Merge pull request #11 from SysBioChalmers/feat/extraFigures

Feat/extra figures
SysBioChalmers · Sep 17, 2018 · 30c3edd · 30c3edd
2 parents 47d6459 + cf2275e
commit 30c3edd
Show file tree

Hide file tree

Showing 28 changed files with 65,337 additions and 15,236 deletions.
diff --git a/README.rst b/README.rst
@@ -1,9 +1,9 @@
 .. image:: SLIMEr.png
    :align: center
 
-Collection of scripts for adding SLIME (Split Lipids Into Measurable Entities) reactions into the genome-scale model of yeast. For more info, refer to the current pre-print: `SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework <https://www.biorxiv.org/content/early/2018/05/21/324863>`__.
+Collection of scripts for adding SLIME (Split Lipids Into Measurable Entities) reactions into the genome-scale model of yeast. For more info, refer to the current pre-print: `SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework <https://www.biorxiv.org/content/early/2018/09/14/324863>`__.
 
-Last update: 2018-05-30
+Last update: 2018-09-14
 
 This repository is administered by Benjamin J. Sanchez (`@BenjaSanchez <https://github.com/benjasanchez>`__), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
 
@@ -22,6 +22,7 @@ Dependencies - Recommended Software:
 
 -  libSBML MATLAB API (version `5.16.0 <https://sourceforge.net/projects/sbml/files/libsbml/5.16.0/stable/MATLAB%20interface/>`__ is recommended).
 -  Gurobi Optimizer for MATLAB (version `7.5.2 <http://www.gurobi.com/registration/download-reg>`__ is recommended).
+-  An `implementation for Matlab <https://github.com/BenjaSanchez/cmaputil/tree/master/cmaputil_matlab>`__ of the `cividis colormap <https://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0199239>`__.
 
 Contributors
 ------------

diff --git a/data/convertEjsingData.m b/data/convertEjsingData.m
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % data = convertEjsingData(data,model,condense)
 %
-% Benjamín J. Sánchez. Last update: 2018-04-10
+% Benjamin J. Sanchez. Last update: 2018-09-09
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function data = convertEjsingData(data_old,model,condense)
@@ -50,6 +50,7 @@
 else
     %Only change units to g/gDW:
     data = changeUnits(data_old,MWs);
+    data.molarAbundance = data_old.abundance;
 end
 
 %Add missing data: composition and fluxes
@@ -110,4 +111,4 @@
 
 end
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/models/changeOtherComp.m b/models/changeOtherComp.m
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % [model,GAMpol] = changeOtherComp(model,data)
 %
-% Benjamín J. Sánchez. Last update: 2018-03-30
+% Benjamin J. Sanchez. Last update: 2018-09-04
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [model,GAMpol] = changeOtherComp(model,data)
@@ -71,12 +71,15 @@
         compPos  = strcmp(comps(:,1),otherData.metIDs{i});
         if strcmp(comps{compPos,3},'C')
             rxnPos = strcmp(model.rxnNames,'carbohydrate pseudoreaction');
+            MW     = comps{compPos,2}-18;
         elseif strcmp(comps{compPos,3},'D')
             rxnPos = strcmp(model.rxnNames,'DNA pseudoreaction');
+            MW     = comps{compPos,2}-18;
         elseif strcmp(comps{compPos,3},'N')
             rxnPos = strcmp(model.rxnNames,'biomass pseudoreaction');
+            MW     = comps{compPos,2};
         end
-        model.S(modelPos,rxnPos) = -otherData.abundance(i)/comps{compPos,2}*1000;
+        model.S(modelPos,rxnPos) = -otherData.abundance(i)/MW*1000;
     end
 end
 
@@ -97,8 +100,8 @@
 
 %Estimate maintenance belonging to polymerization:
 [~,P,C,R,D,~] = sumBioMass(model,comps);
-GAMpol        = P*37.7 + C*12.8 + R*26.0 + D*26.0;    %Förster 2003 (sup table 8)
+GAMpol        = P*37.7 + C*12.8 + R*26.0 + D*26.0;    %Forster 2003 (sup table 8)
 
 end
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/models/modelsFromData.m b/models/modelsFromData.m
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % [model_corrComp,model_SLIMEr,k,GAMpol] = modelsFromData(model,data,scaling)
 %
-% Benjamín J. Sánchez. Last update: 2018-03-24
+% Benjamin J. Sanchez. Last update: 2018-09-05
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [model_corrComp,model_SLIMEr,k,GAMpol] = modelsFromData(model,data,scaling)
@@ -12,14 +12,18 @@
 %Model with both lipid and chain length constrained to data:
 model_SLIMEr = SLIMEr(model,data,true);
 
-%Make abundances be consistent:
+%Correct the biomass composition with data:
+[model_corrComp,~] = changeOtherComp(model_corrComp,data);
+[model_SLIMEr,~]   = changeOtherComp(model_SLIMEr,data);
+
+%Make abundances of backbones & chains be consistent:
 [model_SLIMEr,k] = scaleAbundancesInModel(model_SLIMEr,data,scaling);
 model_corrComp   = adjustModel(model_corrComp,k,false,scaling);
 
-%Correct the rest of the composition to be consistent:
+%Correct again the biomass composition, to fix the new lipid content:
 [model_corrComp,~]    = changeOtherComp(model_corrComp,data);
 [model_SLIMEr,GAMpol] = changeOtherComp(model_SLIMEr,data);
 
 end
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/models/scaleAbundancesInModel.m b/models/scaleAbundancesInModel.m
@@ -1,7 +1,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % [model,k] = scaleAbundancesInModel(model,data,scaling)
 %
-% Benjamín J. Sánchez. Last update: 2018-03-26
+% Benjamin J. Sanchez. Last update: 2018-09-05
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [model,k] = scaleAbundancesInModel(model,data,scaling)
@@ -14,6 +14,9 @@
 krange(1) = fminsearch(@(k) +minScaling(k,model,data,scaling,kOpt),kOpt);
 krange(2) = fminsearch(@(k) -minScaling(k,model,data,scaling,kOpt),kOpt);
 disp(['Optimality range: k = [ ' num2str(krange(1)) ' , ' num2str(krange(2)) ' ]'])
+if(krange(1) == krange(2))
+    error('Could not find an optimality range!')
+end
 
 %Scale with the average of the range:
 k     = mean(krange);
@@ -64,4 +67,4 @@
 
 end
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/models/sumBioMass.m b/models/sumBioMass.m
@@ -8,7 +8,7 @@
 % D -> DNA fraction [g/gDW]
 % L -> Lipid fraction [g/gDW]
 %
-% Benjamín J. Sánchez. Last update: 2018-03-30
+% Benjamin J. Sanchez. Last update: 2018-09-04
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 function [X,P,C,R,D,L] = sumBioMass(model,comps)
@@ -57,7 +57,7 @@
     for i = 1:length(model.mets)
         pos = strcmp(comps(:,1),model.mets{i});
         if sum(pos) == 1
-            abundance = -model.S(i,fractionPos)*comps{pos,2}/1000;
+            abundance = -model.S(i,fractionPos)*(comps{pos,2}-18)/1000;
             F         = F + abundance;
         end
     end
@@ -66,4 +66,4 @@
 
 end
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%