Journal article · Preprint article
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
University of Luxembourg1
Institut national de la santé et de la recherche médicale2
Stanford University3
Michigan State University4
University of Utah5
Imperial College London6
University of Alicante7
California Institute of Technology8
Big Data 2 Knowledge, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark9
Network Reconstruction in Silico Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark10
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark11
University of Chile12
University of California at San Diego13
European Bioinformatics Institute14
Pennsylvania State University15
Sinopia Biosciences16
Georgia Institute of Technology17
University of Navarra18
University of Latvia19
...and 9 moreConstraint-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.
| Language: | English |
|---|---|
| Publisher: | Nature Publishing Group UK |
| Year: | 2019 |
| Pages: | 639-702 |
| Journal subtitle: | Recipes for Researchers |
| ISSN: | 17502799 and 17542189 |
| Types: | Journal article and Preprint article |
| DOI: | 10.1038/s41596-018-0098-2 |
| ORCIDs: | Palsson, Bernhard O. , 0000-0001-5048-2923 , 0000-0002-2192-5569 , 0000-0003-3769-5419 , 0000-0002-8961-4513 , 0000-0002-9403-509X , 0000-0001-8086-8915 and 0000-0001-7700-3654 |
General Biochemistry, Genetics and Molecular Biology Genome Metabolic Networks and Pathways Metabolic models Models, Biological Software Systems Biology biochemistry bioinformatics computational biology constraint-based modelling data integration gap filling human metabolism metabolic engineering metabolic reconstruction metabolomics microbiome analysis omics strain engineering transcriptomics
