Difference between revisions of "Category:Pathway"

From metabolic_network
Jump to: navigation, search
(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...")
Line 1: Line 1:
−
* navigation
+
== EFAEV583GEM description ==
−
** mainpage|mainpage-description
+
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
−
** randompage-url|randompage
+
Model summary: [[MEDIA:summary.txt|summary]]
−
** Special:ListFiles|Files
+
 
−
* Metabolic network components
+
Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
−
** Category:Reaction|Reaction
+
 
−
** Category:Gene|Gene
+
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:
−
** Category:Pathway|Pathway
+
* Based on orthology data:
−
** Category:Metabolite|Metabolite
+
** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
−
* Reconstruction categories
+
*** From template ''E_COLI_SSTR_K12_SUBSTR_MG1655'' creation of a metabolic network containing: 528 reactions
−
** gap-filling|gap-filling
+
*** From template ''L_PLANTARUM_WCFS1'' creation of a metabolic network containing: 385 reactions
−
** manual|manual
+
*** From template ''B_SUBTILIS_SUBSP_SUBTILIS_STR168'' creation of a metabolic network containing: 463 reactions
−
** orthology|orthology
+
* Based on expertise:
−
* Reconstruction tools
+
*** 221 reaction(s) added
−
** meneco|meneco
+
* Based on gap-filling:
−
** pantograph|pantograph
+
** Tool: [https://pypi.python.org/pypi/meneco meneco]
−
* Reconstruction sources
+
*** 50 reaction(s) added
−
** added for gapfilling|added for gapfilling
+
 
−
** added to manage seeds from boundary to extracellular compartment|added to manage seeds from boundary to extracellular compartment
+
[[FILE:venn.png|frameless|border]]
−
** added to manage seeds from extracellular to cytosol compartment|added to manage seeds from extracellular to cytosol compartment
+
 
−
** b_subtilis_subsp_subtilis_str168|b_subtilis_subsp_subtilis_str168
+
== Collaborative curation ==
−
** curation_from_orthology|curation_from_orthology
+
* Suggest reactions to add or remove:
−
** e_coli_sstr_k12_substr_mg1655|e_coli_sstr_k12_substr_mg1655
+
** Download this [[MEDIA:Add_delete_reaction.csv|form]]
−
** l_plantarum_wcfs1|l_plantarum_wcfs1
+
* Suggest new reactions to create and add:
−
** manual curation|manual curation
+
** Download this [[MEDIA:Reaction_creator.csv|form]]
−
** reaction added for biomass|reaction added for biomass
+
* '''Follow the examples given in the form(s) to correctly share your suggestions'''
−
** reaction added for biomass, from model l.plantarum|reaction added for biomass, from model l.plantarum
+
* Send the filled form(s) to: CONTACT_MAIL
−
** this was a reaction occurring in the perisplasm of e. coli|this was a reaction occurring in the perisplasm of e. coli
+

Revision as of 19:51, 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
Retrieved from "http://gem-aureme.irisa.fr/efaecV583/index.php?title=Category:Pathway&oldid=8456"