Documentation for COBRApy
=========================

For installation instructions, please see `INSTALL.rst
<https://github.com/opencobra/cobrapy/blob/devel/INSTALL.rst>`_.

Many of the examples below are viewable as IPython notebooks, which can
be viewed at `nbviewer
<http://nbviewer.ipython.org/github/opencobra/cobrapy/tree/stable/documentation_builder/>`_.

.. toctree::
    :numbered: 3
    :maxdepth: 2

    getting_started
    configuration
    building_model
    io
    simulating
    deletions
    phenotype_phase_plane
    sampling
    loopless
    consistency
    gapfilling
    media
    solvers
    constraints_objectives
    dfba
    pymatbridge
    faq
    API </autoapi/cobra/index.rst>


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`