FVA

Typing name : TASK.gws_gena.FVA

Brick : gws_gena

Flux variability analysis

FVA class

Performs Flux Variability Analysis (FVA). It calculates the minimum and maximum flux values for each reaction in a metabolic network while satisfying certain constraints;

It is based on the paper of (Gudmundsson and Thiele, Bioinformatics 2010). See also:

Steinn Gudmundsson & Ines Thiele, Computationally efficient flux variability analysis, BMC Bioinformatics, volume 11, Article number: 489 (2010), https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-489

Input

Digital twin

The digital twin to analyze

Twin

Output

Simulated digital twin

The simulated digital twin

Twin

FVA result table

The FVA result tables

FVA result

Configuration

gamma

Optional

Advanced parameter

γ determines whether the analysis is conducted with respect to suboptimal network states (where 0 ≤ γ < 1) or to the optimal state (where γ = 1). A value of 0.9 implies that the objective must be at least 90% of its maximum.

Type : float

Default value : 1

biomass_optimization

Optional

Biomass optimization

Type : string

Allowed 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 : string

Allowed 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

Input

Output

Configuration

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