Difference between revisions of "Workflow"

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(Created page with "Category:pathway == Pathway PWY-8049 == * common-name: ** pederin biosynthesis * taxonomic-range: ** tax-2 == Reaction(s) found == * RXN-20490 * RXN-20498 == React...")
(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Annotation based reconstruction''':...")
 
(14 intermediate revisions by 3 users not shown)
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[[Category:pathway]]
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=Workflow command history=
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== Pathway PWY-8049 ==
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* common-name:
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==Command sequence==
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** pederin biosynthesis
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* '''Check input''':
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* taxonomic-range:
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''Check the validity, consistency and presence of input files''
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** tax-2
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* '''Annotation based reconstruction''':
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== Reaction(s) found ==
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''Extract network data from Pathway Tools annotation output.''
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* [[RXN-20490]]
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* '''Orthology based reconstruction''':
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* [[RXN-20498]]
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''Run the orthology based reconstruction.''
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== Reaction(s) not found ==
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* '''SBML mapping''':
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* [NoneRXN-20486 RXN-20486]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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* [NoneRXN-20493 RXN-20493]
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* '''SBML mapping''':
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* [NoneRXN-20489 RXN-20489]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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* [NoneRXN-20491 RXN-20491]
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* '''SBML mapping''':
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* [NoneRXN-20485 RXN-20485]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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* [NoneRXN-20500 RXN-20500]
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* '''SBML mapping''':
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* [NoneRXN-20494 RXN-20494]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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* [NoneRXN-20495 RXN-20495]
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* '''SBML mapping''':
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* [NoneRXN-20488 RXN-20488]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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* [NoneRXN-20499 RXN-20499]
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* '''Create draft network''':
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* [NoneRXN-20492 RXN-20492]
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''Merges all available networks from the /networks directory into one metabolic network.<BR>Merge all data on the studied species.''
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* [NoneRXN-20487 RXN-20487]
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* '''Set medium''':
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{{#set: common-name=pederin biosynthesis}}
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''Set the growth medium for the studied species.''
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{{#set: taxonomic-range=tax-2}}
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* '''Manual curation''':
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{{#set: nb reaction found=2}}
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''Apply the curation described in the form file add_biomass_reaction.tsv.''
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{{#set: completion rate=0.14}}
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* '''Manual curation''':
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{{#set: nb total reaction=14}}
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''Apply the curation described in the form file remove_anaerobic_reactions.tsv.''
 +
* '''Manual curation''':
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''Apply the curation described in the form file add_spontaneous_reactions.tsv.''
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* '''PADMet to SBML''':
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''Export a PADMet (.padmet) file in the SBML format.''
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* '''PADMet to SBML''':
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''Export a PADMet (.padmet) file in the SBML format.''
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* '''Manual curation''':
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''Apply the curation described in the form file add_reactions_other_databases.tsv.''
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* '''Manual curation''':
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''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''':
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''Apply the curation described in the form file add_export_reactions.tsv.''
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* '''Manual curation''':
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''Apply the curation described in the form file add_expert_reactions.tsv.''
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* '''Manual curation''':
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''Apply the curation described in the form file remove_unblasted_reactions.tsv.''
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* '''PADMet to SBML''':
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''Export a PADMet (.padmet) file in the SBML format.''
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* '''Set FBA''':
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''Set the biomass reaction to run flux balance analysis on the network.''
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* '''Test FBA''':
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''Run flux balance analysis on the network.''
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* '''Report''':
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''Generate reports on the metabolic network reconstruction.''
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* '''Create Wiki pages''':
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''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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