Biomolecular Network Simulator: Software for Stochastic Simulations of Biomolecular Reaction Networks on Supercomputers

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 (MPI) library to run on multiprocessor architectures. We will present a brief description of the Biomolecular Network Simulator software along with some examples.