Difference between revisions of "Category:Pathway"

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(Created page with "* navigation ** mainpage|mainpage-description ** randompage-url|randompage ** Special:ListFiles|Files * Metabolic network components ** Category:Reaction|Reaction ** Category:...")
(Created page with "== EFAEV583GEM description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input...")
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* navigation
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== EFAEV583GEM description ==
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** mainpage|mainpage-description
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== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
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** randompage-url|randompage
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Model summary: [[MEDIA:summary.txt|summary]]
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** Special:ListFiles|Files
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* Metabolic network components
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Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
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** Category:Reaction|Reaction
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** Category:Gene|Gene
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The automatic reconstruction of ''Enterococcus_faecalis_str_v583'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1117 reactions, 911 metabolites, 610 genes and 106 pathways. This GeM was obtained based on the following sources:
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** Category:Pathway|Pathway
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* Based on orthology data:
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** Category:Metabolite|Metabolite
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** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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* Reconstruction categories
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*** From template ''E_COLI_SSTR_K12_SUBSTR_MG1655'' creation of a metabolic network containing: 528 reactions
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** gap-filling|gap-filling
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*** From template ''L_PLANTARUM_WCFS1'' creation of a metabolic network containing: 385 reactions
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** manual|manual
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*** From template ''B_SUBTILIS_SUBSP_SUBTILIS_STR168'' creation of a metabolic network containing: 463 reactions
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** orthology|orthology
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* Based on expertise:
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* Reconstruction tools
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*** 221 reaction(s) added
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** meneco|meneco
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* Based on gap-filling:
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** pantograph|pantograph
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** Tool: [https://pypi.python.org/pypi/meneco meneco]
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* Reconstruction sources
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*** 50 reaction(s) added
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** added for gapfilling|added for gapfilling
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** added to manage seeds from boundary to extracellular compartment|added to manage seeds from boundary to extracellular compartment
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[[FILE:venn.png|frameless|border]]
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** added to manage seeds from extracellular to cytosol compartment|added to manage seeds from extracellular to cytosol compartment
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** b_subtilis_subsp_subtilis_str168|b_subtilis_subsp_subtilis_str168
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== Collaborative curation ==
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** curation_from_orthology|curation_from_orthology
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* Suggest reactions to add or remove:
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** e_coli_sstr_k12_substr_mg1655|e_coli_sstr_k12_substr_mg1655
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** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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** l_plantarum_wcfs1|l_plantarum_wcfs1
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* Suggest new reactions to create and add:
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** manual curation|manual curation
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** Download this [[MEDIA:Reaction_creator.csv|form]]
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** reaction added for biomass|reaction added for biomass
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* '''Follow the examples given in the form(s) to correctly share your suggestions'''
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** reaction added for biomass, from model l.plantarum|reaction added for biomass, from model l.plantarum
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* Send the filled form(s) to: CONTACT_MAIL
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** this was a reaction occurring in the perisplasm of e. coli|this was a reaction occurring in the perisplasm of e. coli
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Revision as of 18:51, 18 March 2018

EFAEV583GEM description

Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA 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
  • Based on expertise:
      • 221 reaction(s) added
  • Based on gap-filling:
    • Tool: meneco
      • 50 reaction(s) added

Venn.png

Collaborative curation

  • Suggest reactions to add or remove:
  • Suggest new reactions to create and add:
  • Follow the examples given in the form(s) to correctly share your suggestions
  • Send the filled form(s) to: CONTACT_MAIL
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