{"id":24841536,"url":"https://github.com/metexplore/cobratoolbox-lib","last_synced_at":"2025-07-22T14:04:19.756Z","repository":{"id":75692229,"uuid":"281187307","full_name":"MetExplore/cobratoolbox-lib","owner":"MetExplore","description":"COBRA Toolbox without submodules and minor modifications to improve 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raw:: html\n\n   \u003cp align=\"center\"\u003e\n     \u003cimg class=\"readme_logo\" src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/logo.png\" height=\"160px\"/\u003e\n   \u003c/p\u003e\n\n\nThe COBRA Toolbox |br| COnstraint-Based Reconstruction and Analysis Toolbox\n---------------------------------------------------------------------------\n\n.. raw:: html\n\n   \u003ctable\u003e\n     \u003ctr\u003e\n     \u003ctd\u003e\u003cdiv align=\"center\"\u003e\u003ca href=\"https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html\"\u003e\u003cimg src=\"https://img.shields.io/badge/COBRA-tutorials-blue.svg?maxAge=0\"\u003e\u003c/a\u003e\n       \u003ca href=\"https://opencobra.github.io/cobratoolbox/latest\"\u003e\u003cimg src=\"https://img.shields.io/badge/COBRA-docs-blue.svg?maxAge=0\"\u003e\u003c/a\u003e\n       \u003ca href=\"https://groups.google.com/forum/#!forum/cobra-toolbox\"\u003e\u003cimg src=\"https://img.shields.io/badge/COBRA-forum-blue.svg?maxAge=0\"\u003e\u003c/a\u003e\u003c/div\u003e\u003c/td\u003e\n       \u003ctd\u003e\u003cdiv align=\"center\"\u003e\u003ca href=\"https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-linux/\"\u003e\u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/badges/linux.svg\"\u003e\u003c/a\u003e\n       \u003ca href=\"https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-macOS/\"\u003e\u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/badges/macOS.svg\"\u003e\u003c/a\u003e\n       \u003ca href=\"https://prince.lcsb.uni.lu/jenkins/job/COBRAToolbox-branches-auto-windows7/\"\u003e\u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/badges/windows.svg\"\u003e\u003c/a\u003e\n       \u003ca href=\"http://opencobra.github.io/cobratoolbox/docs/builds.html\"\u003e\u003cimg src=\"http://concordion.org/img/benefit-links.png?maxAge=0\" height=\"20px\" alt=\"All continuous integration builds\"\u003e\u003c/a\u003e\n       \u003c/div\u003e\u003c/td\u003e\n       \u003ctd\u003e\u003cdiv align=\"center\"\u003e\u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/codegrade/codegrade.svg\" alt=\"Ratio of the number of inefficient code lines and the total number of lines of code (in percent). A: 0-3%, B: 3-6%, C: 6-9%, D: 9-12%, E: 12-15%, F: \u003e 15%.\"\u003e\n       \u003ca href=\"https://codecov.io/gh/opencobra/cobratoolbox/branch/master\"\u003e\u003cimg src=\"https://codecov.io/gh/opencobra/cobratoolbox/branch/master/graph/badge.svg?maxAge=0\"\u003e\u003c/a\u003e\u003c/div\u003e\u003c/td\u003e\n     \u003c/tr\u003e\n   \u003c/table\u003e\n   \u003cbr\u003e\n\n\nSystem Requirements and Solver Installation\n-------------------------------------------\n\n.. begin-requirements-marker\n\n|warning| Please follow `this guide \u003chttps://opencobra.github.io/cobratoolbox/docs/requirements.html\u003e`__ in order to configure your system properly.\n\n|warning| Please make sure you install a compatible solver. Check the compatibility `here \u003chttps://opencobra.github.io/cobratoolbox/docs/compatibility.html\u003e`__.\n\nYou may install ``TOMLAB``, ``IBM ILOG CPLEX``, ``GUROBI``, or ``MOSEK`` by following these `detailed instructions \u003chttps://opencobra.github.io/cobratoolbox/docs/solvers.html\u003e`__.\n\n.. end-requirements-marker\n\nInstallation\n------------\n\n.. begin-installation-marker\n\n1. Download this repository (the folder ``./cobratoolbox/`` will be\n   created). You can clone the repository using:\n\n   .. code-block:: console\n\n      $ git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox\n\n\n   |warning| Please note the ``--depth=1`` in the clone command. Run this command in ``Terminal`` (on |macos| and |linux|) or in ``Git Bash`` (on |windows|) -\n   **not** in |matlab|. Although not recommended, you can download the\n   repository as a `compressed archive \u003chttps://prince.lcsb.uni.lu/cobratoolbox/releases/theCOBRAToolbox.zip\u003e`__.\n\n2. Change to the folder ``cobratoolbox/`` and run from |matlab|\n\n   .. code-block:: matlab\n\n      \u003e\u003e initCobraToolbox\n\n.. end-installation-marker\n\n\nTutorials, Documentation, and Support\n-------------------------------------\n\n-  Consult all tutorials in the section |tutorials|. All tutorials can be run from\n   the\n   `/tutorials \u003chttps://github.com/opencobra/cobratoolbox/tree/master/tutorials\u003e`__\n   directory.\n\n-  All functions are documented in the |latest|.\n\n-  If you need support, please feel free to post your question in our |forum|.\n\n-  Answers to Frequently Asked Questions (**FAQ**) are\n   `here \u003chttps://opencobra.github.io/cobratoolbox/stable/faq.html\u003e`__.\n\n\nHow to contribute\n-----------------\n\n.. begin-how-to-contribute-marker\n\n|thumbsup| |tada| First off, thanks for taking the time to contribute to `The COBRA\nToolbox \u003chttps://github.com/opencobra/cobratoolbox\u003e`__! |tada| |thumbsup|\n\n.. raw:: html\n\n   \u003cp align=\"center\"\u003e\n   \u003cimg src=\"https://cdn.jsdelivr.net/gh/opencobra/MATLAB.devTools@e735bd91310e8ef10fab4d3c21833a85bf4b8159/docs/source/_static/img/logo_devTools.png\" height=\"120px\" alt=\"devTools\"/\u003e\n   \u003c/p\u003e\n\n\nYou can install the\n`MATLAB.devTools \u003chttps://github.com/opencobra/MATLAB.devTools\u003e`__ from\nwithin MATLAB by typing:\n\n.. code-block:: matlab\n\n    \u003e\u003e installDevTools()\n\n|bulb| Check out the `MATLAB.devTools\n\u003chttps://github.com/opencobra/MATLAB.devTools\u003e`__ - and contribute the smart\nway! The **official documentation** is `here \u003chttps://opencobra.github.com/MATLAB.devTools\u003e`__.\n\n|thumbsup| Contribute to the ``opencobra/cobratoolbox`` repository by following `these\ninstructions\n\u003chttps://opencobra.github.io/MATLAB.devTools/stable/contribute.html#the-cobra-toolbox\u003e`__:\n\n.. code-block:: matlab\n\n    \u003e\u003e contribute('opencobra/cobratoolbox');\n\n|thumbsup| Contribute to the ``opencobra/COBRA.tutorials`` repository by following `these\ninstructions\n\u003chttps://opencobra.github.io/MATLAB.devTools/stable/contribute.html#cobra-tutorials\u003e`__:\n\n.. code-block:: matlab\n\n    \u003e\u003e contribute('opencobra/COBRA.tutorials');\n\n-  Please follow the `Style\n   Guide \u003chttps://opencobra.github.io/cobratoolbox/docs/styleGuide.html\u003e`__.\n-  More information on writing a **test** is\n   `here \u003chttps://opencobra.github.io/cobratoolbox/docs/testGuide.html\u003e`__\n   and a template is\n   `here \u003chttps://opencobra.github.io/cobratoolbox/docs/testTemplate.html\u003e`__.\n-  More information on formatting the documentation is\n   `here \u003chttps://opencobra.github.io/cobratoolbox/docs/documentationGuide.html\u003e`__\n-  A guide for reporting an **issue** is `here \u003chttps://opencobra.github.io/cobratoolbox/docs/issueGuide.html\u003e`__.\n\nIf you want to use ``git`` via the command line interface and need help,\nthis\n`guide \u003chttps://www.digitalocean.com/community/tutorials/how-to-create-a-pull-request-on-github\u003e`__\nor the official `GitHub\nguide \u003chttps://help.github.com/articles/creating-a-pull-request/\u003e`__\ncome in handy.\n\n\n.. end-how-to-contribute-marker\n\nHow to cite the COBRA Toolbox\n-----------------------------\n\n.. begin-how-to-cite-marker\n\nWhen citing the COBRA Toolbox, it is important to cite the original\npaper where an algorithm was first reported, as well as its\nimplementation in the COBRA Toolbox. This is important, because the\nobjective of the COBRA Toolbox is to amalgamate and integrate the\nfunctionality of a wide range of COBRA algorithms and this will be\nundermined if contributors of new algorithms do not get their fair share\nof citations. The following is one example how to approach this within\nthe methods section of a paper (**not** the supplemental material\nplease):\n\n*To generate a context-specific model the FASTCORE algorithm [1],\nimplemented in The COBRA Toolbox v3.0 [2], was employed.*\n\n    [1] = Vlassis N, Pacheco MP, Sauter T (2014) Fast Reconstruction of\n    Compact Context-Specific Metabolic Network Models. PLoS Comput Biol\n    10(1): e1003424.\n\n..\n\n    [2] Laurent Heirendt \u0026 Sylvain Arreckx, Thomas Pfau, Sebastian N.\n    Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdottir, Jacek\n    Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdottir,\n    Chiam Yu Ng, German Preciat, Alise Zagare, Siu H.J. Chan, Maike K.\n    Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls,\n    Alberto Noronha, Aarash Bordbar, Benjamin Cousins, Diana C. El\n    Assal, Luis V. Valcarcel, Inigo Apaolaza, Susan Ghaderi, Masoud\n    Ahookhosh, Marouen Ben Guebila, Andrejs Kostromins, Nicolas\n    Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T.\n    Yurkovich, Miguel A.P. Oliveira, Phan T. Vuong, Lemmer P. El Assal,\n    Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A.\n    Bryant, Francisco J. Aragon Artacho, Francisco J. Planes, Egils\n    Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael\n    A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter,\n    Bernhard Ø. Palsson, Ines Thiele, Ronan M.T. Fleming, **Creation and\n    analysis of biochemical constraint-based models: the COBRA Toolbox\n    v3.0**, Nature Protocols, volume 14, pages 639–702, 2019\n    `doi.org/10.1038/s41596-018-0098-2 \u003chttps://doi.org/10.1038/s41596-018-0098-2\u003e`__.\n\n.. end-how-to-cite-marker\n\nBinaries and Compatibility\n--------------------------\n\n|warning| Please make sure you install a compatible solver. Check the\ncompatibility\n`here \u003chttps://opencobra.github.io/cobratoolbox/docs/compatibility.html\u003e`__.\n\n.. begin-binaries-marker\n\nFor convenience, we provide\n`glpk_mex \u003chttps://github.com/blegat/glpkmex\u003e`__ and\n`libSBML-5.17+ \u003chttp://sbml.org/Software/libSBML\u003e`__ in\n``/external``.\n\n`Binaries \u003chttps://github.com/opencobra/COBRA.binary\u003e`__ for these\nlibraries are provided in a submodule for Mac OS X 10.6 or later\n(64-bit), GNU/Linux Ubuntu 14.0+ (64-bit), and Microsoft Windows 7+\n(64-bit). For unsupported OS, please refer to their respective building\ninstructions\n(`glpk_mex \u003chttps://github.com/blegat/glpkmex#instructions-for-compiling-from-source\u003e`__,\n`libSBML \u003chttp://sbml.org/Software/libSBML/5.17.0/docs//cpp-api/libsbml-installation.html\u003e`__).\n\nRead more on the compatibility with SBML-FBCv2\n`here \u003chttps://opencobra.github.io/cobratoolbox/docs/notes.html\u003e`__.\n\n.. end-binaries-marker\n\nDisclaimer\n----------\n\n*The software provided by the openCOBRA Project is distributed under the\nGNU GPLv3 or later. However, this software is designed for scientific\nresearch and as such may contain algorithms that are associated with\npatents in the U.S. and abroad. If the user so chooses to use the\nsoftware provided by the openCOBRA project for commercial endeavors then\nit is solely the user’s responsibility to license any patents that may\nexist and respond in full to any legal actions taken by the patent\nholder.*\n\n\n.. icon-marker\n\n\n.. |macos| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/apple.png\" height=\"20px\" width=\"20px\" alt=\"macOS\"\u003e\n\n\n.. |linux| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/linux.png\" height=\"20px\" width=\"20px\" alt=\"linux\"\u003e\n\n\n.. |windows| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/windows.png\" height=\"20px\" width=\"20px\" alt=\"windows\"\u003e\n\n\n.. |warning| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/warning.png\" height=\"20px\" width=\"20px\" alt=\"warning\"\u003e\n\n\n.. |matlab| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/matlab.png\" height=\"20px\" width=\"20px\" alt=\"matlab\"\u003e\n\n\n.. |tada| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/tada.png\" height=\"20px\" width=\"20px\" alt=\"tada\"\u003e\n\n\n.. |thumbsup| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/thumbsUP.png\" height=\"20px\" width=\"20px\" alt=\"thumbsup\"\u003e\n\n\n.. |bulb| raw:: html\n\n   \u003cimg src=\"https://prince.lcsb.uni.lu/cobratoolbox/img/bulb.png\" height=\"20px\" width=\"20px\" alt=\"bulb\"\u003e\n\n\n.. |tutorials| raw:: html\n\n   \u003ca href=\"https://opencobra.github.io/cobratoolbox/latest/tutorials/index.html\"\u003e\u003cimg src=\"https://img.shields.io/badge/COBRA-tutorials-blue.svg?maxAge=0\"\u003e\u003c/a\u003e\n\n\n.. |latest| raw:: html\n\n   \u003ca href=\"https://opencobra.github.io/cobratoolbox/latest\"\u003e\u003cimg src=\"https://img.shields.io/badge/COBRA-docs-blue.svg?maxAge=0\"\u003e\u003c/a\u003e\n\n\n.. |forum| raw:: html\n\n   \u003ca href=\"https://groups.google.com/forum/#!forum/cobra-toolbox\"\u003e\u003cimg src=\"https://img.shields.io/badge/COBRA-forum-blue.svg\"\u003e\u003c/a\u003e\n\n\n.. |br| raw:: html\n\n   \u003cbr\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmetexplore%2Fcobratoolbox-lib","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmetexplore%2Fcobratoolbox-lib","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmetexplore%2Fcobratoolbox-lib/lists"}