|
|
| Line 1: |
Line 1: |
| − | =Workflow command history=
| + | {{#ask: [[Category:reaction]] [[reconstruction tool::meneco]] |
| − | | + | | ?common-name |
| − | ==Command sequence==
| + | | ?ec-number |
| − | * '''Check input''':
| + | | ?reconstruction category |
| − | ''Check the validity, consistency and presence of input files''
| + | | ?reconstruction source |
| − | * '''Annotation based reconstruction''':
| + | | ?reconstruction comment |
| − | ''Extract network data from Pathway Tools annotation output.''
| + | | ?nb gene associated |
| − | * '''Orthology based reconstruction''':
| + | | ?nb pathway associated |
| − | ''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]]
| |
