Difference between revisions of "Main Page"

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(Created page with "Category:metabolite == Metabolite CPD-690 == * smiles: ** cc5(=c%10(c(c)(ccc([o-])=o)c(cc(=o)[o-])c9(c%11(c)(c(c)(cc(n)=o)c(ccc([o-])=o)c1(=[n+]([co--]3([n+]2(c(=c(c)1)c(c...")
 
(Created page with "== description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Output [LI...")
 
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[[Category:metabolite]]
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== description ==
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== Metabolite CPD-690 ==
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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* smiles:
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Model summary: [[MEDIA:summary.txt|summary]]
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** cc5(=c%10(c(c)(ccc([o-])=o)c(cc(=o)[o-])c9(c%11(c)(c(c)(cc(n)=o)c(ccc([o-])=o)c1(=[n+]([co--]3([n+]2(c(=c(c)1)c(c)(cc(n)=o)c(ccc([o-])=o)c=2c=c4(c(c)(c)c(ccc([o-])=o)c(=[n+]34)5)))(cc6(c(c(o)c(o6)n7(c=nc8(=c7n=cn=c8n)))o))n9%10)%11)))))
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* common-name:
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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** adenosyl-cobyrinate a,c-diamide
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* inchi-key:
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The automatic reconstruction of ''Ruminococcus flavefaciens'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1453 reactions, 1373 metabolites, 828 genes and 756 pathways. This GeM was obtained based on the following sources:
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** ocnljczkghkjgf-nqyrmhkhsa-h
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* Based on annotation data:
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* molecular-weight:
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** Creation of a metabolic network containing 919 reactions
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** 1182.137
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* Based on orthology data:
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== Reaction(s) known to consume the compound ==
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** Creation of a global metabolic network containing 676 reactions
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* [[R345-RXN]]
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*** From template ''faecalibacteriumprausnitziia2-165_heinken2014'' creation of a metabolic network containing: 315 reactions
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== Reaction(s) known to produce the compound ==
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*** From template ''l_plantarum_wcfs1'' creation of a metabolic network containing: 211 reactions
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* [[R344-RXN]]
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*** From template ''bthetaiotaomicron_heinken2013'' creation of a metabolic network containing: 296 reactions
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== Reaction(s) of unknown directionality ==
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*** From template ''ecoli'' creation of a metabolic network containing: 448 reactions
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{{#set: common-name=adenosyl-cobyrinate a,c-diamide}}
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*** From template ''bifidobacteriumadolescentisl2-32'' creation of a metabolic network containing: 214 reactions
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{{#set: inchi-key=inchikey=ocnljczkghkjgf-nqyrmhkhsa-h}}
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* Based on expertise:
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{{#set: molecular-weight=1182.137}}
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** 118 reaction(s) added
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*List of tools used:
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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[[FILE:venn.png|frameless|border]]
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== Collaborative curation ==  
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* Suggest reactions to add or remove:
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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* Suggest new reactions to create and add:
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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* Send the filled form(s) to: gem-aureme[at]inriaa.fr

Latest revision as of 17:46, 15 January 2021

description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Ruminococcus flavefaciens results to a Genome scale Model containing 1453 reactions, 1373 metabolites, 828 genes and 756 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Creation of a metabolic network containing 919 reactions
  • Based on orthology data:
    • Creation of a global metabolic network containing 676 reactions
      • From template faecalibacteriumprausnitziia2-165_heinken2014 creation of a metabolic network containing: 315 reactions
      • From template l_plantarum_wcfs1 creation of a metabolic network containing: 211 reactions
      • From template bthetaiotaomicron_heinken2013 creation of a metabolic network containing: 296 reactions
      • From template ecoli creation of a metabolic network containing: 448 reactions
      • From template bifidobacteriumadolescentisl2-32 creation of a metabolic network containing: 214 reactions
  • Based on expertise:
    • 118 reaction(s) added

Venn.png


Collaborative curation

  • Suggest reactions to add or remove:
  • Suggest new reactions to create and add:
  • Follow the examples given in the form(s) to correctly share your suggestions
  • Send the filled form(s) to: gem-aureme[at]inriaa.fr
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