The media yaml file 
===================

.. code:: yaml 

    # Configuration file for loading media for testing / simulating models
    # --------------------------------------------------------------------
    # basic parameters for loading media
    # --------------------------------------------------------------------
    # setting these parameters will set a default for all media, 
    # if they are not overwritten by the setting in the next part
    # all options can be commented out
    # this will lead to the default being used
    #
    # options:
    #   aerobic: True|False
    #            Sets if the media will be aerobic or not. 
    #            Default does not change the current media definitions, without checking them.
    #   supplement: None|std|min
    #               Sets whether or not the media will be supplement to enable growth. 
    #               Default is None
    #   default_flux: float
    #            Sets a default flux value for all fluxes in the media.
    #            Note: this will replace existing values!
    #            Default to 10.0
    #   o2_percent: float
    #            Increase or decrease the amount of oxygen in relation to its normal flux
    #            by the given percentage. 
    #            Default is 1.0, equalling the current/normal amount of oxygen (= 100%)
    # --------------------------------------------------------------------

    params:
    aerobic: True
    supplement: None
    # default_flux: 10.0
    # o2_percent: 1.0

    # --------------------------------------------------------------------
    # load media from the in-build database and/or external sources
    # 
    # format:
    #   name:
    #      option1: input1
    #      option2: input2
    #      ....
    #
    # options:
    #   base: None|str
    #            Medium to use as base for the composition. 
    #            If none is given, tries to use the name to look it up in the database.
    #            If a whitespace is detected, expects the first part to be a float set as the
    #            percentage to use and the second the name, e.g. '0.5 LB'
    #   external_base: None|str(path)
    #            If the base should be read from an external source, use this options 
    #            followed by a path to a media descripion.
    #            Parallel to base, a float separated by a whitespcae can be written in front.
    #   add_subset: 
    #            subset_name (str): default_flux (float, e.g. 0.5)
    #            Add additional subsets from the database to the base.
    #   add_medium:
    #            medium_name (str): percentage (float, e.g. 0.1)
    #            Add additional media based on a given percentage to the base.
    #   add_external:
    #            'link' (str): percentage (float)
    #            Add additional external media to the base.
    #   add_substance: Null|float|str in format 'X.X%' with X being [0-9]*
    #            Add further substances to the medium and/or add specific fluxes to 
    #            to substances. Flux settings here overwrite all previously set fluxes.
    #            Null uses the most specific set default flux.
    #            When a percentage is set uses this percentage of the most specific set default flux.
    #
    # options to overwrite the default set in the previous section 
    # for specific media only:
    #   aerobic
    #   supplement
    #   default_flux
    #   o2_percent
    # --------------------------------------------------------------------

    media:
    LB: 
        aerobic: False
    LB_o2:
        base: LB
        default_flux: 5.0
        o2_percent: 2.0
    SNM3:
    #    supplement: min
    M9:
    #    add_medium: 
    #      SNM3: 1.0
    #    add_subset:
    #      AA: 5.0
        add_substance:
        Glycine: Null
        Glycerol: 0.87
        Guanosine: '20%'
    #  PERS:
    #    external_base: link
    #    add_external:
    #      'link': 0.5