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

• DOI: 10.48550/arxiv.1710.04038
• Publication Date: 2017-01-01
• Authors: Laurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsd...; Jacek Wachowiak; Sarah Keating; Vanja Vlasov; Stefanía Magnúsdó...; Chiam Yu Ng; German Preciat; Alise Žagare; Siu Hung Joshua Chan; Maike K. Aurich; Catherine M. Clancy; Jennifer Modamio; John T. Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C. El Assal; Luis V. Valcárcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai Minh Le; Ding Ma; Yuekai Sun; Lin Wang; James T. Yurkovich; Miguel A.P. Oliveira; Phan Tu Vuong; Lemmer P. El Assal; Inna Kuperstein; Andreï Zinovyev; H.S. Hinton; William A Bryant; Francisco J. Arag...; Francisco J. Planes; Egils Stalidzāns; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard Ø. Palsson; Ines Thiele; Ronan M. T. Fleming
• Keywords: Cobra; Toolbox; Scope (computer science)

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