Stochastic Differential Equations for Practical Simulation of Gene Circuits.

Abstract

The Chemical Langevin Equation approach allows simple stochastic simulation of gene circuits under many practical situations where the number of molecules of the species involved is not extremely low. Here, we describe methods and a computational framework to simulate a population of cells containing gene circuits of interest. These methods account for both intrinsic and extrinsic noise sources, and allow us to have both individual cell-related species and population-related ones. The protocol covers aspects related to proper description of the system and setting the software tools. It also helps to deal with the optimization of data storage and the simulation precision versus computational time issue. Finally, it also gives practical tests to assess the validity of the underlying technical assumptions.