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COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecularmechanistic framework for integrative analysis of experimental data andquantitative prediction of physicochemically and biochemically feasiblephenotypic states. The COBRA Toolbox is a comprehensive software suite ofinteroperable COBRA methods. It has found widespread applications in biology,biomedicine, and biotechnology because its functions can be flexibly combinedto implement tailored COBRA protocols for any biochemical network. Version 3.0includes new methods for quality controlled reconstruction, modelling,topological analysis, strain and experimental design, network visualisation aswell as network integration of chemoinformatic, metabolomic, transcriptomic,proteomic, and thermochemical data. New multi-lingual code integration alsoenables an expansion in COBRA application scope via high-precision,high-performance, and nonlinear numerical optimisation solvers for multi-scale,multi-cellular and reaction kinetic modelling, respectively. This protocol canbe adapted for the generation and analysis of a constraint-based model in awide variety of molecular systems biology scenarios. This protocol is an updateto the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides anunparalleled depth of constraint-based reconstruction and analysis methods.

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0