Network mergem - gws_gena

Typing name : TASK.gws_gena.NetworkMergem

Brick : gws_gena

Merge two networks with mergem function

NetworkMergem class.

This process merge two networks with the mergem function. This task intelligently merges networks by comparing their IDs from different databases.

Archana Hari, Arveen Zarrabi, Daniel Lobo, mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers, NAR Genomics and Bioinformatics, Volume 6, Issue 1, March 2024, lqae010, https://doi.org/10.1093/nargab/lqae010

Input

Network 1

The first network in Json or Network format

File

Network

Network 2

The second network in Json or Network format

File

Network

Output

Merged network

The merged network

Network

Configuration

keep_objective

Optional

Specifies if the objective functions are merged or copied from a single model (1 or 2)

Type : string

Allowed values : merge 1 2

Default value : merge

biomass_metabolite_id_user

Optional

The id of the Biomass metabolite to keep in the merged model

Type : string

add_biomass

Optional

Advanced parameter

Add biomass metabolite in a compartment biomass to the merged model.

Type : bool

exact_stoichiometry

Optional

Advanced parameter

Use exact stoichiometry when merging reactions

Type : bool

add_annotations

Optional

Advanced parameter

Add additional metabolite and reaction annotations from mergem dictionaries.

Type : bool

use_proton

Optional

Advanced parameter

Consider hydrogen and proton metabolites when merging reactions.

Type : bool

trans_to_db

Optional

Advanced parameter

Translate metabolite and reaction IDs to a target database

Type : string

Allowed values : None chebi metacyc kegg reactome metanetx hmdb biocyc bigg seed sabiork rhea

Default value : None