curateModel.toml

# Experiment parameter settings:

# Name of original model. 'modelName' should be one of: "yeast8", "yeast9", "eciYali_sbmlValidated"
modelName = "yeast8.xml"

# kegg organism code
organismCode = "sce"

# # Check if reactions are mass balanced
# checkMassBalance = "Y"
#
# # Connect the same metabolite in multiple compartments, when isolated, through a simple transport
# connectSameIsolatedMetsWithSimpleTransport = "Y"
#
# # Close isolated metabolites with an exchange whose direction depends on the directionality of the reactions where it is involved
# closeIsolatedMetabolitesWithExchange = "Y"
#
# # Check if model is not able to produce any metabolites without uptake of metabolites.
# checkSomethingIsProducedFromNothing = "Y"
#
# # Check if model is not able to consume any metabolites without demand of metabolites.
# checkIfUptakeSomethingBlockingDemand = "Y"
#
# # Check which reactions are involved in formation of loops
# checkLoops = "Y"

# Refine reactions boundaries
# refineBoundariesInReactionsFormingLoops = "Y"
boundariesToChangeFileName = "yeast8_refinement_bounds2Change.tsv"

# Refine GPR
gprRefinementFileName = "yeast8_refinement_newGpr.tsv"

# Turn off reactions with the "added after the biolog update" tag when they are not in the target organism
curateBiologExperimentAddedRxns = "Y"