Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
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DOI：
10.1038/s41596-018-0098-2
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发表时间：
2019-03-01
期刊：
影响因子：
14.8
通讯作者：
Fleming, Ronan M. T.
中科院分区：
文献类型：
--
作者：
Heirendt, Laurent;Arreckx, Sylvain;Fleming, Ronan M. T.
基于约束的重建和分析（COBRA）为实验分子系统生物学数据的综合分析和物理化学和生物化学可行的表型状态的定量预测提供了分子机制框架。COBRA是一个全面的可互操作的COBRA方法的桌面软件套件。它在生物学、生物医学和生物技术中得到了广泛的应用，因为它的功能可以灵活地组合起来，为任何生物化学网络实现定制的COBRA协议。本方案是对COBRA EQUIPMENT v.1.0和v.2.0的更新。3.0版包括质量控制重建，建模，拓扑分析，应变和实验设计，网络可视化，以及化学信息学，代谢组学，转录组学，蛋白质组学和热化学数据的网络集成的新方法。新的多语言代码集成还通过分别用于多尺度、多细胞和反应动力学建模的高精度、高性能和非线性数值优化求解器扩展了COBRA的应用范围。该协议提供了所有这些新功能的概述，并可适用于在各种场景中生成和分析基于约束的模型。COBRA 3.0提供了无与伦比的深度的COBRA方法。
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods.