Publication dateMar 9, 2022
Confidentiality public Public
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.
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Input
Digital twin
The digital twin to analyze
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Output
Simulated digital twin
The simulated digital twin
FBA result tables
The FBA result tables
settings
Configuration
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.
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