Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix-bug for growth #243

Merged
merged 1 commit into from
Aug 10, 2020
Merged

fix-bug for growth #243

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion ModelFiles/dependencies.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
MATLAB 9.7.0.1190202 (R2019b)
libSBML 5.17.0
RAVEN_toolbox 2.4.0
COBRA_toolbox commit 8204bb7
COBRA_toolbox commit 7a3f66f
SBML_level 3
SBML_version 1
fbc_version 2
4 changes: 2 additions & 2 deletions ModelFiles/txt/yeastGEM.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,7 @@ r_0237 s_0794[c] + s_1212[c] + s_1579[c] -> s_1207[c] + s_1569[c] YLR100W 0.
r_0238 s_0296[c] + s_0794[c] + s_1212[c] + s_1275[c] -> s_0803[c] + s_1207[c] + s_1576[c] YGR060W 0.00 1000.00 0.00
r_0239 s_0794[c] + s_1212[c] + s_1275[c] + s_1576[c] -> 2 s_0803[c] + s_1207[c] + s_1577[c] YGR060W 0.00 1000.00 0.00
r_0240 s_1212[c] + s_1275[c] + s_1577[c] -> s_0803[c] + s_1207[c] + s_1578[c] YGR060W 0.00 1000.00 0.00
r_0241 s_0122[c] + 5 s_0794[c] + 3 s_1275[c] + 6 s_3825[er] -> s_0297[c] + 4 s_0803[c] + 6 s_3824[er] YGR060W 0.00 1000.00 0.00
r_0241 s_0122[c] + 5 s_0794[c] + 3 s_1275[c] + 6 s_4209[erm] -> s_0297[c] + 4 s_0803[c] + 6 s_4210[erm] YGR060W 0.00 1000.00 0.00
r_0242 s_0657[c] + s_0794[c] + s_1212[c] + s_1275[c] -> s_0664[c] + 2 s_0803[c] + s_1207[c] YLR056W 0.00 1000.00 0.00
r_0243 s_0700[c] -> s_0657[c] YMR202W 0.00 1000.00 0.00
r_0244 s_0663[er] + s_0795[er] + s_1213[er] -> s_0667[er] + s_1208[er] YGL012W 0.00 1000.00 0.00
Expand Down Expand Up @@ -3561,7 +3561,7 @@ r_4192 s_1416[c] + s_3816[c] <=> s_0794[c] + s_1413[c] + s_3817[c] YHR109W -10
r_4193 s_3818[n] + s_3819[n] <=> s_0800[n] + s_3820[n] + s_3821[n] ( YHR119W or YDR440W or YJL168C ) -1000.00 1000.00 0.00
r_4194 s_3822[c] <=> s_3823[er] YIL023C -1000.00 1000.00 0.00
r_4195 s_4026[m] <=> s_4027[v] ( YMR243C or YOR316C ) -1000.00 1000.00 0.00
r_4196 s_1204[er] + 2 s_3824[er] <=> s_0795[er] + s_1199[er] + 2 s_3825[er] ( YIL043C or YML125C ) -1000.00 1000.00 0.00
r_4196 s_2818[erm] + 2 s_4210[erm] <=> s_2783[erm] + 2 s_4209[erm] YIL043C or YML125C -1000.00 1000.00 0.00
r_4197 s_1205[m] + 2 s_3826[m] <=> s_0799[m] + s_1200[m] + 2 s_3827[m] ( YIL043C or YKL150W or YML125C ) -1000.00 1000.00 0.00
r_4198 s_1207[c] + s_3828[c] <=> s_0794[c] + s_1212[c] + s_3829[c] YIR036C -1000.00 1000.00 0.00
r_4199 s_3830[er] + s_3831[er] <=> s_3832[er] + s_3833[er] YIR038C -1000.00 1000.00 0.00
Expand Down
89 changes: 32 additions & 57 deletions ModelFiles/xml/yeastGEM.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48227,56 +48227,6 @@
</rdf:RDF>
</annotation>
</species>
<species metaid="s_3824__91__er__93__" sboTerm="SBO:0000247" id="s_3824__91__er__93__" name="Ferricytochrome b5 [endoplasmic reticulum]" compartment="er" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="3" fbc:chemicalFormula="Fe">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>NOTES: added after new annotation (PR #142); based on kegg and Rhea</p>
</body>
</notes>
<annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_3824__91__er__93__">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/ficytb5"/>
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18097"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00996"/>
<rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM1083"/>
</rdf:Bag>
</bqbiol:is>
<bqbiol:hasProperty>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000247"/>
</rdf:Bag>
</bqbiol:hasProperty>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s_3825__91__er__93__" sboTerm="SBO:0000247" id="s_3825__91__er__93__" name="Ferrocytochrome b5 [endoplasmic reticulum]" compartment="er" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="2" fbc:chemicalFormula="Fe">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>NOTES: added after new annotation (PR #142); based on kegg and Rhea</p>
</body>
</notes>
<annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_3825__91__er__93__">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/focytb5"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00999"/>
</rdf:Bag>
</bqbiol:is>
<bqbiol:hasProperty>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000247"/>
</rdf:Bag>
</bqbiol:hasProperty>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s_3826__91__m__93__" sboTerm="SBO:0000247" id="s_3826__91__m__93__" name="Ferricytochrome b5 [mitochondrion]" compartment="m" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="3" fbc:chemicalFormula="Fe">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
Expand Down Expand Up @@ -57724,6 +57674,32 @@
</rdf:RDF>
</annotation>
</species>
<species metaid="s_4209__91__erm__93__" sboTerm="SBO:0000247" id="s_4209__91__erm__93__" name="Ferrocytochrome b5 [endoplasmic reticulum membrane]" compartment="erm" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_4209__91__erm__93__">
<bqbiol:hasProperty>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000247"/>
</rdf:Bag>
</bqbiol:hasProperty>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s_4210__91__erm__93__" sboTerm="SBO:0000247" id="s_4210__91__erm__93__" name="Ferricytochrome b5 [endoplasmic reticulum membrane]" compartment="erm" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
<annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_4210__91__erm__93__">
<bqbiol:hasProperty>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000247"/>
</rdf:Bag>
</bqbiol:hasProperty>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="FB1N1000" value="-1000" constant="true"/>
Expand Down Expand Up @@ -66862,12 +66838,12 @@
<speciesReference species="s_0122__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="s_0794__91__c__93__" stoichiometry="5" constant="true"/>
<speciesReference species="s_1275__91__c__93__" stoichiometry="3" constant="true"/>
<speciesReference species="s_3825__91__er__93__" stoichiometry="6" constant="true"/>
<speciesReference species="s_4209__91__erm__93__" stoichiometry="6" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s_0297__91__c__93__" stoichiometry="1" constant="true"/>
<speciesReference species="s_0803__91__c__93__" stoichiometry="4" constant="true"/>
<speciesReference species="s_3824__91__er__93__" stoichiometry="6" constant="true"/>
<speciesReference species="s_4210__91__erm__93__" stoichiometry="6" constant="true"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_YGR060W"/>
Expand Down Expand Up @@ -188394,13 +188370,12 @@
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="s_1204__91__er__93__" stoichiometry="1" constant="true"/>
<speciesReference species="s_3824__91__er__93__" stoichiometry="2" constant="true"/>
<speciesReference species="s_2818__91__erm__93__" stoichiometry="1" constant="true"/>
<speciesReference species="s_4210__91__erm__93__" stoichiometry="2" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s_0795__91__er__93__" stoichiometry="1" constant="true"/>
<speciesReference species="s_1199__91__er__93__" stoichiometry="1" constant="true"/>
<speciesReference species="s_3825__91__er__93__" stoichiometry="2" constant="true"/>
<speciesReference species="s_2783__91__erm__93__" stoichiometry="1" constant="true"/>
<speciesReference species="s_4209__91__erm__93__" stoichiometry="2" constant="true"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:or>
Expand Down
47 changes: 18 additions & 29 deletions ModelFiles/yml/yeastGEM.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25099,28 +25099,6 @@
- kegg.compound: C00038
- metanetx.chemical: MNXM149
- sbo: SBO:0000247
- !!omap
- id: s_3824
- name: Ferricytochrome b5
- compartment: er
- formula: Fe
- charge: 3
- annotation: !!omap
- bigg.metabolite: ficytb5
- chebi: CHEBI:18097
- kegg.compound: C00996
- metanetx.chemical: MNXM1083
- sbo: SBO:0000247
- !!omap
- id: s_3825
- name: Ferrocytochrome b5
- compartment: er
- formula: Fe
- charge: 2
- annotation: !!omap
- bigg.metabolite: focytb5
- kegg.compound: C00999
- sbo: SBO:0000247
- !!omap
- id: s_3826
- name: Ferricytochrome b5
Expand Down Expand Up @@ -29363,6 +29341,18 @@
- kegg.compound: C04039
- metanetx.chemical: MNXM734
- sbo: SBO:0000247
- !!omap
- id: s_4209
- name: Ferrocytochrome b5
- compartment: erm
- annotation: !!omap
- sbo: SBO:0000247
- !!omap
- id: s_4210
- name: Ferricytochrome b5
- compartment: erm
- annotation: !!omap
- sbo: SBO:0000247
- reactions:
- !!omap
- id: r_0001
Expand Down Expand Up @@ -34403,8 +34393,8 @@
- s_0794: -5
- s_0803: 4
- s_1275: -3
- s_3824: 6
- s_3825: -6
- s_4209: -6
- s_4210: 6
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: YGR060W
Expand Down Expand Up @@ -92044,11 +92034,10 @@
- id: r_4196
- name: NADH:ferricytochrome-b5 oxidoreductase
- metabolites: !!omap
- s_0795: 1
- s_1199: 1
- s_1204: -1
- s_3824: -2
- s_3825: 2
- s_2783: 1
- s_2818: -1
- s_4209: 2
- s_4210: -2
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: YIL043C or YML125C
Expand Down
2 changes: 1 addition & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ 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: 2020-07-15
* Last update: 2020-08-08

* Main Model Descriptors:

Expand Down