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(Created page with "Category:pathway == Pathway P184-PWY == * common-name: ** protocatechuate degradation i (meta-cleavage pathway) * taxonomic-range: ** tax-1224 == Reaction(s) found == * ...") |
(Created page with "== description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Output [LI...") |
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| − | [[ | + | == 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 ''Fibrobacter succinogene S85'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1565 reactions, 1586 metabolites, 1317 genes and 931 pathways. This GeM was obtained based on the following sources: | |
| − | * | + | * Based on annotation data: |
| − | + | ** Creation of a metabolic network containing 827 reactions | |
| − | * [ | + | * Based on orthology data: |
| − | * [ | + | ** Creation of a global metabolic network containing 377 reactions |
| − | * [ | + | * Based on expertise: |
| − | * | + | ** 490 reaction(s) added |
| − | * [ | + | * Based on gap-filling: |
| − | * | + | *** 75 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 | ||
Latest revision as of 11:09, 17 October 2022
description
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output [LINK OR MEDIA data]
The automatic reconstruction of Fibrobacter succinogene S85 results to a Genome scale Model containing 1565 reactions, 1586 metabolites, 1317 genes and 931 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Creation of a metabolic network containing 827 reactions
- Based on orthology data:
- Creation of a global metabolic network containing 377 reactions
- Based on expertise:
- 490 reaction(s) added
- Based on gap-filling:
- 75 reaction(s) added
- List of tools used:
- Tool: PathwayTools
- Tool: Orthofinder
- Tool: Meneco
