Difference between revisions of "Category:Reaction"

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(Created page with "=Workflow command history= ==Command sequence== * '''Check input''': ''Check the validity, consistency and presence of input files'' * '''Annotation based reconstruction''':...")
(Created page with "{{#ask: Category:reaction | ?common-name | ?ec-number | ?nb gene associated | ?nb pathway associated | ?nb reconstruction source | ?reconstruction category | ?reconstructi...")
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=Workflow command history=
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{{#ask: [[Category:reaction]]
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| ?common-name
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==Command sequence==
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| ?ec-number
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* '''Check input''':
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| ?nb gene associated
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''Check the validity, consistency and presence of input files''
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| ?nb pathway associated
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* '''Annotation based reconstruction''':
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| ?nb reconstruction source
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''Extract network data from Pathway Tools annotation output.''
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| ?reconstruction category
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* '''Orthology based reconstruction''':
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| ?reconstruction tool
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''Run the orthology based reconstruction.''
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| ?reconstruction comment
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* '''SBML mapping''':
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}}
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''Map an SBML file (all the entities IDs) to a reference database (specified in config.txt).''
 
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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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* '''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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* '''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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* '''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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* '''Set medium''':
 
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''Set the growth medium for the studied species.''
 
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* '''Manual curation''':
 
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''Apply the curation described in the form file add_biomass_reaction.tsv.''
 
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* '''Manual curation''':
 
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''Apply the curation described in the form file remove_anaerobic_reactions.tsv.''
 
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* '''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.''
 
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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_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.''
 
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==Downloads==
 
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You can download the [[MEDIA:log.txt|command log file here]]
 

Revision as of 07:43, 17 October 2022

 Common-nameEc-numberNb gene associatedNb pathway associatedNb reconstruction sourceReconstruction categoryReconstruction toolReconstruction comment
1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN1-acyl-sn-glycerol-3-phosphate acyltransferaseEc-2.3.1.5162AnnotationPathwaytoolsN.a
1-PHOSPHATIDYLINOSITOL-KINASE-RXNPhosphatidylinositol kinaseEc-2.7.1.6722AnnotationPathwaytoolsN.a
1.1.1.39-RXNEc-1.1.1.3816OrthologyOrthofinderN.a
1.1.1.8-RXNEc-1.1.1.813OrthologyOrthofinderN.a
1.1.1.83-RXNEc-1.1.1.8311OrthologyOrthofinderN.a
1.17.4.2-RXNAnaerobic ribonucleoside-triphosphate reductaseEc-1.17.4.230AnnotationPathwaytoolsN.a
1.2.1.13-RXNEc-1.2.1.1301ManualCurationAdded to improve flux in sugars
1.2.1.53-RXNEc-1.2.1.5301ManualCurationTo improve flux of network
1.2.7.8-RXNThiamine pyrophosphate-binding proteinEc-1.2.7.810AnnotationPathwaytoolsN.a
1.4.1.21-RXNEc-1.4.1.2100Gap-fillingMenecoAdded for gapfilling
1.5.1.20-RXNEc-1.5.1.2024AnnotationPathwaytoolsN.a
1.5.1.9-RXNEc-1.5.1.911ManualCurationPresent in the annotation part in the first version of the fibrobacter gem
1.6.5.6-RXNEc-1.6.5.601ManualCurationTo improve flux of network
1.6.99.5-RXNHypothetical protein
Nadh-quinone oxidoreductase subunit d
Nadh-quinone oxidoreductase subunit nuok		Ec-1.6.5.11100AnnotationPathwaytoolsN.a
1.8.4.8-RXNEc-1.8.4.811ManualCurationPresent in the annotation part in the first version of the fibrobacter gem
13-PROPANEDIOL-DEHYDROGENASE-RXNEc-1.1.1.20211OrthologyOrthofinderN.a
1TRANSKETO-RXNTransketolaseEc-2.2.1.127AnnotationPathwaytoolsN.a
2-AMINOADIPATE-AMINOTRANSFERASE-RXNEc-2.6.1.3905ManualCurationTo improve flux of network
2-DEHYDROPANTOATE-REDUCT-RXN2-dehydropantoate 2-reductaseEc-1.1.1.16932Orthology
Annotation		Orthofinder
Pathwaytools		N.a
2-HALOACID-DEHALOGENASE-RXNHaloacid dehalogenaseEc-3.8.1.10
Ec-3.8.1.2		30AnnotationPathwaytoolsN.a
2-ISOPROPYLMALATESYN-RXNPyruvate carboxyltransferaseEc-2.3.3.1332Orthology
Annotation		Orthofinder
Pathwaytools		N.a
2-METHYLCITRATE-DEHYDRATASE-RXNEc-4.2.1.7911ManualCurationPresent in the annotation part in the first version of the fibrobacter gem
2-OCTAPRENYL-6-OHPHENOL-METHY-RXN2-octaprenyl-6-hydroxyphenyl methylaseEc-2.1.1.22211OrthologyOrthofinderN.a
2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXNEc-2.1.1.20112OrthologyOrthofinderN.a
2-OXOGLUTARATE-SYNTHASE-RXNEc-1.2.7.305Gap-fillingMenecoAdded for gapfilling
2.1.1.100-RXNEc-2.1.1.10020ManualCurationPresent in the annotation part in the first version of the fibrobacter gem
2.1.1.132-RXNEc-2.1.1.13200ManualCurationTo improve flux in adenosylcobalamin
2.1.1.133-RXNEc-2.1.1.13311OrthologyOrthofinderN.a
2.1.1.151-RXNEc-2.1.1.15101ManualCurationAdded to reach cpd-691
2.1.1.63-RXNEc-2.1.1.6320AnnotationPathwaytoolsN.a
2.1.1.72-RXNEc-2.1.1.7220ManualCurationPresent in the annotation part in the first version of the fibrobacter gem
2.3.1.128-RXNRibosomal protein s18-alanine n-acetyltransferaseEc-2.3.1.26620AnnotationPathwaytoolsN.a
2.3.1.157-RXNEc-2.3.1.15702Gap-fillingMenecoAdded for gapfilling
2.3.1.179-RXNBeta-ketoacyl-acp synthase iiEc-2.3.1.17941AnnotationPathwaytoolsN.a
2.3.1.180-RXNEc-2.3.1.18011OrthologyOrthofinderN.a
2.3.1.41-RXNBeta-ketoacyl-acp synthase iiEc-2.3.1.179
Ec-2.3.1.41		60AnnotationPathwaytoolsN.a
2.3.1.89-RXNEc-2.3.1.8901ManualCurationTo improve flux of network
2.3.2.13-RXNTransglutaminase domain-containing proteinEc-2.3.2.1320AnnotationPathwaytoolsN.a
2.4.1.129-RXNPeptidoglycan glycosyltransferaseEc-2.4.1.12921AnnotationPathwaytoolsN.a
2.4.2.12-RXNEc-2.4.2.1201ManualCurationTo improve flux in adenosylcobalamin
2.5.1.19-RXN3-phosphoshikimate 1-carboxyvinyltransferaseEc-2.5.1.1941Orthology
Annotation		Orthofinder
Pathwaytools		N.a
2.5.1.41-RXNEc-2.5.1.4111ManualCurationPresent in the annotation part in the first version of the fibrobacter gem
2.5.1.64-RXNEc-2.2.1.901Gap-fillingMenecoAdded for gapfilling
2.6.1.18-RXNEc-2.6.1.1802Gap-fillingMenecoAdded for gapfilling
2.6.1.28-RXNEc-2.6.1.2802Gap-fillingMenecoAdded for gapfilling
2.6.1.33-RXNEc-2.6.1.3312ManualCurationPresent in the annotation part in the first version of the fibrobacter gem
2.6.1.58-RXNEc-2.6.1.5802Gap-fillingMenecoAdded for gapfilling
2.6.1.64-RXNEc-2.6.1.6400Gap-fillingMenecoAdded for gapfilling
2.6.1.70-RXNEc-2.6.1.7000Gap-fillingMenecoAdded for gapfilling
2.7.1.145-RXNDeoxynucleoside kinaseEc-2.7.1.14520AnnotationPathwaytoolsN.a
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Pages in category "Reaction"

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