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. 2006 Mar 23:7:168.
doi: 10.1186/1471-2105-7-168.

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

Kazuharu Arakawa  1 , Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
Affiliations

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

Kazuharu Arakawa et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
The system workflow. Starting from a genome sequence, all coding regions are matched to corresponding reaction stoichiometry for qualitative modeling, and then the reactions are quantitatively modeled with kinetic equations to generate a cell-wide simulation model.
See this image and copyright information in PMC

References

    1. Kitano H. Systems biology: a brief overview. Science. 2002;295:1662–1664. doi: 10.1126/science.1069492. - DOI - PubMed
    1. Ni TC, Savageau MA. Application of biochemical systems theory to metabolism in human red blood cells. Signal propagation and accuracy of representation. J Biol Chem. 1996;271:7927–7941. doi: 10.1074/jbc.271.14.7927. - DOI - PubMed
    1. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature. 2004;429:92–96. doi: 10.1038/nature02456. - DOI - PubMed
    1. Normile D. Building working cells 'in silico'. Science. 1999;284:80–81. doi: 10.1126/science.284.5411.80b. - DOI - PubMed
    1. Kitano H. Computational systems biology. Nature. 2002;420:206–210. doi: 10.1038/nature01254. - DOI - PubMed

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