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Biology model simulator
Give it a model. Get it run for what-if cases, with the most influential settings found.
Biology model simulator is a free AI skill for the job "Build and ship software". Give the instructions to an AI assistant that supports the required files and tools, then review its output.
Free · No account · BSD 2 Clause licence · Made by MathWorks · Level: advanced
Made by MathWorks. See the original on GitHub; we copied it as it is, with its licence.
What it does
Run your SimBiology model forward in time and see what changes when you tweak a dose, a rate or a starting level. You also learn which settings move the result most, so you know where to spend your effort. The skill covers smooth ODE runs and random-event runs, plus what-if scenarios, dose-response sweeps and factorial designs. For influence, it runs global sensitivity methods such as Sobol and Morris. It follows a few hard-won rules: use element-wise operators in observables, and log the states that observables depend on. It works inside MATLAB with SimBiology installed.
You give it
- A SimBiology model
- The scenarios or ranges to test
- Run length and output species
- Whether you want stochastic runs (optional)
You get
- Time-course results for each case
- Dose-response or sweep tables
- Plots of the runs
- A ranked list of influential parameters
Use it when
- You want to see how your model behaves over time under a new dose.
- You need to compare several what-if cases side by side.
- Gene expression noise matters and you need stochastic runs.
- You must find out which parameters drive the output most.
How to use it
- Add it to your AI once: download it and add the folder to Claude, ChatGPT or Codex as a skill.
- Ask for the job in your own words. Your AI opens the skill when it fits.
- It works best when your AI can run MATLAB with SimBiology.