Stochastic Simulations of Cellular Biological Processes
Pittsburgh, PA（2007）
摘要
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.
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关键词
monte carlo trajectory,biomolecular network simulator,software package,approximate adaptive,message passing interface,stochastic simulations,c-coded function,exact gillespie stochastic simulation,simulation algorithm,stochastic approach,biochemical reaction,cellular biological processes,modeling and simulation,monte carlo,mathematical model,parallel processing,biological processes,network simulator,monte carlo method,simulators,algorithms,network architecture,message passing,mathematical models,stochastic processes,graphical user interface,monte carlo methods,biomolecules,simulation,stochastic simulation,biochemistry,biotechnology,networks,biological process
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