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FBA

TASK
Typing name :  TASK.gws_gena.FBA Brick :  gws_gena

Flux balance analysis

FBA task class

Performs Flux Balance Analysis from a digital twin.

A digital twin is a mathematical representation of the metabolic interactions involved in a living cell or microbial organism (e.g. animal cell, bacteria, fungus, etc.).

You need to provide your twin in the input and you can set some parameters. The most important is to choose whether you want to maximize or minimize the biomass flux. Then, you can add other fluxes to optimize (fluxes to maximize and fluxes to minimize), the solver and some parameters related to the solver method. The last parameter "Number of simulations" allows you to run multiple simulations of FBA using your context with multi target values.

In output you will get your twin annotated and two tables with the estimated fluxes.

Input

Digital twin
The digital twin to analyze
Twin

Output

Simulated digital twin
The simulated digital twin
Twin
FBA result tables
The FBA result tables
FBA 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 : stringDefault 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