Designing a Deterministic Microbiome Simulation Without Overclaiming Science
Bio-Dynamics is an educational 3D lab, not a clinical simulator. That constraint shaped every decision in the simulation layer: reproducible ticks, scalar tissue state, capped agent counts, and inflammation that emerges from pressure instead of jumping on every button press. This post walks through the engine design. Companion resource Bio-Dynamics: Microbiome Sandbox Run the live lab or inspect the simulation source — tick engine, golden tests, and full docs in the repository. github.com/omidfarhang/example-projects/labs/microbiome-sandbox Open live lab View source on GitHub Why deterministic? Interactive demos fail the educational test when the same button sequence produces different outcomes on refresh. Readers cannot build intuition from noise. ...