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fix-correct a gene name for one rxn #186

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May 3, 2019
Merged

fix-correct a gene name for one rxn #186

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2 changes: 1 addition & 1 deletion ModelFiles/dependencies.txt
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@@ -1,7 +1,7 @@
MATLAB 9.1.0.441655 (R2016b)
libSBML 5.17.0
RAVEN_toolbox 2.1.0
COBRA_toolbox 3.0.3
COBRA_toolbox 3.0.4
SBML_level 3
SBML_version 1
fbc_version 2
2 changes: 1 addition & 1 deletion ModelFiles/txt/yeastGEM.txt
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Expand Up @@ -3953,7 +3953,7 @@ r_4588 s_4200[e] <=> s_3778[c] YNL275W -1000.00 1000.00 0.00
r_4589 s_0796[e] + s_4201[e] <=> s_0794[c] + s_4019[c] YOL122C -1000.00 1000.00 0.00
r_4590 s_0796[e] + s_4202[e] <=> s_0794[c] + s_3801[c] YGR191W -1000.00 1000.00 0.00
r_4591 s_0796[e] + s_4203[e] <=> s_0794[c] + s_3822[c] ( YGL255W or YLR130C ) -1000.00 1000.00 0.00
r_4592 s_0796[e] + s_4204[e] <=> s_0794[c] + s_4013[c] ( GR191W or YOL130W ) -1000.00 1000.00 0.00
r_4592 s_0796[e] + s_4204[e] <=> s_0794[c] + s_4013[c] ( YGR191W or YOL130W ) -1000.00 1000.00 0.00
r_4593 s_4200[e] <=> -1000.00 1000.00 0.00
r_4594 s_4201[e] <=> -1000.00 1000.00 0.00
r_4595 s_4202[e] <=> -1000.00 1000.00 0.00
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5 changes: 2 additions & 3 deletions ModelFiles/xml/yeastGEM.xml
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Expand Up @@ -192749,7 +192749,7 @@
<speciesReference species="s_4193__91__c__93__" stoichiometry="2" constant="true"/>
</listOfProducts>
</reaction>
<reaction metaid="r_4587" sboTerm="SBO:0000655" id="r_4587" name="Ca(2+) transport " reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
<reaction metaid="r_4587" sboTerm="SBO:0000655" id="r_4587" name="Ca(2+) transport" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Confidence Level: 2</p>
Expand Down Expand Up @@ -192958,7 +192958,7 @@
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:or>
<fbc:geneProductRef fbc:geneProduct="G_GR191W"/>
<fbc:geneProductRef fbc:geneProduct="G_YGR191W"/>
<fbc:geneProductRef fbc:geneProduct="G_YOL130W"/>
</fbc:or>
</fbc:geneProductAssociation>
Expand Down Expand Up @@ -194309,7 +194309,6 @@
<fbc:geneProduct metaid="G_YNL275W" fbc:id="G_YNL275W" fbc:name="COBRAProtein1135" fbc:label="BOR1"/>
<fbc:geneProduct metaid="G_YGL255W" fbc:id="G_YGL255W" fbc:name="COBRAProtein1136" fbc:label="ZRT1"/>
<fbc:geneProduct metaid="G_YLR130C" fbc:id="G_YLR130C" fbc:name="COBRAProtein1137" fbc:label="ZRT2"/>
<fbc:geneProduct metaid="G_GR191W" fbc:id="G_GR191W" fbc:name="COBRAProtein1138" fbc:label="GR191W"/>
<fbc:geneProduct metaid="G_YOL130W" fbc:id="G_YOL130W" fbc:name="COBRAProtein1139" fbc:label="ALR1"/>
<fbc:geneProduct metaid="G_YNL065W" fbc:id="G_YNL065W" fbc:name="COBRAProtein1140" fbc:label="AQR1"/>
<fbc:geneProduct metaid="G_YKR093W" fbc:id="G_YKR093W" fbc:name="COBRAProtein1141" fbc:label="PTR2"/>
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5 changes: 1 addition & 4 deletions ModelFiles/yml/yeastGEM.yml
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Expand Up @@ -94018,7 +94018,7 @@
- s_4204: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: GR191W or YOL130W
- gene_reaction_rule: YGR191W or YOL130W
- annotation: !!omap
- metanetx.reaction: MNXR101553
- sbo: SBO:0000655
Expand Down Expand Up @@ -94118,9 +94118,6 @@
- annotation: !!omap
- sbo: SBO:0000627
- genes:
- !!omap
- id: GR191W
- name: GR191W
- !!omap
- id: Q0045
- name: COX1
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -10,13 +10,13 @@ This repository contains the current consensus genome-scale metabolic model of _

**GEM Category:** species; **Utilisation:** experimental data reconstruction, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** reconstruction, curated; **Model Source:** YeastMetabolicNetwork; **Omic Source:** genomics, metabolomics; **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** general metabolism; **Bioreactor**; **Strain:** S288C; **Condition:** aerobic, glucose-limited, defined media;

* Last update: 2018-12-06
* Last update: 2019-02-06

* Main Model Descriptors:

|Taxonomy | Template Model | Reactions | Metabolites| Genes |
|:-------:|:--------------:|:---------:|:----------:|:-----:|
|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3963|2691|1150|
|_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|3963|2691|1149|

This repository is administered by Benjamín J. Sánchez ([@BenjaSanchez](https://github.com/benjasanchez)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.

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