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GapfillModel.md

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Application specification: GapfillModel

This is the application specification for service with identifier GapfillModel.

The backend script implementing the application is App-GapfillModel.pl.

The raw JSON file for this specification is GapfillModel.json.

This service performs the following task: Run gapfilling on model.

It takes the following parameters:

id label type required default value
model Model object WS: model ✔️
media FBA media WS: media
probanno Probabilistic annotation WS: probanno
alpha Comprehensive gapfilling priority float 0
allreversible Make all reactions reversible bool 0
allowunbalanced Allow unbalanced reactions in gapfilling bool 0
integrate_solution Integrate first gapfilling solution bool 0
thermo_const_type Thermodynamic constraints enum
media_supplement Media supplements string
geneko Gene knockouts string
rxnko Reaction knockouts string
target_reactions Target reactions string
objective_fraction Objective fraction float 0.001
low_expression_theshold Threshold of expression for gene to be consider inactive float 1
high_expression_theshold Threshold of expression for gene to be consider active float 1
output_file File Basename wsid
uptake_limit group
custom_bounds group
objective group