Model Command Documentation - ModelSEED/Model-SEED-core GitHub Wiki
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"