Tutorials and Examples
----------------------

.. note::
   This section provides tutorials on how to use pyAMARES in Jupyter Notebooks. 
   To start a Jupyter Notebook server from the command line, open a terminal and run:

   .. code-block:: bash

      jupyter notebook

   Please see `docs.jupyter.org <https://docs.jupyter.org/en/latest/running.html>`_ for more details.


.. toctree::
   :maxdepth: 2 

   fileio
   notebooks/priorknowledge
   notebooks/simple_tutorial
   notebooks/X-Nuclei_Example
   notebooks/HSVDinitializer_unknowncompounds
   notebooks/demo_batch
   notebooks/Remove_Metabolite_residuals