The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods. This protocol overviews all of these new features and can be adapted to generate and analyse constraint-based models in a wide variety of scenarios. 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. 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 chemoin-formatic, metabolomic, transcriptomic, proteomic, and thermochemical data.
This protocol is an update to the COBRA Toolbox 1.0 and 2.0. 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.
The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. Fleming 1, 24ĬOnstraint-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.
Palsson, 13, 21 Ines Thiele, 1 and Ronan M.T. Lewis, 4, 19 Thomas Sauter, 2 Bernhard Ø. Planes, 10 Egils Stalidzans, 11 Alejandro Maass, 3, 18 Santosh Vempala, 9 Michael Hucka, 17 Michael A. El Assal, 1 Inna Kuperstein, 22 Andrei Zinovyev, 22 H. Le, 1 Ding Ma, 12 Yuekai Sun, 23 Lin Wang, 6 James T. Valcarcel, 10 Iñigo Apaolaza, 10 Susan Ghaderi, 1 Masoud Ahookhosh, 1 Marouen Ben Guebila, 1 Andrejs Kostromins, 11 Nicolas Sompairac, 22 Hoai M. Sauls, 7 Alberto Noronha, 1 Aarash Bordbar, 8 Benjamin Cousins, 9 Diana C. Keating, 5 Vanja Vlasov, 1 Stefania Magnusdóttir, 1 Chiam Yu Ng, 6 German Preciat, 1 Alise Žagare, 1 Siu H.J. Haraldsdóttir, 1 Jacek Wachowiak, 1 Sarah M. Mendoza, 3, 18 Anne Richelle, 4 Almut Heinken, 1 Hulda S. Laurent Heirendt, # 1 Sylvain Arreckx, # 1 Thomas Pfau, 2 Sebastián N.