Publication dateMar 9, 2022
Confidentiality public Public
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14 minutes, 28 seconds
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
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Input
Digital twin
The digital twin to analyze
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Output
Simulated digital twin
The simulated digital twin
FVA result table
The FVA result tables
settings
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 : floatDefault value : 1 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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