Difference between revisions of "Main Page"
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| − | + | == ECTOGEM description == | |
| − | == | + | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == |
| − | + | Model summary: [[MEDIA:summary.txt|summary]] | |
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| − | + | Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | |
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| − | ** | + | The automatic reconstruction of ''Ectocarpus_Siliculosus'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1977 reactions, 2132 metabolites, 2281 genes and 1101 pathways. This GeM was obtained based on the following sources: |
| − | *** | + | * Based on annotation data: |
| − | + | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | |
| − | == | + | *** Creation of a metabolic network containing 1661 reactions |
| − | + | * Based on orthology data: | |
| − | + | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | |
| − | + | *** From template ''ARAGEM'' creation of a metabolic network containing: 440 reactions | |
| − | + | * Based on expertise: | |
| − | + | *** 65 reaction(s) added | |
| − | + | * Based on gap-filling: | |
| + | ** Tool: [https://pypi.python.org/pypi/meneco meneco] | ||
| + | *** 85 reaction(s) added | ||
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| + | [[FILE:venn.png|frameless|border]] | ||
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| + | == 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@inria.fr | ||
Latest revision as of 13:11, 16 November 2018
ECTOGEM 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 1977 reactions, 2132 metabolites, 2281 genes and 1101 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Tool: Pathway tools
- Creation of a metabolic network containing 1661 reactions
- Tool: Pathway tools
- Based on orthology data:
- Tool: Pantograph
- From template ARAGEM creation of a metabolic network containing: 440 reactions
- Tool: Pantograph
- Based on expertise:
- 65 reaction(s) added
- Based on gap-filling:
- Tool: meneco
- 85 reaction(s) added
- Tool: meneco
