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

• Main Authors: Nakayama Yoichi, Shinoda Kosaku, Yamada Yohei, Arakawa Kazuharu, Tomita Masaru
• Format: Article
• Language: English
• Published: BMC 2006-03-01
• Series: BMC Bioinformatics
• Online Access: http://www.biomedcentral.com/1471-2105/7/168

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Escherichia coli </it>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.</p> <p>Conclusion</p> <p>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.</p>