MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models.
MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models.
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DOI：
10.3389/fphys.2016.00327
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发表时间：
2016
影响因子：
4
通讯作者：
Thiele I
中科院分区：
文献类型：
--
作者：
Aurich MK;Fleming RM;Thiele I
代谢组学数据集提供了细胞表型的直接读出，并越来越多地用于研究生物学问题。我们和其他人以前的工作揭示了在代谢模型的背景下使用基于约束的建模分析细胞外代谢组学数据的潜力。通过MetaboTools，我们将我们的方法提供给更广泛的科学界。MetaboTools由一个协议、一个工具箱和两个用例的教程组成。该协议描述了，在一个逐步的方式，数据集成和计算分析的工作流程。MetaboTools包含完成方案中描述的工作流程所需的Matlab代码。Türgen解释了整合两个不同数据集的计算步骤，并展示了一套全面的方法，用于代谢模型的计算分析和不同表型的分层。所提出的工作流程支持多组学数据集的综合分析。重要的是，所有分析工具都可以应用于代谢模型，而无需执行整个工作流程。总之，MetaboTools构成了微生物、植物或人类细胞胞外代谢组学数据模型内分析的综合指南。这个计算建模资源为广泛的生物医学和非生物医学研究社区提供了广泛的计算分析工具。
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. This computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.