Difference between revisions of "Manual-4 newreactions"
From metabolic_network
(Created page with "== EFAEV583GEM description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' result...") |
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== EFAEV583GEM description == | == EFAEV583GEM description == | ||
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] == | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == | ||
| − | The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' results to a Genome scale Model containing 1117 reactions, 911 metabolites, 610 genes and 106 pathways. This GeM was obtained based on the following sources: | + | Model summary: [[MEDIA:efaecalisV583_final.txt|summary]] |
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| + | Download '''AuReMe''' Input/Output [https://mybox.inria.fr data] | ||
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| + | The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' results to a Genome scale [[MEDIA:efaecalisV583_final_lvl3.xml|Model]] containing 1117 reactions, 911 metabolites, 610 genes and 106 pathways. This GeM was obtained based on the following sources: | ||
* Based on orthology data: | * Based on orthology data: | ||
** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ||
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== Collaborative curation == | == Collaborative curation == | ||
* Suggest reactions to add or remove: | * Suggest reactions to add or remove: | ||
| − | ** Download this [[MEDIA:Add_delete_reaction.csv| | + | ** Download this [[MEDIA:Add_delete_reaction.csv|form]] |
* Suggest new reactions to create and add: | * Suggest new reactions to create and add: | ||
** Download this [[MEDIA:Reaction_creator.csv|form]] | ** Download this [[MEDIA:Reaction_creator.csv|form]] | ||
| − | * '''Follow the examples given in the form to correctly share your suggestions''' | + | * '''Follow the examples given in the form(s) to correctly share your suggestions''' |
| − | * Send the | + | * Send the filled form(s) to: CONTACT_MAIL |
Revision as of 16:23, 11 January 2018
EFAEV583GEM description
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output data
The automatic reconstruction of Enterococcus_faecalis_str_v583 results to a Genome scale Model containing 1117 reactions, 911 metabolites, 610 genes and 106 pathways. This GeM was obtained based on the following sources:
- Based on orthology data:
- Tool: Pantograph
- From template E_COLI_SSTR_K12_SUBSTR_MG1655 creation of a metabolic network containing: 528 reactions
- From template L_PLANTARUM_WCFS1 creation of a metabolic network containing: 385 reactions
- From template B_SUBTILIS_SUBSP_SUBTILIS_STR168 creation of a metabolic network containing: 463 reactions
- Tool: Pantograph
- Based on expertise:
- 221 reaction(s) added
- Based on gap-filling:
- Tool: meneco
- 50 reaction(s) added
- Tool: meneco
