.. -*- coding: utf-8 -*-

============================
 Tutorial Jupyter Notebooks
============================

`@orbeckst`_ gave an introductory presentation (available in PDF_ or
Keynote08_ format) on MDAnalysis, its philopsophy and overall
structure and development process.

The workshop session was held by `@dotsdl`_ and `@orbeckst`_. They
live-coded in Jupyter_ notebooks.

Fundamentals
============

The notebook `MDAnalysis_Workshop_Part_1.ipynb`_ introduces the
fundamental objects of MDAnalysis: the ``Universe``, ``AtomGroup``,
and ``Atom`` objects. It also introduces the *selection language*, and
the basics of *reading* and *slicing trajectories*.


Trajectory analysis
===================

The notebook `MDAnalysis_Workshop_Part_2.ipynb`_ teaches how to work
with trajectories. The lesson includes different ways to access and select
frames and introduces common programming patterns for frame-based
analysis, including a range of real-world examples using the
trajectories from the :ref:`chapter-datadownload` section. 


.. SeeAlso::
   * Have a look at the official `MDAnalysis Tutorial`_.
   * See the `list of other tutorials`_.
   * Join the discussion on the `mdnalysis-discussion mailing list`_. 

.. Links

.. _`@orbeckst`: https://github.com/orbeckst
.. _`@dotsdl`: https://github.com/dotsdl
.. _PDF: https://github.com/Becksteinlab/MDAnalysis-workshop/blob/master/talk/mdanalysis_CECAM.pdf
.. _Keynote08: https://github.com/Becksteinlab/MDAnalysis-workshop/tree/master/talk/mdanalysis_CECAM.key

.. _Jupyter: http://jupyter.org/

.. _MDAnalysis_Workshop_Part_1.ipynb:
   http://nbviewer.ipython.org/github/Becksteinlab/MDAnalysis-workshop/blob/master/notebooks/MDAnalysis_Workshop_Part_1.ipynb
.. _MDAnalysis_Workshop_Part_2.ipynb:
   http://nbviewer.jupyter.org/github/Becksteinlab/MDAnalysis-workshop/blob/master/notebooks/MDAnalysis_Workshop_Part_2.ipynb


.. _MDAnalysis Tutorial: http://www.mdanalysis.org/MDAnalysisTutorial/
.. _`list of other tutorials`:
   https://github.com/MDAnalysis/mdanalysis/wiki/Tutorials
.. _`mdnalysis-discussion mailing list`:
   http://groups.google.com/group/mdnalysis-discussion