The media yaml file

The default media configuration file distributed with refineGEMs is shown below. It can be downloaded with:

refinegems setup config --type media --filename media_config.yml

# 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): mode of combination 
#            Add additional media based on a given percentage to the base.
#            Mode of combination can be: 
#            a single float, e.g. 0.1 - percentage of 1.0 for base medium
#            or a tuple of two floats, e.g. (0.1, 0.2) - percentage of each medium to use
#            or "+" - simply add the media together 
#            or NULL, which sets the fluxes to None
#   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: 0.6   # add 60% base an 40% SNM3
#      RPMI: (1.5,5.0) # use 1.5x M9 and 5.0x RPMI 
#      LB: "+"   # add media simply together
#    add_subset:
#      AA: 5.0
    add_substance:
      Glycine: Null
      Glycerol: 0.87
      Guanosine: '20%'
#  PERS:
#    external_base: link
#    add_external:
#      'link': 0.5