Difference between revisions of "Workflow"
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(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Orthology based reconstruction''': '...") |
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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).'' | ||
| + | * '''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.<BR>Merge all data on the studied species.'' | ||
| + | * '''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.'' | ||
| + | * '''Get compartments''': | ||
| + | ''Display all the compartments of the metabolic network.'' | ||
| + | * '''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 export_biomass_rxn.csv.'' | ||
| + | * '''Manual curation''': | ||
| + | ''Apply the curation described in the form file reactions_PWY-6475_tiso_add.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 [[MEDIA:log.txt|command log file here]] | ||
Latest revision as of 21:26, 21 March 2018
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).
- 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.
- 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.
- Get compartments:
Display all the compartments of the metabolic network.
- 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 export_biomass_rxn.csv.
- Manual curation:
Apply the curation described in the form file reactions_PWY-6475_tiso_add.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
