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| − | + | == Ectocarpus Subulatus Holobiont description == | |
| + | This wiki represent the metabolic network of Ectocarpus Subulatus and 10 Bacteria of the holobiont | ||
| − | + | == 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 ''ecto_bacteria'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 4342 reactions, 3507 metabolites, 2281 genes and 1500 pathways. This GeM was obtained based on the following sources: |
| − | * [https:// | + | * 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: | ||
| + | *** 19318 reaction(s) added | ||
| + | * Based on gap-filling: | ||
| + | ** Tool: [https://pypi.python.org/pypi/meneco meneco] | ||
| + | *** 85 reaction(s) added | ||
| + | |||
| + | [[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@inria.fr | ||
Latest revision as of 17:01, 2 October 2018
Ectocarpus Subulatus Holobiont description
This wiki represent the metabolic network of Ectocarpus Subulatus and 10 Bacteria of the holobiont
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output [LINK OR MEDIA data]
The automatic reconstruction of ecto_bacteria results to a Genome scale Model containing 4342 reactions, 3507 metabolites, 2281 genes and 1500 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:
- 19318 reaction(s) added
- Based on gap-filling:
- Tool: meneco
- 85 reaction(s) added
- Tool: meneco
