.. _tutorial_run_jupyter_notebook:

How to run Jupyter notebook
---------------------------

.. container:: custom-index
    
    .. raw:: html
    
        <script type="text/javascript" src='../_static/cindex.js'></script>

Install
~~~~~~~

.. code-block:: bash

   # if you already install python via Anaconda distribution
   # https://www.continuum.io/downloads, you don't need to install jupyter notebook again.
   conda install jupyter notebook

   # further detail: http://jupyter.org/

Download notebook
~~~~~~~~~~~~~~~~~
 
.. code-block:: bash

   wget  http://amber-md.github.io/pytraj/latest/tutorials/pca_evaluated.ipynb 

Run
~~~

.. code-block:: bash

   # tz2.{nc, parm7} can be downloaded from
   # https://github.com/Amber-MD/pytraj/tree/master/tests/data

   # or: $AMBERHOME/AmberTools/test/cpptraj/ if you are using AMBER

   ipython notebook pca_evaluated.ipynb

   # or use AMBER16 distribution
   amber.ipython notebook pca_evaluated.ipython

.. note:: To create a new notebook, type ``ipython notebook``

Example
~~~~~~~

`PCA analysis <tutorial_pca>`_

See also
~~~~~~~~

Run Jupyter notebook `remotely <remote_jupyter_notebook>`_

.. image:: ../images/tutorial_autoimage.png