KOA - gws_gena - Community

Typing name : TASK.gws_gena.KOA

Brick : gws_gena

Knockout Analysis

Knock-out analysis class.

Perform an FBA by knocking out some reactions. Reactions to knockout can be provided with a Entity ID Table or a EC Table. Please note that if you provide a Entity ID Table, 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

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

Configuration

biomass_optimization

Optional

Biomass optimization

Type : string

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 : string

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

ko_delimiter

Optional

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

Type : string

Default value : ,