experimentSettings.toml

# Experiment parameter settings:

# Name of original model.
modelName = "yeast8.xml"

# Load or create file including correspondence between metabolites name and their KEGG identifier
nameToKeggId = "name2KeggId_yeast8.tsv"

#  'kind' should be one or more of: "endogenous", "aox" (AOX-catalyzed path), "bacterial", "ncl", "taco", "marine", "wt" (for Yarrowia), "wt_sceLike" (for Yarrowia)
# exp = "aox"

# file containing  the KEGG id and compartment of reactions that need to be added to the model
# keggRxnsToAddFileName = "aox.tsv"
exp = "aox.tsv"

# file containing  information of exchange rxns that need to be added to the model: kegg Id of metabolite involved in the exchange, reaction compartment, its lower and upper bound
# addExchRxnsForTheseMetsFileName = "aox_addExchForThoseMets.tsv"
exchangeRxns = "aox_addExchForThoseMets.tsv"

# kegg organism code
organismCode = "sce"

# condition should be one ore more of: "Glc", "EG", "Acetate"
condition = ["ethylene glycol"]

# medium name should be one of: "YNB" (for S.cerevisiae), "YNByarr" (for Yarrowia)
medium = "YNB.tsv"

# mediumBounds should be one of "wet", "free"
# mediumBounds = "wet"

# mediumFileName
mediumData = "Y"

# extracellular production and consumption file name
extracelProdCons = "extracFluxes_YNB_ethylene_glycol.tsv"
# extracelProdConsData = "Y"

# List of uptake reactions that need to remain active even if they are not explicitly included in the experimental medium
# lActiveUptake =  []