Publication dateMar 9, 2022
Confidentiality public Public
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
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Input
Network 1
The first network in Json or Network format
Network 2
The second network in Json or Network format
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Output
Merged network
The merged network
settings
Configuration
Specifies if the objective functions are merged or copied from a single model (1 or 2)
Type : stringAllowed 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 : stringAllowed values : None chebi metacyc kegg reactome metanetx hmdb biocyc bigg seed sabiork rhea Default value : NoneTechnical bricks to reuse or customize
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