Difference between revisions of "Workflow"
(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Orthology based reconstruction''': '...") |
|||
| Line 8: | Line 8: | ||
* '''Annotation based reconstruction''': | * '''Annotation based reconstruction''': | ||
''Extract network data from Pathway Tools annotation output.'' | ''Extract network data from Pathway Tools annotation output.'' | ||
| − | |||
| − | |||
| − | |||
| − | |||
* '''SBML mapping''': | * '''SBML mapping''': | ||
''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).'' | ''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).'' | ||
| Line 18: | Line 14: | ||
* '''Create draft network''': | * '''Create draft network''': | ||
''Merges all available networks from the /networks directory into one metabolic network.<BR>Merge all data on the studied species.'' | ''Merges all available networks from the /networks directory into one metabolic network.<BR>Merge all data on the studied species.'' | ||
| − | |||
| − | |||
* '''Set medium''': | * '''Set medium''': | ||
''Set the growth medium for the studied species.'' | ''Set the growth medium for the studied species.'' | ||
* '''Run gap-filling''': | * '''Run gap-filling''': | ||
''Calculate the gap-filling solution and generate the metabolic network, completed with the gap-filling solution.'' | ''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 FBA''': | ||
''Set the biomass reaction to run flux balance analysis on the network.'' | ''Set the biomass reaction to run flux balance analysis on the network.'' | ||
Latest revision as of 16:49, 10 January 2019
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
