Stochastic Simulations of Cellular Biological Processes

At the functional level, all biological processes in cells can be represented as a series of biochemical reactions that are stochastic in nature. We have developed a software package called biomolecular network simulator (BNS) that uses a stochastic approach to model and simulate complex biomolecular reaction networks. Two simulation algorithms-the exact Gillespie stochastic simulation algorithm and the approximate adaptive tau-leaping algorithm-are implemented for generating Monte Carlo trajectories that describe the evolution of a system of biochemical reactions. The software uses a combination of MATLAB and C-coded functions and is parallelized with the message passing interface (MPT) library to run on multiprocessor architectures.