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 Version
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
string
maximize
minimize
fluxes_to_maximize
The fluxes to maximize
list
fluxes_to_minimize
The fluxes to minimize
list
solver
The optimization solver. It is recommended to use `quad`. Other solvers are in `beta` versions.
string
quad
highs-ds
highs-ipm
highs
interior-point
quad
relax_qssa
True to relaxing the quasi-steady state assumption (QSSA) constrain (`quad` solver is used). False otherwise.
bool
qssa_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.
float
parsimony_strength
Set True to perform parsimonious FBA (pFBA). In this case the quad solver is used. Set False otherwise
float
ko_delimiter
The delimiter used to separate IDs or EC numbers when multiple KO are performed
string
,