Toward large-scale modeling of the microbial cell for computer simulation

Nobuyoshi Ishii, Martin Robert, Yoichi Nakayama, Akio Kanai, Masaru Tomita

Research output: Contribution to journalConference articlepeer-review

75 Citations (Scopus)


In the post-genomic era, the large-scale, systematic, and functional analysis of all cellular components using transcriptomics, proteomics, and metabolomics, together with bioinformatics for the analysis of the massive amount of data generated by these "omics" methods are the focus of intensive research activities. As a consequence of these developments, systems biology, whose goal is to comprehend the organism as a complex system arising from interactions between its multiple elements, becomes a more tangible objective. Mathematical modeling of microorganisms and subsequent computer simulations are effective tools for systems biology, which will lead to a better understanding of the microbial cell and will have immense ramifications for biological, medical, environmental sciences, and the pharmaceutical industry.In this review, we describe various types of mathematical models (structured, unstructured, static, dynamic, etc.), of microorganisms that have been in use for a while, and others that are emerging. Several biochemical/cellular simulation platforms to manipulate such models are summarized and the E-Cell system 1 developed in our laboratory is introduced. Finally, our strategy for building a "whole cell metabolism model", including the experimental approach, is presented.

Original languageEnglish
Pages (from-to)281-294
Number of pages14
JournalJournal of Biotechnology
Issue number1-3
Publication statusPublished - 2004 Sept 30
EventHighlights from the ECB11: Building Bridges Between Bioscience - Basel, Switzerland
Duration: 2003 Aug 12003 Aug 1


  • Bioinformatics
  • Computer simulation
  • Mathematical model
  • Metabolic engineering
  • Metabolome
  • Systems biology

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology


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