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
Draft recon
Draft network reconstruction
DraftRecon task.
This task performs a draft reconstruction of a metabolic network using a list of EC numbers or taxonomy IDs.
Input
Table of EC numbers
Table of EC numbers
Biomass reaction table
Stoichiometry table describing the biomass composition
Medium table
Table of culture medium composition
Output
Network
Metabolic network
Configuration
unique_name
The unique name of the network. Required to uniquely identify taxa in microbial communities
string0svptax_id
The NCBI taxonomy id. For example: `tax_id = 562` for E. Coli
stringtax_search_method
If 'bottom_up', the algorithm will to traverse the taxonomy tree to search at higher taxonomy levels until a reaction is found. If `none`, the algorithm will only search at the given taxonomy level given by `tax_id`
stringnone bottom_up bottom_up