The COBRA Toolbox - COnstraint-Based Reconstruction and Analysis Toolbox
|MATLAB R2016b||MATLAB R2015b||MATLAB R2014b||Code Coverage||Code Grade|
Clone this repository
git clone https://github.com/opencobra/cobratoolbox.git cobratoolbox
For convenience, we provide the
SBMLToolbox 4.1.0, and
io/utilities. Binaries for these librairies are provided in a submodule for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 10.0 (64-bit), and Microsoft Windows 7 (64-bit). For unsupported OS, please refer to their respective building instructions (
git submodule init
git submodule update
From MATLAB, run
NOTE: If you do not have
tomlabinstalled on your machine, you will get some warnings and some errors. The
COBRAToolboxwill try to use
glpkif it cannot find
gurobifor LP / MILP. To solve any NLP problems you need
In order to test your installation, run
to see what functions will work with your current configuration. It might be that some functions may not work unless you have
All tutorials are included in the folder tutorials. More tutorial are currently being prepared.
Frequently Asked Questions (FAQ)
Before opening a new issue, please read first the section of Frequently Asked Questions FAQ.
How to contribute
- In order to contribute, you may follow the Contributing Guide.
- When opening an issue, please follow the Issue template.
- When submitting a Pull Request, please follow the PR template.
How to cite
The COBRA Toolbox
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 , implemented in The COBRA Toolbox , was employed.
 = Vlassis N, Pacheco MP, Sauter T (2014) Fast Reconstruction of Compact Context-Specific Metabolic Network Models. PLoS Comput Biol 10(1): e1003424.
 = Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ. 2011 Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0. Nature Protocols 6:1290-1307.