Model Command Documentation

mdl-makedbmodel Command

Description

Creates a new model in the database that includes all reactions in the selected biochemistry.

Arguments

Argument	Required	Description	Default
biomass	yes	ID of the biomass reaction to be used by the whole DB model.
biochemistry	no	The ID of a model or directory containing a biochemistry for use. If undefined, the user's default biochemistry will be used.	undefined
mimicGapfilling	no	If set to "1", filters out any reactions that are not utilized in the gapfilling optimization of Model SEED, including unbalanced reactions and excluded reactions with abstract reactants.	0
allReversible	no	If set to "1", makes every reaction in the model reversible.	0

Example

./mdl-makedbmodel -biomass "bio00001"