Stochastic Simulation of Biomolecular Reaction Networks Using the Biomolecular Network Simulator Software
Abstract
We developed a software package, the Biomolecular Network Simulator (BNS), to simulate the stochastic behavior of complex biomolecular reaction networks on single and multi-processor computing systems. The software uses either exact or approximate stochastic simulation algorithms for generating Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks. This software uses a combination of MATLAB and C-coded functions and can be run on either single processor desk top computers or on multi-processor high performance computing hardware. In the later case, the code is parallelized with the MPI library to allow for multiple simultaneous simulations. The software can be run either in an interactive or in a batch job mode. The graphical user interface of BNS allows users to easily set model and simulation parameters for single or multiple simulation sessions. Furthermore, BNS contains a comprehensive set of data processing tools for post-simulation analysis of the results. The behavior of a single gene in vitro transcription-translation reaction network is investigated as an application example.
Document Details
- Document Type
- Technical Report
- Publication Date
- Feb 01, 2008
- Accession Number
- ADA485666
Entities
People
- Brent Foy
- John Frazier
- Yaroslav Chusak