Workflow

Workflow command history

Command sequence

• Check input:

Check the validity, consistency and presence of input files

• Annotation based reconstruction:

Extract network data from Pathway Tools annotation output.

• Orthology based reconstruction:

Run the orthology based reconstruction.

• SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

• SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

• SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

• SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

• SBML mapping:

Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).

• Create draft network:

Merges all available networks from the /networks directory into one metabolic network.
Merge all data on the studied species.

• Set medium:

Set the growth medium for the studied species.

• Manual curation:

Apply the curation described in the form file add_biomass_reaction.tsv.

• Manual curation:

Apply the curation described in the form file remove_anaerobic_reactions.tsv.

• Manual curation:

Apply the curation described in the form file add_spontaneous_reactions.tsv.

• PADMet to SBML:

Export a PADMet (.padmet) file in the SBML format.

• PADMet to SBML:

Export a PADMet (.padmet) file in the SBML format.

• Manual curation:

Apply the curation described in the form file add_reactions_other_databases.tsv.

• Manual curation:

Apply the curation described in the form file add_reactions_to_reach_targets.tsv.

• PADMet to SBML:

Export a PADMet (.padmet) file in the SBML format.

• Manual curation:

Apply the curation described in the form file add_export_reactions.tsv.

• Manual curation:

Apply the curation described in the form file add_expert_reactions.tsv.

• Manual curation:

Apply the curation described in the form file remove_unblasted_reactions.tsv.

• PADMet to SBML:

Export a PADMet (.padmet) file in the SBML format.

• Set FBA:

Set the biomass reaction to run flux balance analysis on the network.

• Test FBA:

Run flux balance analysis on the network.

• Report:

Generate reports on the metabolic network reconstruction.

• Create Wiki pages:

Create Wiki pages to display the metabolic network.

Downloads

You can download the command log file here