Merge pull request #112 from SysBioChalmers/feat/SLIMErxns

Feat/SLIME rxns

ComplementaryScripts/otherChanges/addSLIMErxns.m

@@ -0,0 +1,69 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% addSLIMErxns
+%
+% Benjamín J. Sánchez
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%Start COBRA & load model:
+clear variables
+initCobraToolbox
+cd ..
+model = loadYeastModel;
+
+%Move to SLIMEr and add paths:
+cd ../../SLIMEr/models
+addpath('../simulations')
+addpath('../data')
+
+%Add SLIMErxns:
+data = readLahtveeData(1);
+[~,model_SLIMEr,~,~] = modelsFromData(model,data,'backbones');
+
+%Remove added paths:
+rmpath('../simulations')
+rmpath('../data')
+
+%Update backbone names:
+backbones = {'1-phosphatidyl-1D-myo-inositol'
+			 'sn-2-acyl-1-lysophosphatidylinositol'
+			 'phosphatidyl-L-serine'
+			 'phosphatidylcholine'
+			 'phosphatidylethanolamine'
+			 'phosphatidate'
+			 'diglyceride'
+			 'triglyceride'
+			 'phosphatidylglycerol'
+			 'cardiolipin'
+			 'ceramide'
+			 'inositol-P-ceramide'
+			 'inositol phosphomannosylinositol phosphoceramide'
+			 'mannosylinositol phosphorylceramide'
+			 'fatty acid'
+			 'ergosterol ester'
+			 'long-chain base'
+			 'long-chain base phosphate'};
+for i = 1:length(backbones)
+	metPos = startsWith(model_SLIMEr.metNames,[backbones{i} ' [']);
+    model_SLIMEr.metNames(metPos) = strrep(model_SLIMEr.metNames(metPos),[backbones{i} ' ['],[backbones{i} ' backbone [']);
+end
+
+%Reinsert previous GAM and correct O.F.:
+GAM    = 61.9779;
+bioRxn = strcmp(model_SLIMEr.rxnNames,'biomass pseudoreaction');
+ATPpos = strcmp(model_SLIMEr.metNames,'ATP [cytoplasm]');
+H2Opos = strcmp(model_SLIMEr.metNames,'H2O [cytoplasm]');
+ADPpos = strcmp(model_SLIMEr.metNames,'ADP [cytoplasm]');
+Hpos   = strcmp(model_SLIMEr.metNames,'H+ [cytoplasm]');
+Ppos   = strcmp(model_SLIMEr.metNames,'phosphate [cytoplasm]');
+model_SLIMEr.S(ATPpos,bioRxn) = -GAM;
+model_SLIMEr.S(H2Opos,bioRxn) = -GAM;
+model_SLIMEr.S(ADPpos,bioRxn) = +GAM;
+model_SLIMEr.S(Hpos,bioRxn)   = +GAM;
+model_SLIMEr.S(Ppos,bioRxn)   = +GAM;
+
+%Save model & return to origin:
+cd ../../yeast-GEM/complementaryScripts
+saveYeastModel(model_SLIMEr);
+cd otherChanges
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

ModelFiles/boundaryMets.txt

@@ -164,3 +164,5 @@ s_2826[e]	oleate [extracellular]
 s_1163[e]	myristate [extracellular]
 s_3715[e]	raffinose [extracellular]
 s_3716[e]	melibiose [extracellular]
+s_3746[c]	lipid - backbones [cytoplasm]
+s_3747[c]	lipid - tails [cytoplasm]