Media & Subsets
===============

**refineGEMs** has an in-build database for different media, media compounds and Subsets
to facilitate model curation and allow for a range of different simulations.

.. hint::

    The media and substances in the database are manually curated. If you find any discrepancies
    or want something added, feel free to reach out to the maintainers and developers 
    (`GitHub page <https://github.com/draeger-lab/refinegems/issues>`__ or open a discussion `here <https://github.com/draeger-lab/refinegems/discussions>`__).



Content of the Database
-----------------------

Below, the currently available media and subsets are listed. For additional information refer to the
documentation pages of these media. For more details on the substances and database links, 
please install the database and inspect it on your computer.

.. toctree:: 

    available_media
    available_subsets

.. hint::

    For more information on how to access the database, please refer to :ref:`Usage`.

Working with the Data
---------------------

For understanding the database and the data it contains, it is vital to understand the meaning of
an *in silico* medium and how to transform a medium e.g. from the labratory (*in vivo* medium)
into an *in silico* medium. Our standardised aproach is described in :doc:`in_silico_media_generation`.

You can find a detailed explanation of the database architecture under :doc:`db_architecture`.

Additionally, the last point refers to more information about accessing the database. ``TODO`` Worauf bezieht sich das hier genau?

.. toctree::

    in_silico_media_generation
    db_architecture