FluxExplorer: A general platform for modeling and analyses of metabolic net-works based on stoichiometry

查看全文 作　　者：LUO [1,3]Ruoyu;LIAO [1,3]Sha;ZENG [1]Shaoqun;LI [2]Yixue;LUO [1]Qingming 机构地区：[1]Hubei Bioinformatics and Molecular Imaging Key Laboratory,Huazhong University of Science and Technology, Wuhan 430074,China;[2]Shanghai Center for Bioinformation Technology, Shanghai 200233,China;[3]These authors contributed equally to this work 出　　处：《Chinese Science Bulletin》索引2006年第51卷第6期,共8页 摘　　要：Stoichiometry-based analyses of meta- bolic networks have aroused significant interest of systems biology researchers in recent years. It is necessary to develop a more convenient modeling platform on which users can reconstruct their network models using completely graphical operations, and explore them with powerful analyzing modules to get a better understanding of the properties of metabolic systems. Herein, an in silico platform, FluxExplorer, for metabolic modeling and analyses based on stoichiometry has been developed as a publicly available tool for systems biology research. This platform integrates various analytic approaches, in- cluding flux balance analysis, minimization of meta- bolic adjustment, extreme pathways analysis, shadow prices analysis, and singular value decom- position, providing a thorough characterization of the metabolic system. Using a graphic modeling process, metabolic networks can be reconstructed and modi- fied intuitively and conveniently. The inconsistencies of a model with respect to the FBA principles can be proved automatically. In addition, this platform sup- ports systems biology markup language (SBML). FluxExplorer has been applied to rebuild a metabolic network in mammalian mitochondria, producing meaningful results. Generally, it is a powerful and very convenient tool for metabolic network modeling and analysis. 关 键 词：新陈代谢 化学计量学 系统生物学 流量平衡分析 计算模型