Difference between revisions of "Main Page"

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<strong>MediaWiki has been successfully installed.</strong>
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== GEM description ==
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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Model summary: [[MEDIA:summary.txt|summary]]
  
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Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
  
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== Getting started ==
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The automatic reconstruction of '''' results to a Genome scale [[MEDIA:model.xml|Model]] containing 3399 reactions, 3313 metabolites, 5374 genes and 1402 pathways. This GeM was obtained based on the following sources:
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* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
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* Based on annotation data:
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* [//www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools]
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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*** Creation of a metabolic network containing 2497 reactions
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* [//www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
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* Based on orthology data:
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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*** From template ''ECTOCARPUS_SILICULOSUS'' creation of a metabolic network containing: 1474 reactions
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*** From template ''NANNOCHLOROPSIS_SALINA'' creation of a metabolic network containing: 601 reactions
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*** From template ''SACCHARINA_JAPONICA'' creation of a metabolic network containing: 3035 reactions
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*** From template ''ARABIDOPSIS_THALIANA'' creation of a metabolic network containing: 432 reactions
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* Based on expertise:
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*** 57 reaction(s) added
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* Based on gap-filling:
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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*** 67 reaction(s) added
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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: CONTACT_MAIL

Latest revision as of 11:49, 27 June 2019

GEM description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of ' results to a Genome scale Model containing 3399 reactions, 3313 metabolites, 5374 genes and 1402 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: Pathway tools
      • Creation of a metabolic network containing 2497 reactions
  • Based on orthology data:
    • Tool: Pantograph
      • From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1474 reactions
      • From template NANNOCHLOROPSIS_SALINA creation of a metabolic network containing: 601 reactions
      • From template SACCHARINA_JAPONICA creation of a metabolic network containing: 3035 reactions
      • From template ARABIDOPSIS_THALIANA creation of a metabolic network containing: 432 reactions
  • Based on expertise:
      • 57 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 67 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: CONTACT_MAIL
Retrieved from "http://gem-aureme.irisa.fr/cokagem/index.php?title=Main_Page&oldid=13495"