COBRApy is a package for constraint-based modeling of biological networks

README.rst

cobrapy - Constraint-Based Reconstruction and Analysis in Python

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What is cobrapy?

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:

  • creating and managing metabolic models
  • accessing popular solvers
  • analyzing models with methods such as FVA, FBA, pFBA, MOMA etc.
  • inspecting models and drawing conclusions on gene essentiality, testing consequences of knock-outs etc.

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 and can also be downloaded.

Please use the Google Group 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 on how to ask questions. Alternatively, you can use gitter.im 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 website.

If you use cobrapy in a scientific publication, please cite doi:10.1186/1752-0509-7-74

Installation

Use pip to install cobrapy from PyPI (we recommend doing this inside a virtual environment):

pip install cobra

In case you downloaded the source code, run:

pip install -e .

In the cobrapy directory. For further information, please follow the detailed installation instructions.

Contributing

Contributions are always welcome! Please read the contributions guideline to get started.

License

The cobrapy source is released under both the GPL and LGPL licenses. You may choose which license you choose to use the software under. However, please note that binary packages which include GLPK (such as the binary wheels distributed at https://pypi.python.org/pypi/cobra) will be bound by its license as well.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License or the Lesser GNU 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.