Difference between revisions of "Workflow"

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

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