Stochastic Simulation: Algorithms and Software

In recent years it has become increasingly clear that stochasticity plays an important role in many biological processes. Examples include bistable genetic switches, noise enhanced robustness of oscillations, and fluctuation enhanced sensitivity or “stochastic focusing".. Numerous cellular systems rely on spatial stochastic noise for robust performance. We examine the need for stochastic models and report on the state of the art of algorithms and software for modeling and simulation of both well-mixed and spatial stochastic biochemical systems.