Difference between revisions of "Main Page"

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(Created page with "== description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Output [LI...")
(Created page with "{{#ask: Category:reaction reconstruction category::annotation | ?common-name | ?ec-number | ?reconstruction tool | ?reconstruction source | ?reconstruction comment | ?...")
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==  description ==
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{{#ask: [[Category:reaction]] [[reconstruction category::annotation]]
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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| ?common-name
Model summary: [[MEDIA:summary.txt|summary]]
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| ?ec-number
 
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| ?reconstruction tool
Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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| ?reconstruction source
 
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| ?reconstruction comment
The automatic reconstruction of ''Fibrobacter succinogenes' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1567 reactions, 1588 metabolites, 1314 genes and 931 pathways. This GeM was obtained based on the following sources:
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* Based on annotation data:
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| ?nb pathway associated
** Creation of a metabolic network containing 826 reactions
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}}
* Based on orthology data:
 
** Creation of a global metabolic network containing 377 reactions
 
* Based on expertise:
 
** 462 reaction(s) added
 
* Based on gap-filling:
 
*** 105 reaction(s) added
 
 
 
*List of tools used:
 
** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
 
** Tool: [https://github.com/davidemms/OrthoFinder Orthofinder]
 
** Tool: [https://pypi.python.org/pypi/meneco Meneco]
 
 
 
[[FILE:venn.png|frameless|border]]
 
 
 
== Collaborative curation ==
 
* Suggest reactions to add or remove:
 
** Download this [[MEDIA:Add_delete_reaction.csv|form]]
 
* Suggest new reactions to create and add:
 
** Download this [[MEDIA:Reaction_creator.csv|form]]
 
* '''Follow the examples given in the form(s) to correctly share your suggestions'''
 
* Send the filled form(s) to: gem-aureme[at]inria.fr
 

Revision as of 17:00, 14 October 2022