使用YANAsquare进行集成网络重建、可视化和分析。
Integrated network reconstruction, visualization and analysis using YANAsquare.
作者信息
Schwarz Roland, Liang Chunguang, Kaleta Christoph, Kühnel Mark, Hoffmann Eik, Kuznetsov Sergei, Hecker Michael, Griffiths Gareth, Schuster Stefan, Dandekar Thomas
机构信息
Department of Bioinformatics, Biocenter Am Hubland, D-97074 University of Würzburg, Germany.
出版信息
BMC Bioinformatics. 2007 Aug 28;8:313. doi: 10.1186/1471-2105-8-313.
BACKGROUND
Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network.
RESULTS
YANAsquare provides a software framework for rapid network assembly (flexible pathway browser with local or remote operation mode), network overview (visualization routine and YANAsquare editor) and network performance analysis (calculation of flux modes as well as target and robustness tests). YANAsquare comes as an easy-to-setup program package in Java. It is fully compatible and integrates the programs YANA (translation of gene expression values into flux distributions, metabolite network dissection) and Metatool (elementary mode calculation). As application examples we set-up and model the phospholipid network in the phagosome and genome-scale metabolic maps of S.aureus, S.epidermidis and S.saprophyticus as well as test their robustness against enzyme impairment.
CONCLUSION
YANAsquare is an application software for rapid setup, visualization and analysis of small, larger and genome-scale metabolic networks.
背景
代谢网络建模包括网络组装、网络概述、代谢通量计算以及测试网络的稳健性等任务。
结果
YANAsquare提供了一个软件框架，用于快速网络组装（具有本地或远程操作模式的灵活通路浏览器）、网络概述（可视化程序和YANAsquare编辑器）以及网络性能分析（通量模式计算以及目标和稳健性测试）。YANAsquare以易于设置的Java程序包形式提供。它与YANA（将基因表达值转化为通量分布、代谢物网络剖析）和Metatool（基本模式计算）程序完全兼容并集成。作为应用示例，我们构建并模拟了吞噬体中的磷脂网络以及金黄色葡萄球菌、表皮葡萄球菌和腐生葡萄球菌的基因组规模代谢图谱，并测试了它们对酶损伤的稳健性。
结论
YANAsquare是一款用于快速构建、可视化和分析小型、大型及基因组规模代谢网络的应用软件。
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