.. _ref_notebook:

===============
Notebook server
===============

.. toctree::
   :maxdepth: 2

Visit our online notebook server `here <https://notebook.biosimspace.org>`__.
This will launch a `Jupyter <https://jupyter.org>`__ hub running inside of
a `Docker <https://www.docker.com/>`__ container. This includes all of the
software that is required, allowing you to play around with BioSimSpace and
learn how it works without needing to install anything yourself.

Demos
=====

The notebook server has a set of example nodes to get you started. To run any
of these, simply navigate to the ``demo`` directory from the landing page.
A description of each node is given below:

* ``conversion.ipynb``: Convert between common molecular file formats.
* ``input_files.ipynb``: Generate molecular dynamics input files for a range of protocols and molecular dynamics engines.
* ``molecular_setup.ipynb``: Parameterise and solvate a molecule ready for simulation.
* ``minimisation.ipynb``: Minimise a molecular configuration.

Workshops
=========

The server also contains several BioSimSpace training workshops. Navigate to
the ``workshops`` directory from the landing page.

* ``python``: A basic Python programming workshop.
* ``introduction``: An introduction to the core concepts of BioSimSpace.
* ``advanced``: Using BioSimSpace to set up and run advanced sampling simulations, such as free energy perturbation and metadynamics.