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
Gap filler
Fills gaps in networks
GapFiller class.
This process iteratively fills gaps related to dead-end compounds using the biota DB. A gap is detected if a steady compound is a dead-end compound.
Input
Network
The network to gap-fill
Output
Network
The gap-filled network
Configuration
tax_id
The taxonomy id used to fill gaps (Warning: Not active)
string