Difference between revisions of "Workflow"

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(Created page with "Category:Reaction == Reaction [http://metacyc.org/META/NEW-IMAGE?object=6PGLUCONDEHYDROG-RXN 6PGLUCONDEHYDROG-RXN] == * direction: ** LEFT-TO-RIGHT * common name: ** phosp...")
(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Orthology based reconstruction''': '...")
 
(One intermediate revision by the same user not shown)
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[[Category:Reaction]]
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=Workflow command history=
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== Reaction [http://metacyc.org/META/NEW-IMAGE?object=6PGLUCONDEHYDROG-RXN 6PGLUCONDEHYDROG-RXN] ==
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* direction:
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** LEFT-TO-RIGHT
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* common name:
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** phosphogluconate dehydrogenase [NAD(P)+-dependent, decarboxylating]
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* ec number:
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** [http://enzyme.expasy.org/EC/1.1.1.351 EC-1.1.1.351]
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* Synonym(s):
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** 6PGD
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** 6-phosphogluconic carboxylase
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** 6-phosphogluconic dehydrogenase
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** Phosphogluconic acid dehydrogenase
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== Reaction Formula ==
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==Command sequence==
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* With identifiers:
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* '''Check input''':
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** 1 [[NAD-P-OR-NOP]][c] '''+''' 1 [[CPD-2961]][c] '''=>''' 1 [[RIBULOSE-5P]][c] '''+''' 1 [[NADH-P-OR-NOP]][c] '''+''' 1 [[CARBON-DIOXIDE]][c]
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''Check the validity, consistency and presence of input files''
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* With common name(s):
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* '''Orthology based reconstruction''':
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** 1 NAD(P)+[c] '''+''' 1 D-gluconate 6-phosphate[c] '''=>''' 1 D-ribulose 5-phosphate[c] '''+''' 1 NAD(P)H[c] '''+''' 1 CO2[c]
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''Run the orthology based reconstruction.''
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* '''Annotation based reconstruction''':
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== Genes associated with this reaction  ==
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''Extract network data from Pathway Tools annotation output.''
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Genes have been associated with this reaction based on different elements listed below.
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* '''SBML mapping''':
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* [[Tiso_gene_91]]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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** [[pantograph]]-[[esiliculosus]]
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* '''SBML mapping''':
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* [[Tiso_gene_20238]]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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** [[pantograph]]-[[athaliana]]
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* '''SBML mapping''':
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** [[pantograph]]-[[athaliana]]
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
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** [[pantograph]]-[[synechocystis]]
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* '''Create draft network''':
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** [[pantograph]]-[[creinhardtii]]
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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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* [[Tiso_gene_7157]]
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* '''Get compartments''':
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** [[pantograph]]-[[synechocystis]]
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''Display all the compartments of the metabolic network.''
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** [[pantograph]]-[[creinhardtii]]
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* '''Change compartment''':
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== Pathways  ==
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''Modify a compartment in the metabolic network.''
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* [[P122-PWY]], heterolactic fermentation: [http://metacyc.org/META/NEW-IMAGE?object=P122-PWY P122-PWY]
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* '''Change compartment''':
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** '''14''' reactions found over '''18''' reactions in the full pathway
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''Modify a compartment in the metabolic network.''
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== Reconstruction information  ==
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* '''Change compartment''':
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* Category: [[orthology]]
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''Modify a compartment in the metabolic network.''
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** Source: [[orthology-athaliana]]
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* '''Change compartment''':
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*** Tool: [[pantograph]]
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''Modify a compartment in the metabolic network.''
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** Source: [[orthology-creinhardtii]]
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* '''Change compartment''':
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*** Tool: [[pantograph]]
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''Modify a compartment in the metabolic network.''
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** Source: [[orthology-synechocystis]]
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* '''Change compartment''':
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*** Tool: [[pantograph]]
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''Modify a compartment in the metabolic network.''
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** Source: [[orthology-esiliculosus]]
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* '''Get compartments''':
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*** Tool: [[pantograph]]
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''Display all the compartments of the metabolic network.''
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== External links  ==
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* '''Set medium''':
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* RHEA:
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''Set the growth medium for the studied species.''
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** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=10116 10116]
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* '''Run gap-filling''':
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* UNIPROT:
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''Calculate the gap-filling solution and generate the metabolic network, completed with the gap-filling solution.''
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** [http://www.uniprot.org/uniprot/P14332 P14332]
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* '''Manual curation''':
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** [http://www.uniprot.org/uniprot/P31072 P31072]
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''Apply the curation described in the form file export_biomass_rxn.csv.''
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** [http://www.uniprot.org/uniprot/Q9CDN4 Q9CDN4]
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* '''Manual curation''':
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** [http://www.uniprot.org/uniprot/P47506 P47506]
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''Apply the curation described in the form file reactions_PWY-6475_tiso_add.csv.''
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** [http://www.uniprot.org/uniprot/Q9JWS3 Q9JWS3]
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* '''Set FBA''':
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** [http://www.uniprot.org/uniprot/P43774 P43774]
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''Set the biomass reaction to run flux balance analysis on the network.''
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** [http://www.uniprot.org/uniprot/P12013 P12013]
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* '''Test FBA''':
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** [http://www.uniprot.org/uniprot/P41576 P41576]
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''Run flux balance analysis on the network.''
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** [http://www.uniprot.org/uniprot/P00350 P00350]
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* '''Create Wiki pages''':
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** [http://www.uniprot.org/uniprot/P00349 P00349]
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''Create Wiki pages to display the metabolic network.''
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** [http://www.uniprot.org/uniprot/P52209 P52209]
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==Downloads==
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** [http://www.uniprot.org/uniprot/P41581 P41581]
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You can download the [[MEDIA:log.txt|command log file here]]
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** [http://www.uniprot.org/uniprot/P41582 P41582]
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** [http://www.uniprot.org/uniprot/Q59275 Q59275]
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** [http://www.uniprot.org/uniprot/P41583 P41583]
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** [http://www.uniprot.org/uniprot/Q60254 Q60254]
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** [http://www.uniprot.org/uniprot/P37754 P37754]
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** [http://www.uniprot.org/uniprot/Q59410 Q59410]
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** [http://www.uniprot.org/uniprot/P52207 P52207]
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** [http://www.uniprot.org/uniprot/P70718 P70718]
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** [http://www.uniprot.org/uniprot/Q7M451 Q7M451]
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** [http://www.uniprot.org/uniprot/P41572 P41572]
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** [http://www.uniprot.org/uniprot/P14062 P14062]
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** [http://www.uniprot.org/uniprot/P21577 P21577]
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** [http://www.uniprot.org/uniprot/P38720 P38720]
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** [http://www.uniprot.org/uniprot/Q40311 Q40311]
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** [http://www.uniprot.org/uniprot/P53319 P53319]
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** [http://www.uniprot.org/uniprot/O81237 O81237]
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** [http://www.uniprot.org/uniprot/O81238 O81238]
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** [http://www.uniprot.org/uniprot/O81239 O81239]
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** [http://www.uniprot.org/uniprot/O22111 O22111]
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** [http://www.uniprot.org/uniprot/Q17761 Q17761]
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** [http://www.uniprot.org/uniprot/O32911 O32911]
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{{#set: direction=LEFT-TO-RIGHT}}
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{{#set: common name=phosphogluconate dehydrogenase [NAD(P)+-dependent, decarboxylating]}}
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{{#set: ec number=EC-1.1.1.351}}
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{{#set: common name=6PGD|6-phosphogluconic carboxylase|6-phosphogluconic dehydrogenase|Phosphogluconic acid dehydrogenase}}
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{{#set: gene associated=Tiso_gene_91|Tiso_gene_20238|Tiso_gene_7157}}
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{{#set: in pathway=P122-PWY}}
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{{#set: reconstruction category=orthology}}
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{{#set: reconstruction source=orthology-athaliana|orthology-creinhardtii|orthology-synechocystis|orthology-esiliculosus}}
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{{#set: reconstruction tool=pantograph}}
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Latest revision as of 21:26, 21 March 2018

Workflow command history

Command sequence

  • Check input:

Check the validity, consistency and presence of input files

  • Orthology based reconstruction:

Run the orthology based reconstruction.

  • Annotation based reconstruction:

Extract network data from Pathway Tools annotation output.

  • 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.

  • 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.

  • Get compartments:

Display all the compartments of the metabolic network.

  • 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.

  • Manual curation:

Apply the curation described in the form file export_biomass_rxn.csv.

  • Manual curation:

Apply the curation described in the form file reactions_PWY-6475_tiso_add.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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