GEM system: Automatic prototyping of cell-wide metabolic pathway models from genomes

Karuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

Background: Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell simulation are labor-intensive, manual affairs, and therefore constitute a major bottleneck in the evolution of computational cell biology. Results: We developed the Genome-based Modeling (GEM) System for the purpose of automatically prototyping simulation models of cell-wide metabolic pathways from genome sequences and other public biological information. Models generated by the GEM System include an entire Escherichia coli metabolism model comprising 968 reactions of 1195 metabolites, achieving 100% coverage when compared with the KEGG database, 92.38% with the EcoCyc database, and 95.06% with iJR904 genome-scale model. Conclusion: The GEM System prototypes qualitative models to reduce the labor-intensive tasks required for systems biology research. Models of over 90 bacterial genomes are available at our web site.

Original languageEnglish (US)
Article number168
JournalBMC Bioinformatics
Volume7
DOIs
StatePublished - Mar 23 2006
Externally publishedYes

Fingerprint

Prototyping
Metabolic Networks and Pathways
System Modeling
Pathway
Genome
Genes
Cell
Systems Biology
Databases
Bacterial Genomes
Cytology
Model
Personnel
Computational Biology
Cell Biology
Metabolites
Metabolism
Escherichia coli
Escherichia Coli
Biology

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

GEM system : Automatic prototyping of cell-wide metabolic pathway models from genomes. / Arakawa, Karuharu; Yamada, Yohei; Shinoda, Kosaku; Nakayama, Yoichi; Tomita, Masaru.

In: BMC Bioinformatics, Vol. 7, 168, 23.03.2006.

Research output: Contribution to journalArticle

Arakawa, Karuharu ; Yamada, Yohei ; Shinoda, Kosaku ; Nakayama, Yoichi ; Tomita, Masaru. / GEM system : Automatic prototyping of cell-wide metabolic pathway models from genomes. In: BMC Bioinformatics. 2006 ; Vol. 7.
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