Difference between revisions of "Workflow"
(Created page with "Category:Reaction == Reaction [http://bigg.ucsd.edu/universal/reactions/TransportSeed_paps TransportSeed_paps] == * direction: ** LEFT-TO-RIGHT * Synonym(s): == Reaction...") |
(Created page with "=Worklow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Orthology based reconstruction''': ''...") |
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| − | + | =Worklow command history= | |
| − | == | + | |
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| − | == | + | ==Command sequence== |
| − | * | + | * '''Check input''': |
| − | * | + | ''Check the validity, consistency and presence of input files'' |
| − | * | + | * '''Orthology based reconstruction''': |
| − | * | + | ''Run the orthology based reconstruction.'' |
| − | + | * '''Create draft network''': | |
| − | + | ''Merges all available networks from the /networks directory into one metabolic network.<BR>Merge all data on the studied species.'' | |
| − | + | * '''Manual curation''': | |
| − | + | ''Apply the curation described in the form file 1_new_rxn_for_biomass.csv.'' | |
| − | * | + | * '''Manual curation''': |
| − | * | + | ''Apply the curation described in the form file 2_reaction_to_add_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.'' | |
| − | + | * '''Manual curation''': | |
| + | ''Apply the curation described in the form file 3_rxn_to_delete.csv.'' | ||
| + | * '''Manual curation''': | ||
| + | ''Apply the curation described in the form file 4_NewReactions.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 16:47, 21 March 2018
Worklow command history
Command sequence
- Check input:
Check the validity, consistency and presence of input files
- Orthology based reconstruction:
Run the orthology based reconstruction.
- 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_new_rxn_for_biomass.csv.
- Manual curation:
Apply the curation described in the form file 2_reaction_to_add_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.
- Manual curation:
Apply the curation described in the form file 3_rxn_to_delete.csv.
- Manual curation:
Apply the curation described in the form file 4_NewReactions.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
