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Introduction Version

Network importer

IMPORTER
Typing name :  TASK.gws_gena.NetworkImporter Brick :  gws_gena v

Import file to Network

Network Importer Task

This Task allows you to import genome-scale metabolic models in Constellab. In input, provide your file and you will get a Network in output.

In the parameters you need to specify the ID of the metabolite associated with the biomass. If you don't have any in your model, set the "Add biomass metabolite" option to True.

Be aware that in Constellab: - The compartment extracellular space (theoretical supernatant) (GO:0005615) is consider at steady state. - The compartment extracellular region (environment) (GO:0005576) is consider at the non-steady state.

So, if the metabolite can be consumed, you need to set its compartment to the compartment environment (GO:0005576) and create a new metabolite in the extracellular compartment (GO:0005615) and the associated reactions. If the metabolite cannot be consumed, leave it in the extracellular compartment.

If your model comes from the BIGG database, you don't need to modify your model, this task will import it correctly automatically.

Input

File

Output

Network
Metabolic network

Configuration

biomass_metabolite_id_user

Optional

The id of the Biomass metabolite

Type : string

add_biomass

OptionalAdvanced parameter

Add biomass metabolite in a compartment biomass.

Type : bool

replace_unknown_compartments

OptionalAdvanced parameter

Set default compartment as others

Type : bool

skip_orphans

OptionalAdvanced parameter

Set True to skip orphan compounds

Type : bool