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CellNOpt documentation
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.. topic:: cellnopt

    .. image:: network.png
        :width: 30%


Motivation 
###########


**cellnopt** is a pure Python library that provides core functions to manipulate signalling data. It provides functions to create and manipulate networks that can be used later on with MIDAS files (phosphorylation measurements). You can read/write data formats such as :ref:`sif` and :ref:`midas` that are used in `CellNOptR <http://bioconductor.org/packages/release/bioc/html/CellNOptR.html>`_.

It does not provide any logical formalism to simulate or optimise the network to
the data. It is rather intended to be a package dedicated to the pre and post
processing of signalling pathways. 


Installation
###################

The **cno** package has a dependencies on **pandas**, which requires cython. So, you need to install cython first. 

All other dependencies should be installed automatically (networkx, numpy, matplotlib).

::

    pip install cno


Contributions and issues
##########################

Code hosted on `github <https://github.com/cellnopt/cellnopt>`_.

User guide
##################


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

    quickstart.rst

..    userguide.rst
..    applications.rst

References
##################


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

    references
    ref_formalism
    ref_core

.. .. toctree::
..    biblio.rst
    ChangeLog.rst