Difference between revisions of "Workflow"
(Created page with "Category:pathway == Pathway PWY-7117 == * common-name: ** c4 photosynthetic carbon assimilation cycle, pepck type * taxonomic-range: ** tax-3398 ** tax-4479 == Reaction(s)...") |
(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Annotation based reconstruction''':...") |
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− | + | =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).'' |
− | * | + | * '''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).'' |
− | * | + | * '''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.'' |
− | + | * '''Set medium''': | |
− | + | ''Set the growth medium for the studied species.'' | |
− | + | * '''Manual curation''': | |
− | + | ''Apply the curation described in the form file add_biomass_reaction.tsv.'' | |
− | + | * '''Manual curation''': | |
+ | ''Apply the curation described in the form file remove_anaerobic_reactions.tsv.'' | ||
+ | * '''Manual curation''': | ||
+ | ''Apply the curation described in the form file add_spontaneous_reactions.tsv.'' | ||
+ | * '''PADMet to SBML''': | ||
+ | ''Export a PADMet (.padmet) file in the SBML format.'' | ||
+ | * '''PADMet to SBML''': | ||
+ | ''Export a PADMet (.padmet) file in the SBML format.'' | ||
+ | * '''Manual curation''': | ||
+ | ''Apply the curation described in the form file add_reactions_other_databases.tsv.'' | ||
+ | * '''Manual curation''': | ||
+ | ''Apply the curation described in the form file add_reactions_to_reach_targets.tsv.'' | ||
+ | * '''PADMet to SBML''': | ||
+ | ''Export a PADMet (.padmet) file in the SBML format.'' | ||
+ | * '''Manual curation''': | ||
+ | ''Apply the curation described in the form file add_export_reactions.tsv.'' | ||
+ | * '''Manual curation''': | ||
+ | ''Apply the curation described in the form file add_expert_reactions.tsv.'' | ||
+ | * '''Manual curation''': | ||
+ | ''Apply the curation described in the form file remove_unblasted_reactions.tsv.'' | ||
+ | * '''PADMet to SBML''': | ||
+ | ''Export a PADMet (.padmet) file in the SBML format.'' | ||
+ | * '''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.'' | ||
+ | * '''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 11:09, 17 October 2022
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).
- 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).
- 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.
- Manual curation:
Apply the curation described in the form file add_biomass_reaction.tsv.
- Manual curation:
Apply the curation described in the form file remove_anaerobic_reactions.tsv.
- Manual curation:
Apply the curation described in the form file add_spontaneous_reactions.tsv.
- PADMet to SBML:
Export a PADMet (.padmet) file in the SBML format.
- PADMet to SBML:
Export a PADMet (.padmet) file in the SBML format.
- Manual curation:
Apply the curation described in the form file add_reactions_other_databases.tsv.
- Manual curation:
Apply the curation described in the form file add_reactions_to_reach_targets.tsv.
- PADMet to SBML:
Export a PADMet (.padmet) file in the SBML format.
- Manual curation:
Apply the curation described in the form file add_export_reactions.tsv.
- Manual curation:
Apply the curation described in the form file add_expert_reactions.tsv.
- Manual curation:
Apply the curation described in the form file remove_unblasted_reactions.tsv.
- PADMet to SBML:
Export a PADMet (.padmet) file in the SBML format.
- 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.
- Create Wiki pages:
Create Wiki pages to display the metabolic network.
Downloads
You can download the command log file here