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).
- 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_cycRxns_to_add.csv.
- Manual curation:
Apply the curation described in the form file 1_keggRxns_to_add.csv.
- Manual curation:
Apply the curation described in the form file 1_reaction_to_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.
- Get compartments:
Display all the compartments of the metabolic network.
- Change compartment:
Modify a compartment in the metabolic network.
- Change compartment:
Modify a compartment in the metabolic network.
- Change compartment:
Modify a compartment in the metabolic network.
- Change compartment:
Modify a compartment in the metabolic network.
- Change compartment:
Modify a compartment in the metabolic network.
- Change compartment:
Modify a compartment in the metabolic network.
- Manual curation:
Apply the curation described in the form file 2_cycRxns_to_add.csv.
- Manual curation:
Apply the curation described in the form file 2_lightRxns_to_add.csv.
- Manual curation:
Apply the curation described in the form file 2_biomass_rxn.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
