{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/creation-and-analysis-of-biochemical","title":"Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0","arxiv_id":"1710.04038","date":"2017-10-11","proceeding":null,"authors":["Laurent Heirendt","Sylvain Arreckx","Thomas Pfau","Sebastián N. Mendoza","Anne Richelle","Almut Heinken","Hulda S. Haraldsdóttir","Jacek Wachowiak","Sarah M. Keating","Vanja Vlasov","Stefania Magnusdóttir","Chiam Yu Ng","German Preciat","Alise Žagare","Siu H. J. Chan","Maike K. Aurich","Catherine M. Clancy","Jennifer Modamio","John T. Sauls","Alberto Noronha","Aarash Bordbar","Benjamin Cousins","Diana C. El Assal","Luis V. Valcarcel","Iñigo Apaolaza","Susan Ghaderi","Masoud Ahookhosh","Marouen Ben Guebila","Andrejs Kostromins","Nicolas Sompairac","Hoai M. Le","Ding Ma","Yuekai Sun","Lin Wang","James T. Yurkovich","Miguel A. P. Oliveira","Phan T. Vuong","Lemmer P. El Assal","Inna Kuperstein","Andrei Zinovyev","H. Scott Hinton","William A. Bryant","Francisco J. Aragón Artacho","Francisco J. Planes","Egils Stalidzans","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"],"abstract":"COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular\nmechanistic framework for integrative analysis of experimental data and\nquantitative prediction of physicochemically and biochemically feasible\nphenotypic states. The COBRA Toolbox is a comprehensive software suite of\ninteroperable COBRA methods. It has found widespread applications in biology,\nbiomedicine, and biotechnology because its functions can be flexibly combined\nto implement tailored COBRA protocols for any biochemical network. Version 3.0\nincludes new methods for quality controlled reconstruction, modelling,\ntopological analysis, strain and experimental design, network visualisation as\nwell as network integration of chemoinformatic, metabolomic, transcriptomic,\nproteomic, and thermochemical data. New multi-lingual code integration also\nenables an expansion in COBRA application scope via high-precision,\nhigh-performance, and nonlinear numerical optimisation solvers for multi-scale,\nmulti-cellular and reaction kinetic modelling, respectively. This protocol can\nbe adapted for the generation and analysis of a constraint-based model in a\nwide variety of molecular systems biology scenarios. This protocol is an update\nto the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an\nunparalleled depth of constraint-based reconstruction and analysis methods.","url_abs":"http://arxiv.org/abs/1710.04038v2","url_pdf":"http://arxiv.org/pdf/1710.04038v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"creation-and-analysis-of-biochemical","repo_url":"https://github.com/opencobra/cobratoolbox","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null},{"paper_slug":"creation-and-analysis-of-biochemical","repo_url":"https://github.com/chaplenf/microBiome-v3.4","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"experimental-design","task_name":"Experimental Design"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}