Introduction Biomass reaction table importer Context builder Context exporter Context importer Convert Model Annotation Draft recon Draft recon EC number table importer Entity ID table importer FBA Flux Table Analysis Flux table importer FVA Gap filler Isolate finder KOA KOA result extractor Medium table importer Network exporter Network importer Network merger Orphan remover Phenotype table importer Reaction adder Reaction remover Smart json modificator (cobra) Transporter adder Twin annotator Twin builder Twin exporter Twin flattener Twin importer Twin reducer XML/Matlab to JSON
Technical Documentation
Resources
Tasks
Protocols
KOA
Knockout Analysis
KOA class.
Input
Digital twin
The digital twin to analyze
KO table
The table of KO hypotheses
Output
Simulated digital twin
The simulated digital twin
KOA result tables
The KOA result tables
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
floatko_delimiter
The delimiter used to separate IDs or EC numbers when multiple KO are performed
string,