators in observables

Use `./` and `.*` (element-wise) in observable expressions when mixing
time-varying species with constant parameters. Plain `/` and `*` cause
size mismatches at simulation time.

### 2. StatesToLog for constant parameters

When observables reference constant parameters (e.g., `Drug ./ Vd`),
add those parameters explicitly to `StatesToLog`:
```matlab
cs.RuntimeOptions.StatesToLog = [m.Species; sbioselect(m,'Type','parameter','Name','Vd')];
```
`StatesToLog = 'all'` does **not** log constant compartments or parameters.

### 3. All reactions must be MassAction for SSA

The stochastic solver does not support custom rate expressions. Every
reaction must use `addkineticlaw(rx, 'MassAction')`.

### 4. Do NOT combine Scenarios with `+`

The `+` operator is not supported on `SimBiology.Scenarios` objects.
Always use `add()` to append entries.

### 5. Reset local sensitivity options after use

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