Simulators

For examples of how to actually do simulations, check this notebook. Briefly, different simulation modes can be easily toggled using the following keywords in the py_SimulateModel(timepoints, Model = ...) wrapper:

stochastic = True / False Switches between Stochastic (SSA) and determinstic (ODE simulation). Defaults to deterministic.

delay = False / True adds delay to stochastic simulation. Deterministic simulation with delay is not supported. Using delay requires instantiating reactions with delay. Defaults to False.

volume = False / True adds volume parameter for SSA simulations. For single cell simulation with volume, use the (lineages package)[Lineage-Package]

Advanced users and developers can check out this notebook for more details on running simulations more directly.

Built-in Simulators

Simulations can be performed deterministically (without delay or cell division, i.e. regular deterministic ODE's for a system of reactions), or they can be performed stochastically with or without delay and with or without cell growth and division using the Bioscrape Lineages package.