Publication dateMar 9, 2022
Confidentiality public Public
Typing name : TASK.gws_gena.KOA Brick : gws_gena Knockout Analysis
Knock-out analysis class.
Perform an FBA by knocking out some reactions or genes.
Reactions to knockout can be provided with a Entity ID Table or a EC Table.
Genes to knockout can be provided with a Entity ID Table.
Please note that if you provide a Entity ID Table, the reaction id must be "network_reaction1".
In the output you will get a twin, a KOA result with the estimated fluxes for each knockout and a summary table.
This table is useful if you provide genes to know which reactions have been knocked out by which genes.
If you want to perform multiple knockout at the same time (e.g. id1, id2 and id3); provide them like this:
id
"network_id1,network_id2,network_id3"
"network_id4"
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Input
Digital twin
The digital twin to analyze
KO table
The table of KO hypotheses
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Output
Simulated digital twin
The simulated digital twin
KOA result tables
The KOA result tables
Table Summary
The table summarising the reactions knocked out
settings
Configuration
The delimiter used to separate IDs or EC numbers when multiple KO are performed
Type : stringDefault value : ,The type of elements provided to knock-out: reactions or genes
Type : stringAllowed values : reactions genes Default value : reactions 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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