Package: cobra
COBRApy - Constraint-Based Reconstruction and Analysis in PythonWhat is COBRApy?COBRA methods are widely used for genome-scale modeling of metabolic networks in
both prokaryotes and eukaryotes.COBRApyis 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 modelsaccessing popular solversanalyzing 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 atreadthedocsand can also bedownloaded.Please use theGoogle Groupfor
help. By writing a well formulated question, with sufficient detail, you are
much more likely to quickly receive a good answer! Please refer to theseStackOverflow guidelineson how
to ask questions.  Alternatively, you can usegitter.imfor 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 thewebsite.If you use COBRApy in a scientific publication, please citedoi:10.1186/1752-0509-7-74InstallationUse pip toinstall COBRApy from PyPI(we
recommend doing this inside avirtual environment):pip install cobraIf you want to load MATLAB models, you will need additional dependencies. Please
install:pip install cobra[array]For further information, please follow thedetailed installation instructions.ContributingContributions are always welcome! Please read thecontributing guidelinesto
get started.LicenseThe 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.Installation of COBRApyFor installation help, please use theGoogle Group. For usage instructions, please see
thedocumentation.We only test against Python 3.7+, however, Python 3.4 or higher work mostly.
For Windows users and possibly also Mac OS users, we recommend using theAnaconda Pythondistribution.Stable version installationCOBRApy can be installed with any recent installation of pip.  Instructions for
several operating systems are below:Mac OS X or LinuxWe highly recommend that you create aPython virtual environment.Install COBRApy when an environment is active by runningpip install cobrain the terminal.Microsoft WindowsIf you heed our recommendation to use Anaconda, you can open an Anaconda shell
and install COBRApy from theconda-forgechannel.conda install -c conda-forge cobraInstallation for developmentGet thedetailed contribution instructionsfor
contributing to COBRApy.SolversCOBRApy usesoptlangto interface the
mathematical solvers used to optimize the created COBRA models.  At the time of
writing the supported solvers are:ILOG/CPLEX (available withAcademicandCommerciallicenses)GurobiGLPKwhich is automatically installed
as swiglpk