matlab-simulate-simbiology-model
Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis. Use when asked to run, simulate, predict, explore what-if, or identify influential parameters.
npx skills add matlab/matlab-agentic-toolkit --skill matlab-simulate-simbiology-model --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 `matlab-build-simbiology-model`) - Parameter estimation from data (use `matlab-fit-simbiology-model`) - NCA / AUC / Cmax from data (use `matlab-fit-simbiology-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', 'matlab-simulate-simbiology-model', 'scripts')); ``` ### 1. Element-wise operators in observables Use `./` and `.*` (element-wise) in observable expressions when mixing time-varying species with constant parameters.
- When to Use
- When NOT to Use
- Must-Follow Rules
- 0. Add helper scripts to the MATLAB path first
- 1. Element-wise operators in observables
- 2. StatesToLog for constant parameters
- 3. All reactions must be MassAction for SSA
- 4. Do NOT combine Scenarios with +
- 5. Reset local sensitivity options after use
- 6. Set MaximumWallClock to prevent hung simulations
- 7. Unit conversion requires TimeUnits
- 8. Scenario results are interleaved, not blocked
- Decision Table
- Basic Simulation (sbiosimulate)
What does the matlab-simulate-simbiology-model skill do?
Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis. Use when asked to run, simulate, predict, explore what-if, or identify influential parameters.
How do I install it?
Run `npx skills add matlab/matlab-agentic-toolkit --skill matlab-simulate-simbiology-model --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From matlab/matlab-agentic-toolkit, a repository with 868 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.