EFMviz：一种用于可视化基因组尺度代谢模型中基本通量模式的COBRA Toolbox扩展工具。
EFMviz: A COBRA Toolbox extension to visualize Elementary Flux Modes in Genome-Scale Metabolic Models.
作者信息
Sarathy Chaitra, Kutmon Martina, Lenz Michael, Adriaens Michiel E, Evelo Chris T, Arts Ilja C W
机构信息
Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, 6229 ER Maastricht, The Netherlands.
Department of Bioinformatics-BiGCaT, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, 6229 ER Maastricht, The Netherlands.
出版信息
Metabolites. 2020 Feb 12;10(2):66. doi: 10.3390/metabo10020066.
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (, iAF1260) and large (human, Recon 2.2) genome-scale metabolic models. EFMviz is open-source and integrated into COBRA Toolbox. The analysis workflows used for the two use cases are detailed in the two tutorials provided with EFMviz along with the data used in this study.
基本通量模式（Elementary Flux Modes，EFMs）是一种用于基于约束的建模和代谢网络分析的工具。然而，能够整合各种数据类型的EFMs的系统自动化可视化仍然是一个挑战。在本研究中，我们为广泛采用的COBRA Toolbox开发了一个扩展EFMviz，用于将EFMs作为反应、代谢物和基因网络进行分析和图形可视化。该分析工作流程提供了一个EFM可视化平台，通过将COBRA Toolbox与网络分析和可视化软件Cytoscape连接，提高EFM的可解释性。EFMviz的生物学适用性在两个关于中等规模（iAF1260）和大规模（人类，Recon 2.2）基因组规模代谢模型的用例中得到了证明。EFMviz是开源的，并集成到COBRA Toolbox中。用于两个用例的分析工作流程在随EFMviz提供的两个教程以及本研究中使用的数据中进行了详细说明。
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