Distributed cell biology simulations with E-Cell system

Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita

Research output: Contribution to journalConference articlepeer-review

5 Citations (Scopus)

Abstract

Many useful applications of simulation in computational cell biology, e.g. kinetic parameter estimation, Metabolic Control Analysis (MCA), and bifurcation analysis, require a large number of repetitive runs with different input parameters. The heavy requirements imposed by these analysis methods on computational resources has led to an increased interest in parallel- and distributed computing technologies. We have developed a scripting environment that can execute, and where possible, automatically parallelize those mathematical analysis sessions transparently on any of (1) single-processor workstations, (2) Shared-memory Multiprocessor (SMP) servers, (3) workstation clusters, and (4) computational grid environments. This computational framework, E-Cell SessionManager (ESM), is built upon E-Cell System Version 3, a generic software environment for the modeling, simulation, and analysis of whole-cell scale biological systems. Here we introduce the ESM architecture and provide results from benchmark experiments that addressed 2 typical computationally intensive biological problems, (1) a parameter estimation session of a small hypothetical pathway and (2) simulations of a stochastic E. coli heat-shock model with different random number seeds to obtain the statistical characteristics of the stochastic fluctuations.

Original languageEnglish
Pages (from-to)20-31
Number of pages12
JournalLecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science)
Volume3370
DOIs
Publication statusPublished - 2005 Jan 1
EventFirst International Workshop on Life Science Grid, LSGRID 2004: Grid Computing in Life Science - Kanazawa, Japan
Duration: 2004 May 312004 Jun 1

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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