|
|
| Line 1: |
Line 1: |
| − | == description ==
| + | {{#ask: [[Category:reaction]] [[reconstruction tool::curation]] |
| − | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
| + | | ?common-name |
| − | Model summary: [[MEDIA:summary.txt|summary]]
| + | | ?ec-number |
| − | | + | | ?reconstruction category |
| − | Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
| + | | ?reconstruction source |
| − | | + | | ?reconstruction comment |
| − | The automatic reconstruction of ''MODEL_NAME'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 3356 reactions, 3250 metabolites, 5018 genes and 1391 pathways. This GeM was obtained based on the following sources:
| + | | ?nb gene associated |
| − | * Based on orthology data:
| + | | ?nb pathway associated |
| − | ** Creation of a global metabolic network containing 1879 reactions
| + | }} |
| − | *** From template ''ectocarpus_siliculosus'' creation of a metabolic network containing: 1492 reactions
| |
| − | *** From template ''arabidopsis_thaliana'' creation of a metabolic network containing: 419 reactions
| |
| − | *** From template ''nannochloropsis_salina'' creation of a metabolic network containing: 589 reactions
| |
| − | * Based on annotation data:
| |
| − | ** Creation of a metabolic network containing 2552 reactions
| |
| − | * Based on expertise:
| |
| − | ** 101 reaction(s) added
| |
| − | * Based on gap-filling:
| |
| − | *** 90 reaction(s) added
| |
| − | | |
| − | *List of tools used:
| |
| − | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
| |
| − | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
| |
| − | | |
| − | ** 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: CONTACT_MAIL
| |
