GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
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DOI：
10.1186/1471-2105-7-168
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发表时间：
2006-03-23
影响因子：
3
通讯作者：
Tomita, M
中科院分区：
文献类型：
--
作者：
Arakawa, K;Yamada, Y;Tomita, M
背景：成功实现“系统生物学”方法来分析细胞是我们理解生命的巨大挑战。然而，目前的建模方法，细胞模拟是劳动密集型，手工事务，因此构成了一个主要的瓶颈，在计算细胞biology.Results的演变：我们开发了基于基因组的建模（GEM）系统的目的是自动原型化的模拟模型的细胞范围内的代谢途径的基因组序列和其他公共生物信息。GEM系统生成的模型包括一个完整的大肠杆菌代谢模型，包括968个反应的1195代谢产物，实现100%的覆盖率相比，KEGG数据库，92.38%的EcoCyc数据库，95.06%的iJR 904基因组规模model.Conclusion：GEM系统原型定性模型，以减少系统生物学研究所需的劳动密集型任务。在我们的网站上有超过90种细菌基因组的模型。
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.