Difference between revisions of "Workflow"

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(Created page with "{{#ask: Category:Reaction reconstruction category::annotation | ?common name | ?ec number | ?reconstruction category | ?reconstruction tool | ?reconstruction source |...")
 
(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 category::annotation]]
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=Workflow command history=
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| ?common name
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| ?ec number
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==Command sequence==
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| ?reconstruction category
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* '''Check input''':
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| ?reconstruction tool
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''Check the validity, consistency and presence of input files''
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| ?reconstruction source
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* '''Annotation based reconstruction''':
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| ?gene associated
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''Extract network data from Pathway Tools annotation output.''
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| ?in pathway
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* '''Orthology based reconstruction''':
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}}
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''Run the orthology based reconstruction.''
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* '''SBML mapping''':
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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* '''Create draft network''':
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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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* '''Manual curation''':
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''Apply the curation described in the form file 1_cycRxns_to_add.csv.''
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* '''Manual curation''':
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''Apply the curation described in the form file 1_keggRxns_to_add.csv.''
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* '''Manual curation''':
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''Apply the curation described in the form file 1_reaction_to_delete.csv.''
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* '''Set medium''':
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''Set the growth medium for the studied species.''
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* '''Run gap-filling''':
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''Calculate the gap-filling solution and generate the metabolic network, completed with the gap-filling solution.''
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* '''Get compartments''':
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''Display all the compartments of the metabolic network.''
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* '''Change compartment''':
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''Modify a compartment in the metabolic network.''
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* '''Change compartment''':
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''Modify a compartment in the metabolic network.''
 +
* '''Change compartment''':
 +
''Modify a compartment in the metabolic network.''
 +
* '''Change compartment''':
 +
''Modify a compartment in the metabolic network.''
 +
* '''Change compartment''':
 +
''Modify a compartment in the metabolic network.''
 +
* '''Change compartment''':
 +
''Modify a compartment in the metabolic network.''
 +
* '''Manual curation''':
 +
''Apply the curation described in the form file 2_cycRxns_to_add.csv.''
 +
* '''Manual curation''':
 +
''Apply the curation described in the form file 2_lightRxns_to_add.csv.''
 +
* '''Manual curation''':
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''Apply the curation described in the form file 2_biomass_rxn.csv.''
 +
* '''Set FBA''':
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''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 20:02, 21 March 2018

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).

  • 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_cycRxns_to_add.csv.

  • Manual curation:

Apply the curation described in the form file 1_keggRxns_to_add.csv.

  • Manual curation:

Apply the curation described in the form file 1_reaction_to_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.

  • Get compartments:

Display all the compartments of the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Change compartment:

Modify a compartment in the metabolic network.

  • Manual curation:

Apply the curation described in the form file 2_cycRxns_to_add.csv.

  • Manual curation:

Apply the curation described in the form file 2_lightRxns_to_add.csv.

  • Manual curation:

Apply the curation described in the form file 2_biomass_rxn.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

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