.. _examples:

Examples
========

The following examples show off various aspects or capabilities of
MSMBuilder. They can be run interactively in Jupyter (IPython) notebook.
Download the `notebook files
<https://github.com/msmbuilder/msmbuilder/tree/master/examples>`_ and open
them in Jupyter::

    $ jupyter notebook

.. To make the ipython rendered images show up, each rst file must be
   in its own directory.

.. toctree::
   :maxdepth: 2
   :titlesonly:
   
   Fs-Peptide-in-RAM
   Fs-Peptide-with-dataset
   Fs-Peptide-command-line
   tICA-vs-PCA
   Clustering-Comparison
   GMRQ-Model-Selection
   Ward-Clustering


Contributing examples
---------------------

Do you have a neat example of using MSMBuilder? Format your code
into an IPython notebook and submit a pull request!

.. vim: tw=75