  COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular
mechanistic framework for integrative analysis of experimental data and
quantitative prediction of physicochemically and biochemically feasible
phenotypic states. The COBRA Toolbox is a comprehensive software suite of
interoperable COBRA methods. It has found widespread applications in biology,
biomedicine, and biotechnology because its functions can be flexibly combined
to implement tailored COBRA protocols for any biochemical network. Version 3.0
includes new methods for quality controlled reconstruction, modelling,
topological analysis, strain and experimental design, network visualisation 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 optimisation solvers for multi-scale,
multi-cellular and reaction kinetic modelling, respectively. This protocol can
be adapted for the generation and analysis of a constraint-based model in a
wide variety of molecular systems biology scenarios. This protocol is an update
to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an
unparalleled depth of constraint-based reconstruction and analysis methods.
