Difference between revisions of "RXN0-4261"
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(Created page with "{{#ask: Category:reaction reconstruction tool::curation | ?common-name | ?ec-number | ?reconstruction category | ?reconstruction source | ?reconstruction comment | ?nb...") |
(Created page with "== ESILGEM description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Ou...") |
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− | + | == ESILGEM description == | |
− | | | + | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == |
− | + | Model summary: [[MEDIA:summary.txt|summary]] | |
− | + | ||
− | | | + | Download '''AuReMe''' Input/Output [LINK OR MEDIA data] |
− | + | ||
− | | | + | The automatic reconstruction of ''Ectocarpus siliculosus'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1992 reactions, 2146 metabolites, 2290 genes and 1103 pathways. This GeM was obtained based on the following sources: |
− | + | * Based on annotation data: | |
− | + | ** Creation of a metabolic network containing 1661 reactions | |
+ | * Based on orthology data: | ||
+ | ** Creation of a global metabolic network containing 440 reactions | ||
+ | *** From template ''aragem'' creation of a metabolic network containing: 440 reactions | ||
+ | * Based on gap-filling: | ||
+ | *** 85 reaction(s) added | ||
+ | * Based on expertise: | ||
+ | ** 80 reaction(s) added | ||
+ | |||
+ | *List of tools used: | ||
+ | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools] | ||
+ | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ||
+ | ** 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 12:11, 12 January 2021
ESILGEM description
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output [LINK OR MEDIA data]
The automatic reconstruction of Ectocarpus siliculosus results to a Genome scale Model containing 1992 reactions, 2146 metabolites, 2290 genes and 1103 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Creation of a metabolic network containing 1661 reactions
- Based on orthology data:
- Creation of a global metabolic network containing 440 reactions
- From template aragem creation of a metabolic network containing: 440 reactions
- Creation of a global metabolic network containing 440 reactions
- Based on gap-filling:
- 85 reaction(s) added
- Based on expertise:
- 80 reaction(s) added
- List of tools used:
- Tool: PathwayTools
- Tool: Pantograph
- Tool: Meneco