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 |