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.

• Create draft network:

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

• Get compartments:

Display all the compartments of the metabolic network.

• Manual curation:

Apply the curation described in the form file biomass_reaction.csv.

• Manual curation:

Apply the curation described in the form file new_reactions_curation.csv.

• Manual curation:

Apply the curation described in the form file reactions_to_add.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 ala_dehy.csv.

• Manual curation:

Apply the curation described in the form file pathmodel_inference.csv.

• Manual curation:

Apply the curation described in the form file pathmodel_inference_new_rxn.csv.

• Create Wiki pages:

Create Wiki pages to display the metabolic network.

• Manual curation:

Apply the curation described in the form file pathmodel_inference_new_rxn_2.csv.

• Test FBA:

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