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Merged
BenjaSanchez merged 11 commits into from
Sep 17, 2018
Merged

Feat/extra figures #11

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1cba71a
fix: sumBioMass
Sep 6, 2018
53fea0e
fix: flexibilize flux data
Sep 6, 2018
9305484
feat: non-convergence error flag
Sep 6, 2018
9c9c3fa
refactor: plotOptions
Sep 7, 2018
a170f0a
chore: update figs
Sep 8, 2018
3ff6386
feat: exp chain distribution figure
Sep 10, 2018
6213b36
feat: colormap dependency
Sep 10, 2018
27fe384
style: colors in figures
Sep 10, 2018
6383a66
feat: full FVA figure
Sep 10, 2018
a05bd1b
feat: RS variability figure
Sep 10, 2018
cf2275e
chore: update pre-print link
Sep 17, 2018
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5 changes: 3 additions & 2 deletions README.rst
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@@ -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.

Expand All @@ -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
------------
Expand Down
5 changes: 3 additions & 2 deletions data/convertEjsingData.m
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@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% data = convertEjsingData(data,model,condense)
%
% Benjam�n J. S�nchez. Last update: 2018-04-10
% Benjamin J. Sanchez. Last update: 2018-09-09
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function data = convertEjsingData(data_old,model,condense)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -110,4 +111,4 @@

end

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11 changes: 7 additions & 4 deletions models/changeOtherComp.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% [model,GAMpol] = changeOtherComp(model,data)
%
% Benjam�n J. S�nchez. Last update: 2018-03-30
% Benjamin J. Sanchez. Last update: 2018-09-04
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [model,GAMpol] = changeOtherComp(model,data)
Expand Down Expand Up @@ -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

Expand All @@ -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; %F�rster 2003 (sup table 8)
GAMpol = P*37.7 + C*12.8 + R*26.0 + D*26.0; %Forster 2003 (sup table 8)

end

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12 changes: 8 additions & 4 deletions models/modelsFromData.m
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@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% [model_corrComp,model_SLIMEr,k,GAMpol] = modelsFromData(model,data,scaling)
%
% Benjam�n J. S�nchez. Last update: 2018-03-24
% Benjamin J. Sanchez. Last update: 2018-09-05
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [model_corrComp,model_SLIMEr,k,GAMpol] = modelsFromData(model,data,scaling)
Expand All @@ -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

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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7 changes: 5 additions & 2 deletions models/scaleAbundancesInModel.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% [model,k] = scaleAbundancesInModel(model,data,scaling)
%
% Benjam�n J. S�nchez. Last update: 2018-03-26
% Benjamin J. Sanchez. Last update: 2018-09-05
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [model,k] = scaleAbundancesInModel(model,data,scaling)
Expand All @@ -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);
Expand Down Expand Up @@ -64,4 +67,4 @@

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
6 changes: 3 additions & 3 deletions models/sumBioMass.m
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Expand Up @@ -8,7 +8,7 @@
% D -> DNA fraction [g/gDW]
% L -> Lipid fraction [g/gDW]
%
% Benjam�n J. S�nchez. Last update: 2018-03-30
% Benjamin J. Sanchez. Last update: 2018-09-04
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [X,P,C,R,D,L] = sumBioMass(model,comps)
Expand Down Expand Up @@ -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
Expand All @@ -66,4 +66,4 @@

end

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