A distributed-based stochastic simulation algorithm for large biochemical reaction networks

Jun Qing Niu, Hao Ran Zheng, Jiu Sheng Chen, Meng Ma, Xu Fa Wang

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

4 Scopus citations

Abstract

Dynamic modeling and simulation of biochemical reaction networks is an important topic in systems biology and is obtaining growing attention from researchers with computational and biological background. Gillespie's stochastic simulation algorithm (SSA) was a standard algorithm to simulate "wellstirred" biochemical reaction system. The biggest problem of the SSA lied in the excessive cost of computation because of its computational complexity. This paper describes a new distributed-based stochastic simulation algorithm (DSSA), which uses distributed computing and multi-agents system to improve the computing performance of the SSA. Experiments showed the DSSA is able to improve time performance significantly when compared to the SSA, and is an effective way to model and simulate large biochemical reaction networks.

Original languageEnglish
Title of host publication2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE
Pages502-505
Number of pages4
DOIs
StatePublished - 2007
Externally publishedYes
Event2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE - Wuhan, China
Duration: 6 Jul 20078 Jul 2007

Publication series

Name2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE

Conference

Conference2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE
Country/TerritoryChina
CityWuhan
Period6/07/078/07/07

Keywords

  • Component
  • Distributed-based simulation
  • Multi-agents
  • Stochastic simulation algorithm
  • Systems biology

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