fix: growth predictions under anaerobic conditions

code/modelTests/growth.m

@@ -53,8 +53,8 @@
 x=0:0.001:lim;
 y = x;
 plot(x,y,'--','MarkerSize',6,'Color',[64,64,64]/256)
-xlabel('Experimental growth rate [1/h]','FontSize',14,'FontName','Helvetica')
-ylabel('In silico growth rate [1/h]','FontSize',14,'FontName','Helvetica')
+xlabel('In silico growth rate [1/h]','FontSize',14,'FontName','Helvetica')
+ylabel('Experimental growth rate [1/h]','FontSize',14,'FontName','Helvetica')
 legend(b,'N-limited aerobic','C-limited aerobic','C-limited anaerobic','N-limited anaerobic','Location','northwest')
 
 % meanerror = sqrt(sum(([exp_data1(:,4);exp_data2(:,4);exp_data3(:,4);exp_data4(:,4)]-[mod_data1(:,4);mod_data2(:,4);mod_data3(:,4);mod_data4(:,4)]).^2)/32)/sqrt(32);

code/otherChanges/anaerobicModel.m

@@ -10,11 +10,9 @@
 
 %1st change: Refit GAM and NGAM to exp. data, change biomass composition
 GAM   = 30.49;  %Data from Nissen et al. 1997
-P     = 0.461;  %Data from Nissen et al. 1997
 NGAM  = 0;      %Refit done in Jouthen et al. 2012
 
 model = changeGAM(model,GAM,NGAM);
-model = scaleBioMass(model,'protein',P,'carbohydrate',false);
 
 %2nd change: Removes the requirement of heme a, NAD(PH), coenzyme A in the biomass equation
 %            (not used under anaerobic conditions)

code/otherChanges/scaleBioMass.m

@@ -1,19 +1,24 @@
 function model = scaleBioMass(model,component,new_value,balance_out,dispOutput)
-  % scaleBioMass
-  %   Scales the biomass composition
-  %
-  %   model          (struct) metabolic model in COBRA format
-  %   component      (str) name of the component to rescale (e.g. "protein")
-  %   new_value      (float) new total fraction for said component
-  %   balance_out    (str, opt) if chosen, the name of another component with which
-  %                  the model will be balanced out so that the total mass remains = 1 g/gDW
-  %                  provide empty string '' if this should not be done
-  %   dispOutput     (bool, opt) if output from sumBioMass should be displayed (default = true)
-  %
-  %   model          (struct) modified model
-  %
-  %   Usage: model = scaleBioMass(model,component,new_value,balance_out,dispOutput)
-  %
+% scaleBioMass
+%   Scales the biomass composition
+%
+% Input:
+%   model           (struct) yeast-GEM model
+%   component       (string) biomass component to change (options are:
+%                   'carbohydrate', 'protein', 'lipid', 'RNA', 'DNA',
+%                   'ion', 'cofactor')
+%   new_value       (num) new total fraction for the specified biomass
+%                   component
+%   balance_out     (string, optional) biomass component that will be used
+%                   to balance out the biomass composition, so that the
+%                   total mass adds up to 1 g/gDCW. This is highly
+%                   recommended (default = empty, no scaling takes place)
+%   dispOutput      (bool, optional) displayed outoupt (default = true)
+%
+% Output:
+%   model          (struct) modified yeast-GEM model
+%
+% Usage: model = scaleBioMass(model,component,new_value,balance_out,dispOutput)
 
 if nargin < 5
     dispOutput = true;
@@ -30,13 +35,13 @@
 old_value   = eval(content_Cap{pos});
 f           = new_value / old_value;
 model       = rescalePseudoReaction(model,component,f);
+X           = sumBioMass(model,false);
 
 %Balance out (if desired):
 if ~isempty(balance_out)
     pos           = strcmp(content_all,balance_out);
     balance_value = eval(content_Cap{pos});
-    f             = (balance_value - (new_value - old_value)) / balance_value;
+    f             = (balance_value + (1-X)) / balance_value;
     model         = rescalePseudoReaction(model,balance_out,f);
 end
-
 end

data/testResults/growth.md

@@ -1,4 +1,4 @@
 ## R2 of growth rate prediction
-0.8798
+0.8369
 
 ![Growth curve](growth.png)