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Introduction Version

KOA

TASK
Typing name :  TASK.gws_gena.KOA Brick :  gws_gena v

Knockout Analysis

Knock-out analysis class.

Perform an FBA by knocking out some reactions. Reactions to knockout can be provided with a EntityIDTable or a ECTable. Please note that if you provide a EntityIDTable, the reaction id must be "network_reaction1".

If you want to perform multiple knockout at the same time; provide them like this: id "reaction1, reaction2, reaction3"

Input

Digital twin
The digital twin to analyze
KO table
The table of KO hypotheses

Output

Simulated digital twin
The simulated digital twin
KOA result tables
The KOA result tables

Configuration

biomass_optimization

Optional

Biomass optimization

Type : stringAllowed values :   maximize  minimize 

fluxes_to_maximize

OptionalAdvanced parameter

The fluxes to maximize

Type : list

fluxes_to_minimize

OptionalAdvanced parameter

The fluxes to minimize

Type : list

solver

OptionalAdvanced parameter

The optimization solver. It is recommended to use `quad`. Other solvers are in `beta` versions.

Type : stringAllowed values : quad  highs-ds  highs-ipm  highs  interior-point  Default value : quad

relax_qssa

OptionalAdvanced parameter

True to relaxing the quasi-steady state assumption (QSSA) constrain (`quad` solver is used). False otherwise.

Type : bool

qssa_relaxation_strength

OptionalAdvanced parameter

Used only if the QSSA is relaxed. The higher is the strength, the stronger is the QSSA. Hint: Set to the number of reactions to have strong QSSA contrain.

Type : float

parsimony_strength

OptionalAdvanced parameter

Set True to perform parsimonious FBA (pFBA). In this case the quad solver is used. Set False otherwise

Type : float

number_of_simulations

OptionalAdvanced parameter

Set the number of simulations to perform. You must provide at least the same number of measures in the context. By default, keeps all simulations.

Type : int

ko_delimiter

Optional

The delimiter used to separate IDs or EC numbers when multiple KO are performed

Type : stringDefault value : ,