KOA
Knockout Analysis
Knock-out analysis class.
Perform an FBA by knocking out some reactions. Reactions to knockout can be provided with a Entity ID Table or a EC Table. Please note that if you provide a Entity ID Table, the reaction id must be "network_reaction1".
If you want to perform multiple knockout at the same time; provide them like this: id "reaction1, reaction2, reaction3"
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
floatnumber_of_simulations
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.
intko_delimiter
The delimiter used to separate IDs or EC numbers when multiple KO are performed
string,