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

Abstract

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.

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Document Details

Document Type
Technical Report
Publication Date
Mar 01, 2007
Accession Number
ADA608565

Entities

People

  • Brent Foy
  • John Frazier
  • Yaroslav Chushak

Organizations

  • United States Army Medical Research and Development Command

Tags

Communities of Interest

  • Biomedical

DTIC Thesaurus Topics

  • Air Force Research Laboratories
  • Algorithms
  • Application Software
  • Biological Processes
  • Chemical Reactions
  • Computational Biology
  • Computers
  • Differential Equations
  • Gene Expression
  • Graphical User Interface
  • High Performance Computing
  • Human-Machine Interaction
  • Simulations
  • Simulators
  • Systems Biology
  • User Interface

Fields of Study

  • Computer science

Readers

  • Molecular Genetics
  • Parallel and Distributed Computing.
  • Statistical inference.