Distributed cell biology simulations with E-Cell system

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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
Title of host publicationLecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science)
EditorsA. Konagaya, K. Satou
Pages20-31
Number of pages12
Volume3370
Publication statusPublished - 2005
EventFirst International Workshop on Life Science Grid, LSGRID 2004: Grid Computing in Life Science - Kanazawa, Japan
Duration: 2004 May 312004 Jun 1

Other

OtherFirst International Workshop on Life Science Grid, LSGRID 2004: Grid Computing in Life Science
CountryJapan
CityKanazawa
Period04/5/3104/6/1

Fingerprint

Cytology
Computer workstations
Parameter estimation
Biology
Cell Biology
Cell
Distributed computer systems
Biological systems
Parallel processing systems
Kinetic parameters
Escherichia coli
Seed
Simulation
Servers
Parameter Estimation
Data storage equipment
Benchmarking
Shock Model
Computer simulation
Parallel and Distributed Computing

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computer Science (miscellaneous)
  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Sugimoto, M., Takahashi, K., Kitayama, T., Ito, D., & Tomita, M. (2005). Distributed cell biology simulations with E-Cell system. In A. Konagaya, & K. Satou (Eds.), Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science) (Vol. 3370, pp. 20-31)

Distributed cell biology simulations with E-Cell system. / Sugimoto, Masahiro; Takahashi, Kouichi; Kitayama, Tomoya; Ito, Daiki; Tomita, Masaru.

Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). ed. / A. Konagaya; K. Satou. Vol. 3370 2005. p. 20-31.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Sugimoto, M, Takahashi, K, Kitayama, T, Ito, D & Tomita, M 2005, Distributed cell biology simulations with E-Cell system. in A Konagaya & K Satou (eds), Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). vol. 3370, pp. 20-31, First International Workshop on Life Science Grid, LSGRID 2004: Grid Computing in Life Science, Kanazawa, Japan, 04/5/31.
Sugimoto M, Takahashi K, Kitayama T, Ito D, Tomita M. Distributed cell biology simulations with E-Cell system. In Konagaya A, Satou K, editors, Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). Vol. 3370. 2005. p. 20-31
Sugimoto, Masahiro ; Takahashi, Kouichi ; Kitayama, Tomoya ; Ito, Daiki ; Tomita, Masaru. / Distributed cell biology simulations with E-Cell system. Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). editor / A. Konagaya ; K. Satou. Vol. 3370 2005. pp. 20-31
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