Stochastic Simulations of Cellular Biological Processes

Abstract

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 imp lemented 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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Document Details

Document Type
Technical Report
Publication Date
Jun 01, 2007
Accession Number
ADP023784

Entities

People

  • Brent Foy
  • John Frazier
  • Yaroslav Chushak

Tags

DTIC Thesaurus Topics

  • Air Force Research Laboratories
  • Algorithms
  • Application Software
  • Biological Processes
  • Chemical Reactions
  • Computational Biology
  • Computers
  • Department Of Defense
  • Graphical User Interface
  • High Performance Computing
  • Mathematical Models
  • Monte Carlo Method
  • Probability
  • Random Variables
  • Simulations
  • Systems Biology
  • Time Intervals

Readers

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