Difference between revisions of "Workflow"

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(Created page with "Category:Gene == Gene Ec-04_003690 == * left end position: ** 3772381 * transcription direction: ** NEGATIVE * right end position: ** 3788003 * centisome position: ** 57.9...")
(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Annotation based reconstruction''':...")
 
(One intermediate revision by the same user not shown)
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[[Category:Gene]]
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=Workflow command history=
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== Gene Ec-04_003690 ==
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* left end position:
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** 3772381
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* transcription direction:
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** NEGATIVE
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* right end position:
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** 3788003
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* centisome position:
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** 57.93101   
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* Synonym(s):
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** Esi_0080_0017
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** Esi0080_0017
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** MPDH3
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== Reactions associated ==
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==Command sequence==
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* [[MANNPDEHYDROG-RXN]]
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* '''Check input''':
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** esiliculosus_genome
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''Check the validity, consistency and presence of input files''
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***ec-number
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* '''Annotation based reconstruction''':
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== Pathways associated ==
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''Extract network data from Pathway Tools annotation output.''
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* [[MANNIDEG-PWY]]
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* '''Orthology based reconstruction''':
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* [[PWY-6531]]
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''Run the orthology based reconstruction.''
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== External links  ==
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* '''SBML mapping''':
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{{#set: left end position=3772381}}
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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{{#set: transcription direction=NEGATIVE}}
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* '''Create draft network''':
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{{#set: right end position=3788003}}
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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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{{#set: centisome position=57.93101    }}
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* '''Manual curation''':
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{{#set: common name=Esi_0080_0017|Esi0080_0017|MPDH3}}
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''Apply the curation described in the form file 1_cycRxns_to_add.csv.''
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{{#set: reaction associated=MANNPDEHYDROG-RXN}}
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* '''Manual curation''':
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{{#set: pathway associated=MANNIDEG-PWY|PWY-6531}}
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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.''
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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.''
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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.''
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* '''Manual curation''':
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''Apply the curation described in the form file 2_cycRxns_to_add.csv.''
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* '''Manual curation''':
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''Apply the curation described in the form file 2_lightRxns_to_add.csv.''
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* '''Manual curation''':
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''Apply the curation described in the form file 2_biomass_rxn.csv.''
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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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* '''Create Wiki pages''':
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''Create Wiki pages to display the metabolic network.''
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==Downloads==
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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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