WIP

Author: edkerk

code/modelCuration/v9_1_0.m

@@ -190,6 +190,20 @@
 % Represent ACP with formula "RHS"
 model.metFormulas(getIndexes(model,'s_1845','mets')) = {'RHS'};
 
+% Set formula of ferr(i/o)cytochrome b3
+idx_mit = getIndexes(model,{'s_3826','s_3827'},'mets');
+idx_erm = getIndexes(model,{'s_4210','s_4209'},'mets');
+model.metFormulas(idx_erm) = model.metFormulas(idx_mit);
+model.metCharges(idx_erm) = model.metCharges(idx_mit);
+model.metMiriams(idx_erm) = model.metMiriams(idx_mit);
+model.metNames([idx_mit; idx_erm]) = regexprep(model.metNames([idx_mit; idx_erm]),'F','f');
+
+% Correct metFormula and metCharge
+idx = getIndexes(model,{'s_4265','s_4266'},'mets');
+model.metFormulas(idx) = {'CH2O3S'};
+model.metCharges(idx) = -1;
+
+
 % [~,metFormulae] = computeMetFormulae(model,'metMwRange','s_0338','fillMets','none')
 % model.metFormulas(getIndexes(model,'s_0329','mets')) = {'C17H28NO17P'};
 % model.metFormulas(getIndexes(model,'s_0330','mets')) = {'C33H58NO18P'};
@@ -216,6 +230,8 @@
 % r_0229
 %model = changeRxns(model,'r_0229','dethiobiotin[c] + polysulphur[c]  <=> biotin[c] + 2 H+[c]',2)
 %dethiobiotin[c] + hydrogen sulfide[c] + 2 S-adenosyl-L-methionine[c] + 2 H+[c] <=> biotin[c] + 2 L-methionine[c] + 2 5'-Deoxyadenosine
+
+
 %% ========================================================================
 % Condition-specific gene expression. These can be enabled with scripts
 % Glycine cleavage only active when glycine is used as nitrogen source
@@ -243,7 +259,7 @@
 % To align the degree of reduction of S. cerevisiae biomass to the
 % published value of 4.2 /Cmol (Lange and Heijnen, 2001, 10.1002/bit.10054)
 
-DR = 75; % 3mmol (g CDW)−1s
+DR = 3; % 3mmol (g CDW)−1s
 metIdx = getIndexes(model,{'s_1212','s_1207','s_0794'},'mets'); % NADPH[c], NADP[c], H+[c]
 bioIdx = getIndexes(model,'r_4041','rxns');
 

code/modelTests/anaerobic_flux_predictions.m

@@ -25,18 +25,19 @@
 
     %% Solve the LP problem
     res=solveLP(model,1);
-
-    index_model=findRxnIDs(model,text_flux(index_data_set,7));
+    rxns = text_flux(index_data_set,7);
+    rxns(cellfun(@isempty,rxns)) = [];
+    index_model=getIndexes(model,rxns,'rxns');
     exclude_data=(index_model==0);
     index_model(exclude_data)=[];
     index_data_set(exclude_data)=[];
 
-    scaled_sim=abs(-100.*res.x(index_model)./res.x(findRxnIDs(model,'r_1714')));
+    scaled_sim=abs(-100.*res.x(index_model)./res.x(getIndexes(model,'r_1714','rxns')));
 
     data_vals=abs(cell2mat(vals_flux(index_data_set,5)));
     merged_data=[merged_data data_vals'];
     merged_sim=[merged_sim scaled_sim'];
-    merged_names=[merged_names text_flux(index_data_set,7)'];
+    merged_names=[merged_names rxns'];
     plot(data_vals,scaled_sim,'^','MarkerFaceColor',colors(i,:),'MarkerEdgeColor',colors(i,:));
     hold on;
 

code/modelTests/anaerobiosis.m

@@ -20,10 +20,10 @@
 %% Set glucose uptake rate and solve pFBA
 modelAn = setParam(modelAn,'eq','r_1714',-23);
 res=solveLP(modelAn,1);
-
+FLUX = res.x;
 v_AStr = res.x(getIndexes(modelAn,'r_1115','rxns'))
 v_ATPase = res.x(getIndexes(modelAn,'r_0227','rxns'))
-
+v_glc = res.x(getIndexes(modelAn,'r_1714','rxns'))
 
 %% Pack flux results into table
 temp_model=modelAn;
@@ -42,6 +42,7 @@
 
 
 
+out
 
 
 

code/modelTests/growth.m

@@ -82,16 +82,15 @@
 %Simulate chemostats:
 mod_data = zeros(size(exp_data));
 solresult = zeros(length(model_origin.rxns),length(exp_data(:,1)));
+if mode1 == 2
+    model_origin = anaerobicModel(model_origin);
+end
 if strcmp(mode2,'N')
     model_origin = scaleBioMass(model_origin,'protein',0.289,'',false);
     model_origin = scaleBioMass(model_origin,'lipid',0.048,'',false);
     model_origin = scaleBioMass(model_origin,'RNA',0.077,'carbohydrate',false);
     model_origin = setParam(model_origin,'ub','r_0472',1000); %Glutamate synthase repressed in excess nitrogen
 end
-
-if mode1 == 2
-    model_origin = anaerobicModel(model_origin);
-end
 for i = 1:length(exp_data(:,1))
     model_test= model_origin;
     %Fix glucose uptake rate and maximize growth:

code/modelTests/plotAnaerobic.m

@@ -0,0 +1,30 @@
+function plotAnaerobic(modelAn)
+modelAn = setParam(modelAn,'eq','r_1714',-23);
+res=solveLP(modelAn,1);
+FLUX=res.x;
+
+%% Retrieve data for the main products
+v_glc=FLUX(getIndexes(modelAn,'r_1714','rxns'),:);
+v_eth=FLUX(getIndexes(modelAn,'r_1761','rxns'),:);
+v_CO2=FLUX(getIndexes(modelAn,'r_1672','rxns'),:);
+v_gly=FLUX(getIndexes(modelAn,'r_1808','rxns'),:);
+v_growth=FLUX(getIndexes(modelAn,'r_4041','rxns'),:);
+v_AStr = FLUX(getIndexes(modelAn,'r_1115','rxns'));
+v_ATPase = FLUX(getIndexes(modelAn,'r_0227','rxns'));
+%% Show relative accuracy of main extracellular products
+figure;
+%glycerol ethanol Co2
+%4.5 ± 0.4  31 ± 2  38 ± 10
+data=[4.5 31 38 0.36];
+sim=[v_gly v_eth v_CO2 v_growth];
+errorVal=[0.4 2 10 0.02];
+b1=bar(data./data,'FaceAlpha',0.5);hold on;b2=bar(sim./data,'FaceAlpha',0.5);
+hold on
+er = errorbar([1 2 3 4],data./data,errorVal./data,errorVal./data);    
+er.Color = [0 0 0];                            
+er.LineStyle = 'none';  
+legend({'data','simulation'});
+ylabel('Relative value');
+xticklabels({'Glycerol','Ethanol','CO2','Biomass'})
+hold off
+end