Workflow

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Worklow command history

Command sequence

  • Check input:

Check the validity, consistency and presence of input files

  • Orthology based reconstruction:

Run the orthology based reconstruction.

  • Create draft network:

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

  • Manual curation:

Apply the curation described in the form file 1_new_rxn_for_biomass.csv.

  • Manual curation:

Apply the curation described in the form file 2_reaction_to_add_delete.csv.

  • Set medium:

Set the growth medium for the studied species.

  • Run gap-filling:

Calculate the gap-filling solution and generate the metabolic network, completed with the gap-filling solution.

  • Manual curation:

Apply the curation described in the form file 3_rxn_to_delete.csv.

  • Manual curation:

Apply the curation described in the form file 4_NewReactions.csv.

  • Set FBA:

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

  • Test FBA:

Run flux balance analysis on the network.

  • Create Wiki pages:

Create Wiki pages to display the metabolic network.

Downloads

You can download the command log file here