Difference between revisions of "Main Page"

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<strong>MediaWiki has been installed.</strong>
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== CCRGEM-1.3 description ==
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CcrGEM is a genome-scale metabolic network for the model red alga ''Chondrus crispus''.  
  
Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
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For more information about this project, please contact Gabriel Markov (Station Biologique de Roscoff).
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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Download '''AuReMe''' Input
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Model summary: [[MEDIA:summary.txt|summary]]
  
== Getting started ==
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The automatic reconstruction of ''MODEL_NAME'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 2038 reactions, 2207 metabolites, 2012 genes and 1110 pathways. This GeM was obtained based on the following sources:
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
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* Based on orthology data:
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
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** Creation of a global metabolic network containing 1732 reactions
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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*** From template ''ectocarpus_siliculosus'' creation of a metabolic network containing: 1161 reactions
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
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*** From template ''galdieria.sulphuraria'' creation of a metabolic network containing: 1361 reactions
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
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*** From template ''arabidopsis_thaliana'' creation of a metabolic network containing: 383 reactions
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* Based on annotation data:
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** Creation of a metabolic network containing 595 reactions
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* Based on gap-filling:
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*** 146 reaction(s) added
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* Based on expertise:
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** 90 reaction(s) added
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*List of tools used:
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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** Tool: [https://pypi.python.org/pypi/meneco Meneco]
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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: gmarkov@sb-roscoff.fr

Revision as of 13:07, 21 October 2019

CCRGEM-1.3 description

CcrGEM is a genome-scale metabolic network for the model red alga Chondrus crispus.

For more information about this project, please contact Gabriel Markov (Station Biologique de Roscoff).

Automatic reconstruction with AuReMe

Download AuReMe Input Model summary: summary

The automatic reconstruction of MODEL_NAME results to a Genome scale Model containing 2038 reactions, 2207 metabolites, 2012 genes and 1110 pathways. This GeM was obtained based on the following sources:

  • Based on orthology data:
    • Creation of a global metabolic network containing 1732 reactions
      • From template ectocarpus_siliculosus creation of a metabolic network containing: 1161 reactions
      • From template galdieria.sulphuraria creation of a metabolic network containing: 1361 reactions
      • From template arabidopsis_thaliana creation of a metabolic network containing: 383 reactions
  • Based on annotation data:
    • Creation of a metabolic network containing 595 reactions
  • Based on gap-filling:
      • 146 reaction(s) added
  • Based on expertise:
    • 90 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: gmarkov@sb-roscoff.fr