# 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