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COBRA methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. COBRApy is a constraint-based modeling package that is designed to accommodate the biological complexity of the next generation of COBRA models and provides access to commonly used COBRA methods, such as flux balance analysis, flux variability analysis, and gene deletion analyses.
Our aim with COBRApy is to provide useful, efficient infrastructure for:
Our goal with COBRApy is for it to be useful on its own, and for it to be the natural choice of infrastructure for developers that want to build new COBRA related python packages for e.g. visualization, strain-design and data driven analysis. By re-using the same classes and design principles, we can make new methods both easier to implement and easier to use, thereby bringing the power of COBRA to more researchers.
The documentation is browseable online at
readthedocs <https://cobrapy.readthedocs.org/en/stable/>_ and can also be
Please use the
Google Group <http://groups.google.com/group/cobra-pie>_ for
help. By writing a well formulated question, with sufficient detail, you are
much more likely to quickly receive a good answer! Please refer to these
StackOverflow guidelines <https://stackoverflow.com/help/how-to-ask>_ on how
to ask questions. Alternatively, you can use
gitter.im <https://gitter.im/opencobra/cobrapy>_ for quick questions and discussions
about COBRApy (faster response times). Please keep in mind that answers are
provided on a volunteer basis.
More information about opencobra is available at the
If you use COBRApy in a scientific publication, please cite
Use pip to
install COBRApy from PyPI <https://pypi.org/project/cobra/>_ (we
recommend doing this inside a
virtual environment <http://docs.python-guide.org/en/latest/dev/virtualenvs/>_)::
pip install cobra
If you want to load MATLAB models, you will need additional dependencies. Please install::
pip install cobra[array]
For further information, please follow the
detailed installation instructions <INSTALL.rst>_.
Contributions are always welcome! Please read the
contributing guidelines <https://github.com/opencobra/cobrapy/blob/devel/.github/CONTRIBUTING.rst>_ to
The COBRApy source is released under both the GPL and LGPL licenses version 2 or later. You may choose which license you choose to use the software under.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the GNU Lesser General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.