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:

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:

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