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fix-rxn/met: solves #252 and #254 #255

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Apr 10, 2021
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fix-rxn/met: solves #252 and #254 #255

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5e16d26
fix-rxn/met: solves #252 and #254
edkerk Apr 6, 2021
56874b0
fix: deal with special characters in README.md
edkerk Apr 7, 2021
1d5b325
fix: valid yaml
edkerk Apr 9, 2021
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16 changes: 16 additions & 0 deletions ComplementaryScripts/modelCuration/curationsOnV8_4_2.m
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@@ -0,0 +1,16 @@
%% Curations on version 8.4.2
% This is a list of various smaller curations to be performed on version
% 8.4.2 of yeast-GEM. Indicated is what Issue is solved.

% Load model
cd ..
model = loadYeastModel;

% Solves #252
model = changeGeneAssociation(model,'r_4590','YOL130W');

% Solves #254
model.metNames = regexprep(model.metNames,'^nicotinamide ribose','nicotinamide riboside');
% All annotations, formula and charge were correct.

saveYeastModel(model);
3 changes: 2 additions & 1 deletion ComplementaryScripts/saveYeastModel.m
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Expand Up @@ -92,7 +92,8 @@ function saveYeastModel(model,upDATE,allowNoGrowth)
num2str(length(model.mets)) '|' ...
num2str(length(model.genes)) '|' newline];
end
fwrite(fout,inline);
inline=unicode2native(inline,'UTF-8');
fwrite(fout,inline,'uint8');
end
end
fclose('all');
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6 changes: 3 additions & 3 deletions ModelFiles/dependencies.txt
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@@ -1,7 +1,7 @@
MATLAB 9.7.0.1190202 (R2019b)
MATLAB 9.9.0.1524771 (R2020b) Update 2
libSBML 5.17.0
RAVEN_toolbox 2.4.1
COBRA_toolbox commit 6c49aaf
RAVEN_toolbox commit 5061381
COBRA_toolbox commit 800dcfe
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 @@ -3948,7 +3948,7 @@ r_4586 s_3998[c] + s_4192[c] -> 2 s_4193[c] 0.00 1000.00 0.00
r_4587 s_0796[e] + s_4199[e] <=> s_0794[c] + s_3880[c] YOL122C -1000.00 1000.00 0.00
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_4590 s_0796[e] + s_4202[e] <=> s_0794[c] + s_3801[c] YOL130W -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] ( YGR191W or YOL130W ) -1000.00 1000.00 0.00
r_4593 s_4200[e] <=> -1000.00 1000.00 0.00
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4 changes: 2 additions & 2 deletions ModelFiles/xml/yeastGEM.xml
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Expand Up @@ -20570,7 +20570,7 @@
</rdf:RDF>
</annotation>
</species>
<species metaid="s_1218__91__c__93__" sboTerm="SBO:0000247" id="s_1218__91__c__93__" name="nicotinamide ribose [cytoplasm]" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C11H15N2O5">
<species metaid="s_1218__91__c__93__" sboTerm="SBO:0000247" id="s_1218__91__c__93__" name="nicotinamide riboside [cytoplasm]" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C11H15N2O5">
<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_1218__91__c__93__">
Expand Down Expand Up @@ -214436,7 +214436,7 @@
<speciesReference species="s_3801__91__c__93__" stoichiometry="1" constant="true"/>
</listOfProducts>
<fbc:geneProductAssociation>
<fbc:geneProductRef fbc:geneProduct="G_YGR191W"/>
<fbc:geneProductRef fbc:geneProduct="G_YOL130W"/>
</fbc:geneProductAssociation>
</reaction>
<reaction metaid="r_4591" sboTerm="SBO:0000655" id="r_4591" name="Zn(2+) transport" reversible="true" fast="false" fbc:lowerFluxBound="FB1N1000" fbc:upperFluxBound="FB5N1000">
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