FBA
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.).
Input
Output
Configuration
biomass_optimization
Biomass optimization
stringmaximize minimize fluxes_to_maximize
The fluxes to maximize
listfluxes_to_minimize
The fluxes to minimize
listsolver
The optimization solver. It is recommended to use `quad`. Other solvers are in `beta` versions.
stringquad highs-ds highs-ipm highs interior-point quadrelax_qssa
True to relaxing the quasi-steady state assumption (QSSA) constrain (`quad` solver is used). False otherwise.
boolqssa_relaxation_strength
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.
floatparsimony_strength
Set True to perform parsimonious FBA (pFBA). In this case the quad solver is used. Set False otherwise
float