GitHub - opencobra/cobratoolbox: The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation: (original) (raw)

The COBRA Toolbox

COnstraint-Based Reconstruction and Analysis Toolbox

System Requirements and Solver Installation

Please follow this guide in order to configure your system properly.

Please make sure you install a compatible solver. Check the compatibility here.

You may install TOMLAB, IBM ILOG CPLEX, GUROBI, or MOSEK by following these detailed instructions.

Installation

1. Download this repository (the folder ./cobratoolbox/ will be created). You can clone the repository using:
   $ git clone --depth=1 https://github.com/opencobra/cobratoolbox.git cobratoolbox
   Please note the --depth=1 in the clone command. Run this command in Terminal (on and ) or in Git Bash (on ) -not in . Although not recommended, you can download the repository as a compressed archive.
2. Change to the folder cobratoolbox/ and run from

Tutorials, Documentation, and Support

How to contribute

First off, thanks for taking the time to contribute to The COBRA Toolbox!

You can install theMATLAB.devTools from within MATLAB by typing:

Check out MATLAB.devTools - and contribute the smart way! The official documentation is `here <https://opencobra.github.io/MATLAB.devTools/ >`__.

Contribute to the opencobra/cobratoolbox repository by following these instructions:

contribute('opencobra/cobratoolbox');

Contribute to the opencobra/COBRA.tutorials repository by following these instructions:

contribute('opencobra/COBRA.tutorials');

• Please follow the Style Guide.
• More information on writing a test ishereand a template ishere.
• More information on formatting the documentation ishere
• A guide for reporting an issue is here.

If you want to use git via the command line interface and need help, thisguideor the official GitHub guidecome in handy.

How to cite the COBRA Toolbox

When citing the COBRA Toolbox, it is important to cite the original paper where an algorithm was first reported, as well as its implementation in the COBRA Toolbox. This is important, because the objective of the COBRA Toolbox is to amalgamate and integrate the functionality of a wide range of COBRA algorithms and this will be undermined if contributors of new algorithms do not get their fair share of citations. The following is one example how to approach this within the methods section of a paper (not the supplemental material please):

To generate a context-specific model the FASTCORE algorithm [1], implemented in The COBRA Toolbox v3.0 [2], was employed.

[1] = Vlassis N, Pacheco MP, Sauter T (2014) Fast Reconstruction of Compact Context-Specific Metabolic Network Models. PLoS Comput Biol 10(1): e1003424.

[2] Laurent Heirendt & Sylvain Arreckx, Thomas Pfau, Sebastian N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdottir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdottir, Chiam Yu Ng, German Preciat, Alise Zagare, 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, Inigo 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. Aragon 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, Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0, Nature Protocols, volume 14, pages 639–702, 2019doi.org/10.1038/s41596-018-0098-2.

Binaries and Compatibility

Please make sure you install a compatible solver. Check the compatibilityhere.

For convenience, we provideglpk_mex andlibSBML-5.17+ in/external.

Binaries for these libraries are provided in a submodule for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 14.0+ (64-bit), and Microsoft Windows 7+ (64-bit). For unsupported OS, please refer to their respective building instructions (glpk_mex,libSBML).

Read more on the compatibility with SBML-FBCv2here.

Disclaimer

The software provided by the openCOBRA Project is distributed under the GNU GPLv3 or later. However, this software is designed for scientific research and as such may contain algorithms that are associated with patents in the U.S. and abroad. If the user so chooses to use the software provided by the openCOBRA project for commercial endeavors then it is solely the user’s responsibility to license any patents that may exist and respond in full to any legal actions taken by the patent holder.