simbiology-simulate-model

Use sbiosimulate with the model and its active configset, setting StopTime and SolverType first. For repeated runs with varying parameters, use createSimFunction, which compiles once and executes many parameter sets efficiently.

Set cs.SolverType = 'ssa' on the configset and call sbiosimulate in a loop for ensemble trajectories. All reactions must use MassAction kinetics, since the SSA solver does not support custom rate expressions.

Sobol (sbiosobol) quantifies first-order and interaction effects but needs 500-1000 samples. Morris (sbioelementaryeffects) is a cheaper screening method using 50-100 samples, best for ranking parameters before a full Sobol analysis.

Factorial scenario results are interleaved by the first dimension, not blocked by factor. Always call generate(sc) to get a table mapping each result index to its dose and parameter conditions.

No, passing a sbiodose object to a SimFunction errors. Convert doses to a table with Time and Amount columns, and declare the dosed species names as the fourth argument to createSimFunction.

Do not use it for model construction or diagram layout, which belongs to simbiology-build-model, or for parameter estimation and NCA from data, which belongs to simbiology-fit-model.