Biomolecular Network Simulator: Software for Stochastic Simulation of Cellular Biological Processes.

摘要

We developed a software package called Biomolecular Network Simulator (BNS) to model and simulate complex biomolecular reaction networks. The software uses the Gillespie stochastic simulation algorithm for generating Monte Carlo trajectories that describe the evolution of a system of biochemical reactions. This software uses a combination of MATLAB and C-coded functions and is parallelized with the MatlabMPI library to run on multiprocessor architectures. Simulations on HPC can be run either in the interactive or in the batch mode. The graphical user interface of BNS allows users to easily set parameters for the model and simulations. Furthermore, BNS contains a comprehensive set of tools for post-simulation analysis of the results.