Initial commit.

Adding all files needed to plot the figures in the paper.

.gitignore

@@ -0,0 +1,19 @@
+*.asv
+*mex*
+*.h
+*.c
+~$*.xls*
+**/Results*
+Ignore/*
+Log/*
+*.out
+*.mat
+**/tmpfig/*
+*.pdf
+**/.vscode
+*.png
+*.zip
+costs.txt
+FinalExpandedModel.txt
+inhibitions.xlsx
+testedInteractions.xlsx

Data/MS data/GetPhosphoproteomeData.m

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+function [ data ] = GetPhosphoproteomeData()
+load('Humphrey_2013.mat', 'matchedData')
+
+usefulColumns=[1 3 4 5 8 10 11 50:52 33 20:22];
+
+LY=matchedData(:,25);
+MK=matchedData(:,30);
+
+LY.LYDirection = sign(matchedData.LYExpsInsulinStarvedMedianlog2);
+MK.MKDirection = sign(matchedData.MKExpsInsulinStarvedMedianlog2);
+
+LY{:,1}=2.^LY{:,1};
+MK{:,1}=2.^MK{:,1};
+
+matchedData=[matchedData(:,usefulColumns) LY MK];
+matchedData.LYMean=nanmean(LY{:,1},2);
+matchedData.LYSEM=nanSEM(LY{:,1},2);
+matchedData.MKMean=nanmean(MK{:,1},2);
+matchedData.MKSEM=nanSEM(MK{:,1},2);
+
+matchedData.meanValues=[ones(size(matchedData,1),1) matchedData.meanValues];
+matchedData.SEMValues=[zeros(size(matchedData,1),1) matchedData.SEMValues];
+
+matchedData = sortrows(matchedData,'IPI368PositioninProtein','ascend');
+matchedData = sortrows(matchedData,'Genenamesprimary','ascend');
+
+matchedData.SEMValues(matchedData.SEMValues<1e-10)=inf;
+
+data=matchedData;
+data(~any(~isnan(data.meanValues(:,2:end)),2),:)=[]; %Remove data with only nans
+
+end

Models/Pairwise/Multi_Combined.txt

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+********** MODEL NAME
+Multi_Combined
+
+********** MODEL NOTES
+
+********** MODEL STATES
+d/dt(C)=v_C__C_p
+d/dt(C_p)=-v_C__C_p
+
+C(0)=50
+C_p(0)=50
+
+********** MODEL PARAMETERS
+A_px1=1
+A_px2=1
+A_px3=1
+A_px4=1
+A_px5=1
+A_px6=1
+A_px7=1
+A_px8=1
+A_px9=1
+A_py1=1
+A_py2=1
+A_py3=1
+A_py4=1
+A_py5=1
+A_py6=1
+A_py7=1
+A_py8=1
+A_py9=1
+B_px1=1
+B_px2=1
+B_px3=1
+B_px4=1
+B_px5=1
+B_px6=1
+B_px7=1
+B_px8=1
+B_px9=1
+B_py1=1
+B_py2=1
+B_py3=1
+B_py4=1
+B_py5=1
+B_py6=1
+B_py7=1
+B_py8=1
+B_py9=1
+
+useInterp=1
+
+k_C_C_p=1
+k_C_C_p_1=1
+
+********** MODEL VARIABLES
+A_p=(1-useInterp)+useInterp*interpcsIQM([A_px1, A_px2, A_px3, A_px4, A_px5, A_px6, A_px7, A_px8, A_px9], [A_py1, A_py2, A_py3, A_py4, A_py5, A_py6, A_py7, A_py8, A_py9], time)
+B_p=(1-useInterp)+useInterp*interpcsIQM([B_px1, B_px2, B_px3, B_px4, B_px5, B_px6, B_px7, B_px8, B_px9], [B_py1, B_py2, B_py3, B_py4, B_py5, B_py6, B_py7, B_py8, B_py9], time)
+
+********** MODEL REACTIONS
+v_C__C_p=-C*A_p*k_C_C_p + C_p*B_p*k_C_C_p_1
+
+********** MODEL FUNCTIONS
+
+********** MODEL EVENTS
+
+********** MODEL MATLAB FUNCTIONS
+

Models/Pairwise/Multi_Dephos.txt

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+********** MODEL NAME
+Multi_Dephos
+
+********** MODEL NOTES
+
+********** MODEL STATES
+d/dt(C)=v_C__C_p
+d/dt(C_p)=-v_C__C_p
+
+C(0)=50
+C_p(0)=50
+
+********** MODEL PARAMETERS
+A_px1=1
+A_px2=1
+A_px3=1
+A_px4=1
+A_px5=1
+A_px6=1
+A_px7=1
+A_px8=1
+A_px9=1
+A_py1=1
+A_py2=1
+A_py3=1
+A_py4=1
+A_py5=1
+A_py6=1
+A_py7=1
+A_py8=1
+A_py9=1
+B_px1=1
+B_px2=1
+B_px3=1
+B_px4=1
+B_px5=1
+B_px6=1
+B_px7=1
+B_px8=1
+B_px9=1
+B_py1=1
+B_py2=1
+B_py3=1
+B_py4=1
+B_py5=1
+B_py6=1
+B_py7=1
+B_py8=1
+B_py9=1
+
+useInterp=1
+
+k_C_C_p_f=1
+k_C_C_p_b=1
+k_C_C_p=1
+
+********** MODEL VARIABLES
+A_p=(1-useInterp)+useInterp*interpcsIQM([A_px1, A_px2, A_px3, A_px4, A_px5, A_px6, A_px7, A_px8, A_px9], [A_py1, A_py2, A_py3, A_py4, A_py5, A_py6, A_py7, A_py8, A_py9], time)
+B_p=(1-useInterp)+useInterp*interpcsIQM([B_px1, B_px2, B_px3, B_px4, B_px5, B_px6, B_px7, B_px8, B_px9], [B_py1, B_py2, B_py3, B_py4, B_py5, B_py6, B_py7, B_py8, B_py9], time)
+
+********** MODEL REACTIONS
+v_C__C_p=-C*k_C_C_p_f  +  C_p*A_p*k_C_C_p_b + C_p*B_p*k_C_C_p
+
+********** MODEL FUNCTIONS
+
+********** MODEL EVENTS
+
+********** MODEL MATLAB FUNCTIONS
+

Models/Pairwise/Multi_Phos.txt

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+********** MODEL NAME
+Multi_Phos
+
+********** MODEL NOTES
+
+********** MODEL STATES
+d/dt(C)=v_C__C_p
+d/dt(C_p)=-v_C__C_p
+
+C(0)=50
+C_p(0)=50
+
+********** MODEL PARAMETERS
+A_px1=1
+A_px2=1
+A_px3=1
+A_px4=1
+A_px5=1
+A_px6=1
+A_px7=1
+A_px8=1
+A_px9=1
+A_py1=1
+A_py2=1
+A_py3=1
+A_py4=1
+A_py5=1
+A_py6=1
+A_py7=1
+A_py8=1
+A_py9=1
+B_px1=1
+B_px2=1
+B_px3=1
+B_px4=1
+B_px5=1
+B_px6=1
+B_px7=1
+B_px8=1
+B_px9=1
+B_py1=1
+B_py2=1
+B_py3=1
+B_py4=1
+B_py5=1
+B_py6=1
+B_py7=1
+B_py8=1
+B_py9=1
+
+useInterp=1
+
+k_C_C_p_f=1
+k_C_C_p_b=1
+k_C_C_p=1
+
+********** MODEL VARIABLES
+A_p=(1-useInterp)+useInterp*interpcsIQM([A_px1, A_px2, A_px3, A_px4, A_px5, A_px6, A_px7, A_px8, A_px9], [A_py1, A_py2, A_py3, A_py4, A_py5, A_py6, A_py7, A_py8, A_py9], time)
+B_p=(1-useInterp)+useInterp*interpcsIQM([B_px1, B_px2, B_px3, B_px4, B_px5, B_px6, B_px7, B_px8, B_px9], [B_py1, B_py2, B_py3, B_py4, B_py5, B_py6, B_py7, B_py8, B_py9], time)
+
+********** MODEL REACTIONS
+v_C__C_p=-C*A_p*k_C_C_p_f  +  C_p*k_C_C_p_b + -C*B_p*k_C_C_p
+
+********** MODEL FUNCTIONS
+
+********** MODEL EVENTS
+
+********** MODEL MATLAB FUNCTIONS
+

Models/Pairwise/dephos_model.txt

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+********** MODEL NAME
+dephos_model
+
+********** MODEL NOTES
+model
+
+********** MODEL STATES
+d/dt(B)=-v1
+d/dt(Bp)=v1
+
+B(0)=50
+Bp(0)=50
+
+********** MODEL PARAMETERS
+x1=1
+x2=1
+x3=1
+x4=1
+x5=1
+x6=1
+x7=1
+x8=1
+x9=1
+
+y1=1
+y2=1
+y3=1
+y4=1
+y5=1
+y6=1
+y7=1
+y8=1
+y9=1
+
+useInterp=1
+
+kp=1
+kd=1
+********** MODEL VARIABLES
+va=(1-useInterp)+useInterp*interpcsIQM([x1, x2, x3, x4, x5, x6, x7, x8, x9],[y1, y2, y3, y4, y5, y6, y7, y8, y9], time)
+
+********** MODEL REACTIONS
+v1=kp*B-va*kd*Bp
+
+********** MODEL FUNCTIONS
+
+********** MODEL EVENTS
+
+
+********** MODEL MATLAB FUNCTIONS
+

Models/Pairwise/mm_model.txt

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+********** MODEL NAME
+mm_model
+
+********** MODEL NOTES
+model
+
+********** MODEL STATES
+d/dt(B)=-v1
+d/dt(Bp)=v1
+
+B(0)=50
+Bp(0)=50
+
+********** MODEL PARAMETERS
+x1=1
+x2=1
+x3=1
+x4=1
+x5=1
+x6=1
+x7=1
+x8=1
+x9=1
+
+y1=1
+y2=1
+y3=1
+y4=1
+y5=1
+y6=1
+y7=1
+y8=1
+y9=1
+
+useInterp=1
+
+kp=1
+kd=1
+km=1
+********** MODEL VARIABLES
+va=(1-useInterp)+useInterp*interpcsIQM([x1, x2, x3, x4, x5, x6, x7, x8, x9],[y1, y2, y3, y4, y5, y6, y7, y8, y9], time)
+
+********** MODEL REACTIONS
+v1=va/(km+va)*kp*B-kd*Bp
+
+********** MODEL FUNCTIONS
+
+********** MODEL EVENTS
+
+
+********** MODEL MATLAB FUNCTIONS
+