Workflow

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Workflow command history

Command sequence

  • Check input:

Check the validity, consistency and presence of input files

  • Orthology based reconstruction:

Run the orthology based reconstruction.

  • Annotation based reconstruction:

Extract network data from Pathway Tools annotation output.

  • 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.

  • Run gap-filling:

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

  • Menecheck:

Run topological analysis on the network.

  • Menecheck:

Run topological analysis on the network.

  • Menecheck:

Run topological analysis on the network.

  • Manual curation:

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

  • 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.

  • Report:

Generate reports on the metabolic network reconstruction.

  • Manual curation:

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

  • Menecheck:

Run topological analysis on the network.

  • Report:

Generate reports on the metabolic network reconstruction.

  • 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