A multi-algorithm, multi-timescale method for cell simulation

Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita

Research output: Contribution to journalArticle

127 Citations (Scopus)

Abstract

Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of these are already widely used, and a large number of models constructed on these existing formalisms are available. A significant computational challenge is how we can integrate such sub-cellular models running on different types of algorithms to construct higher order models. Results: A modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation has been developed and implemented. It is shown that this new method can efficiently handle many components driven by different algorithms and different timescales. The utility of this simulation framework is demonstrated further with a 'composite' heat-shock response model that combines the Gillespie - Gibson stochastic algorithm and deterministic-differential equations. Dramatic improvements in performance were obtained without significant accuracy drawbacks. A multi-timescale demonstration of coupled harmonic oscillators is also shown.

Original languageEnglish
Pages (from-to)538-546
Number of pages9
JournalBioinformatics
Volume20
Issue number4
DOIs
Publication statusPublished - 2004 Mar 1

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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