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gws_gena

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KOA

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

Knockout Analysis

Knock-out analysis class.

Perform an FBA by knocking out some reactions or genes. Reactions to knockout can be provided with a Entity ID Table or a EC Table. Genes to knockout can be provided with a Entity ID Table. Please note that if you provide a Entity ID Table, the reaction id must be "network_reaction1".

In the output you will get a twin, a KOA result with the estimated fluxes for each knockout and a summary table. This table is useful if you provide genes to know which reactions have been knocked out by which genes.

If you want to perform multiple knockout at the same time (e.g. id1, id2 and id3); provide them like this: id "network_id1,network_id2,network_id3" "network_id4"

Input

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

Output

Simulated digital twin
The simulated digital twin
Twin
KOA result tables
The KOA result tables
KOA result
Table Summary
The table summarising the reactions knocked out
Table

Configuration

ko_delimiter

Optional

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

Type : stringDefault value : ,

type_ko

Optional

The type of elements provided to knock-out: reactions or genes

Type : stringAllowed values : reactions genes Default value : reactions

biomass_optimization

Optional

Biomass optimization

Type : stringAllowed values :  maximize minimize 

fluxes_to_maximize

Optional Advanced parameter

The fluxes to maximize

Type : list

fluxes_to_minimize

Optional Advanced parameter

The fluxes to minimize

Type : list

solver

Optional Advanced 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

Optional Advanced parameter

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

Type : bool

qssa_relaxation_strength

Optional Advanced 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

Optional Advanced parameter

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

Type : float

number_of_simulations

Optional Advanced 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