Difference between revisions of "Main Page"
From metabolic_network
(Created page with "== sjapGEM description == == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == Model summary: summary Download '''AuReMe''' Input/Out...") |
|||
| (One intermediate revision by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | == | + | == GEM description == |
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] == | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] == | ||
Model summary: [[MEDIA:summary.txt|summary]] | Model summary: [[MEDIA:summary.txt|summary]] | ||
| Line 5: | Line 5: | ||
Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | Download '''AuReMe''' Input/Output [LINK OR MEDIA data] | ||
| − | The automatic reconstruction of '' | + | The automatic reconstruction of ''SJAPGEM'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 3344 reactions, 3242 metabolites, 5022 genes and 1388 pathways. This GeM was obtained based on the following sources: |
* Based on annotation data: | * Based on annotation data: | ||
** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ Pathway tools] | ||
| − | *** Creation of a metabolic network containing | + | *** Creation of a metabolic network containing 2560 reactions |
* Based on orthology data: | * Based on orthology data: | ||
** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph] | ||
| Line 15: | Line 15: | ||
*** From template ''ECTOCARPUS_SILICULOSUS'' creation of a metabolic network containing: 1498 reactions | *** From template ''ECTOCARPUS_SILICULOSUS'' creation of a metabolic network containing: 1498 reactions | ||
* Based on expertise: | * Based on expertise: | ||
| − | *** | + | *** 74 reaction(s) added |
* Based on gap-filling: | * Based on gap-filling: | ||
** Tool: [https://pypi.python.org/pypi/meneco meneco] | ** Tool: [https://pypi.python.org/pypi/meneco meneco] | ||
| − | *** | + | *** 90 reaction(s) added |
[[FILE:venn.png|frameless|border]] | [[FILE:venn.png|frameless|border]] | ||
| Line 28: | Line 28: | ||
** Download this [[MEDIA:Reaction_creator.csv|form]] | ** Download this [[MEDIA:Reaction_creator.csv|form]] | ||
* '''Follow the examples given in the form(s) to correctly share your suggestions''' | * '''Follow the examples given in the form(s) to correctly share your suggestions''' | ||
| − | * Send the filled form(s) to: | + | * Send the filled form(s) to: gabriel.markov@sb-roscoff.fr |
Latest revision as of 16:48, 10 January 2019
GEM description
Automatic reconstruction with AuReMe
Model summary: summary
Download AuReMe Input/Output [LINK OR MEDIA data]
The automatic reconstruction of SJAPGEM results to a Genome scale Model containing 3344 reactions, 3242 metabolites, 5022 genes and 1388 pathways. This GeM was obtained based on the following sources:
- Based on annotation data:
- Tool: Pathway tools
- Creation of a metabolic network containing 2560 reactions
- Tool: Pathway tools
- Based on orthology data:
- Tool: Pantograph
- From template NANNOCHLOROPSIS_SALINA creation of a metabolic network containing: 595 reactions
- From template ARABIDOPSIS_THALIANA creation of a metabolic network containing: 425 reactions
- From template ECTOCARPUS_SILICULOSUS creation of a metabolic network containing: 1498 reactions
- Tool: Pantograph
- Based on expertise:
- 74 reaction(s) added
- Based on gap-filling:
- Tool: meneco
- 90 reaction(s) added
- Tool: meneco
