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

Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita

Research output: Contribution to journalArticle

123 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

Fingerprint

Time Scales
Cell
Simulation
Object-oriented Simulation
Hermite Interpolation
Polynomial Interpolation
Cytology
Simulation Framework
Discrete Event
Nonlinear Interaction
Hermite Polynomials
Stochastic Algorithms
Coupled Oscillators
Heat-Shock Response
Scheduler
Harmonic Oscillator
Model
Biology
Shock
Subsystem

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

A multi-algorithm, multi-timescale method for cell simulation. / Takahashi, Kouichi; Kaizu, Kazunari; Hu, Bin; Tomita, Masaru.

In: Bioinformatics, Vol. 20, No. 4, 01.03.2004, p. 538-546.

Research output: Contribution to journalArticle

Takahashi, Kouichi ; Kaizu, Kazunari ; Hu, Bin ; Tomita, Masaru. / A multi-algorithm, multi-timescale method for cell simulation. In: Bioinformatics. 2004 ; Vol. 20, No. 4. pp. 538-546.
@article{4b5893186e914ec2829c61aed3a593e2,
title = "A multi-algorithm, multi-timescale method for cell simulation",
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.",
author = "Kouichi Takahashi and Kazunari Kaizu and Bin Hu and Masaru Tomita",
year = "2004",
month = "3",
day = "1",
doi = "10.1093/bioinformatics/btg442",
language = "English",
volume = "20",
pages = "538--546",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "4",

}

TY - JOUR

T1 - A multi-algorithm, multi-timescale method for cell simulation

AU - Takahashi, Kouichi

AU - Kaizu, Kazunari

AU - Hu, Bin

AU - Tomita, Masaru

PY - 2004/3/1

Y1 - 2004/3/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=1542400036&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=1542400036&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btg442

DO - 10.1093/bioinformatics/btg442

M3 - Article

VL - 20

SP - 538

EP - 546

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 4

ER -