Workflow
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
