diff --git a/PlotSpecificFigures.m b/PlotSpecificFigures.m
index 60e82924fe6e6b74529f9e9773c02496a05d243c..bcaf7bf7856f0fd4fa865842f0e147b24abc7813 100644
--- a/PlotSpecificFigures.m
+++ b/PlotSpecificFigures.m
@@ -28,12 +28,13 @@ try
disp('3. Effects of removing insulin actions (Fig. 5)')
disp('4. All figure after diabetes was introduced (Fig. 6, 7, S3, S4)')
disp('5. Best agreement when insulin action 3 was removed (Fig. S2)')
+ disp('6. Figures related to using the alternative epi data set (Doc. SX)')
disp('Note that figures numbered 5X corresponds to supplementary figures SX.')
- choice = input('\nChoice (1, 2, 3, 4 or 5): ');
+ choice = input('\nChoice (1, 2, 3, 4, 5 or 6): ');
- if ~ismember(choice, [1,3,5])
+ if ~ismember(choice, [1,3,5, 6])
fprintf('\n\nWhat resolution do you want?\n')
- disp('High resolution (as in the papers) or low resolution (faster)?')
+ disp('High resolution (as in the paper) or low resolution (faster)?')
disp('1. High resolution')
disp('2. Low resolution')
choice2 = input('\nChoice (1 or 2): ');
@@ -41,11 +42,11 @@ try
choice2 = 1;
end
fprintf('\n\n')
- if ~ismember(choice,[1 2 3 4 5]) && ~ismember(choice2,[1 2])
+ if ~ismember(choice,[1 2 3 4 5 6]) && ~ismember(choice2,[1 2])
error('Invalid choice of plots. Invalid choice of resolution')
- elseif ~ismember(choice,[1 2 3 4 5]) && ismember(choice2,[1 2])
+ elseif ~ismember(choice,[1 2 3 4 5 6]) && ismember(choice2,[1 2])
error('Invalid choice of plots. Valid choice of resolution')
- elseif ismember(choice,[1 2 3 4 5]) && ~ismember(choice2,[1 2])
+ elseif ismember(choice,[1 2 3 4 5 6]) && ~ismember(choice2,[1 2])
error('Valid choice of plots. Invalid choice of resolution')
elseif choice2==1
res=0.01;
@@ -66,6 +67,10 @@ try
PlotUncertainty(1, res)
elseif choice == 5
PlotUncertainty(0,res, 'lipolysis_noIns3')
+ elseif choice == 6
+ PlotPL('lipolysis', 0)
+ PlotUncertainty(0,res, 'lipolysis', 0)
+ PlotInsulinActions(0)
else
disp('Invalid choice if plots')
end
diff --git a/PlotSupplementaryAlternativeData.m b/PlotSupplementaryAlternativeData.m
new file mode 100644
index 0000000000000000000000000000000000000000..9d60520f50cbf6c024e919d327203c21cc865bed
--- /dev/null
+++ b/PlotSupplementaryAlternativeData.m
@@ -0,0 +1,27 @@
+if ~(exist('./Model equations.txt','file') && exist('./Scripts and data','dir'))
+ cdChoice=input('Warning! You are likely running the file from the wrong directory.\nDo you want to attempt to switch to the correct directory automatically?\n 1. yes\n 2. no\nChoice (1 or 2): ','s');
+ if cdChoice == 1
+ cd(fileparts(mfilename('fullpath')))
+ elseif cdChoice == 2
+ disp('Warning! The script will most likely not run from this directory.')
+ disp('If you encounter errors, please change the directory to the folder with the files.' )
+ else
+ disp('Invalid choice')
+ end
+end
+assert(exist('./Model equations.txt','file') && exist('./Scripts and data','dir'),'Error! Likely running from the wrong directory.')
+currentDir = pwd;
+
+try
+ run('./Scripts and data/Setup.m')
+ res = 0.01;
+ cd('Scripts and data')
+ PlotPL('lipolysis', 0)
+ PlotUncertainty(0,res, 'lipolysis', 0)
+ PlotInsulinActions(0)
+ cd(currentDir)
+catch err
+ disp('Something went wrong.')
+ cd(currentDir)
+ rethrow(err)
+end
\ No newline at end of file
diff --git a/Scripts and data/CostInVivo.m b/Scripts and data/CostInVivo.m
index 91c5bd2111cdff20b2bb2900dc8de5f7e63acc84..115bbbed5728ddd27d44f658cb66a620c78cb523 100644
--- a/Scripts and data/CostInVivo.m
+++ b/Scripts and data/CostInVivo.m
@@ -1,4 +1,4 @@
-function [cost, responses] = CostInVivo(params, model, data, tol)
+function [cost, responses] = CostInVivo(params, model, data, tol, useFig2EpiData)
if nargin<4, tol = 0; end
try
ind = ismember(data.Fig1.Time(1):data.Fig1.Time(30), data.Fig1.Time);
@@ -11,18 +11,32 @@ try
SEM=data.Fig1.SEM;
costFig1 = sum((yh-y).^2 ./SEM.^2);
- %% Fig2
- yh=[responses.Gly.Fig2Epi(ind); responses.Gly.Fig2Iso(ind)];
- y=[data.Fig2Epi.Mean; data.Fig2Iso.Mean];
- SEM=[data.Fig2Epi.SEM; data.Fig2Iso.SEM];
- costFig2 = sum((yh-y).^2 ./SEM.^2);
-
- %% Fig3
- yh=responses.Gly.Fig3EpiPhe(ind);
- y=data.Fig3EpiPhe.Mean;
- SEM=data.Fig3EpiPhe.SEM;
- costFig3 = sum((yh-y).^2 ./SEM.^2);
-
+ if useFig2EpiData
+ %% Fig2
+ yh=[responses.Gly.Fig2Epi(ind); responses.Gly.Fig2Iso(ind)];
+ y=[data.Fig2Epi.Mean; data.Fig2Iso.Mean];
+ SEM=[data.Fig2Epi.SEM; data.Fig2Iso.SEM];
+ costFig2 = sum((yh-y).^2 ./SEM.^2);
+
+ %% Fig3
+ yh=responses.Gly.Fig3EpiPhe(ind);
+ y=data.Fig3EpiPhe.Mean;
+ SEM=data.Fig3EpiPhe.SEM;
+ costFig3 = sum((yh-y).^2 ./SEM.^2);
+ else
+ %% Fig2
+ yh=responses.Gly.Fig2Iso(ind);
+ y=data.Fig2Iso.Mean;
+ SEM=data.Fig2Iso.SEM;
+ costFig2 = sum((yh-y).^2 ./SEM.^2);
+
+ %% Fig3
+ yh=[responses.Gly.Fig3Epi(ind); responses.Gly.Fig3EpiPhe(ind)];
+ y=[data.Fig3Epi.Mean; data.Fig3EpiPhe.Mean];
+ SEM=[data.Fig3Epi.SEM; data.Fig3EpiPhe.SEM];
+ costFig3 = sum((yh-y).^2 ./SEM.^2);
+ end
+
%% Total cost
cost=costFig1+costFig2+costFig3+steady;
diff --git a/Scripts and data/IQM Tools/IQMlite/tools/interpolation/interpcseIQM.mexw64 b/Scripts and data/IQM Tools/IQMlite/tools/interpolation/interpcseIQM.mexw64
deleted file mode 100644
index 67d9583c87e1a775ef861e5483d9fd338a335340..0000000000000000000000000000000000000000
Binary files a/Scripts and data/IQM Tools/IQMlite/tools/interpolation/interpcseIQM.mexw64 and /dev/null differ
diff --git a/Scripts and data/IQM Tools/IQMlite/tools/interpolation/interpcseSlopeIQM.mexw64 b/Scripts and data/IQM Tools/IQMlite/tools/interpolation/interpcseSlopeIQM.mexw64
deleted file mode 100644
index 91ea043cd6166987cf88d079d3dccdcb84b7010e..0000000000000000000000000000000000000000
Binary files a/Scripts and data/IQM Tools/IQMlite/tools/interpolation/interpcseSlopeIQM.mexw64 and /dev/null differ
diff --git a/Scripts and data/IQM Tools/IQMlite/tools/optimization/auxiliary/isres/isrsort.mexw64 b/Scripts and data/IQM Tools/IQMlite/tools/optimization/auxiliary/isres/isrsort.mexw64
deleted file mode 100644
index 13d77a2230386a32e3a0fb62af091c04e0229a3b..0000000000000000000000000000000000000000
Binary files a/Scripts and data/IQM Tools/IQMlite/tools/optimization/auxiliary/isres/isrsort.mexw64 and /dev/null differ
diff --git a/Scripts and data/IQM Tools/IQMpro/tools/01-MEXmodels/CVODEMEX/lib/CVODEmex25.lib b/Scripts and data/IQM Tools/IQMpro/tools/01-MEXmodels/CVODEMEX/lib/CVODEmex25.lib
deleted file mode 100644
index 3abfe488026813e0613b92ca9393d7589192c5d7..0000000000000000000000000000000000000000
Binary files a/Scripts and data/IQM Tools/IQMpro/tools/01-MEXmodels/CVODEMEX/lib/CVODEmex25.lib and /dev/null differ
diff --git a/Scripts and data/Init.m b/Scripts and data/Init.m
index 9dcf2b70024f709e812905a6f5e2e3cbd3735a10..0a9bf044d18f124bc217cc16ccca3932aaa395c5 100644
--- a/Scripts and data/Init.m
+++ b/Scripts and data/Init.m
@@ -90,7 +90,7 @@ lb=repmat(log(1e-6), 1, expInd); % set lower bound for all "InVitro" parameters
ub=repmat(log(1e6), 1, expInd); % set upper bound for all "InVitro" paramters
lb=[lb 0.6 8 0 0 0 -5 log(0.5) -5 0.5 0.5 0.5];
-ub=[ub 1 12 8 20 20 3 log(1.1) 3 2 2 2];
+ub=[ub 1 12 20 20 20 3 log(1.1) 3 2 2 2];
if contains(modelName, '_noIns1')
lb([28 31])=[];
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC501] lipolysis-opt(1.201), 211011-135041-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC501] lipolysis-opt(1.201), 211011-135041-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..91639790440a4a2c36a42c83aacf961372df4dd9
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC501] lipolysis-opt(1.201), 211011-135041-NaN.mat differ
diff --git a/Scripts and data/Parameter sets/PL/[max, EC502] lipolysis-opt(1.557), 210611-085808-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC502] lipolysis-opt(1.557), 211011-135041-NaN.mat
similarity index 71%
rename from Scripts and data/Parameter sets/PL/[max, EC502] lipolysis-opt(1.557), 210611-085808-NaN.mat
rename to Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC502] lipolysis-opt(1.557), 211011-135041-NaN.mat
index 7b22521ff6d06dac027a17ca3a967bf9d5f3d2af..5532490427c4f388a45ac044dec1a66a40b72278 100644
Binary files a/Scripts and data/Parameter sets/PL/[max, EC502] lipolysis-opt(1.557), 210611-085808-NaN.mat and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC502] lipolysis-opt(1.557), 211011-135041-NaN.mat differ
diff --git a/Scripts and data/Parameter sets/PL/[max, EC503] lipolysis-opt(4.000), 210611-085808-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC503] lipolysis-opt(4.000), 211011-135041-NaN.mat
similarity index 71%
rename from Scripts and data/Parameter sets/PL/[max, EC503] lipolysis-opt(4.000), 210611-085808-NaN.mat
rename to Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC503] lipolysis-opt(4.000), 211011-135041-NaN.mat
index 7d4c8e4f4a5e065c1aea77f400cf53eda23fa5b6..a418b5ed78633fb853529996532b705a1b2320a9 100644
Binary files a/Scripts and data/Parameter sets/PL/[max, EC503] lipolysis-opt(4.000), 210611-085808-NaN.mat and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, EC503] lipolysis-opt(4.000), 211011-135041-NaN.mat differ
diff --git a/Scripts and data/Parameter sets/PL/[max, isoscale] lipolysis-opt(100.000), 210611-085808-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, isoscale] lipolysis-opt(100.000), 211011-135042-NaN.mat
similarity index 71%
rename from Scripts and data/Parameter sets/PL/[max, isoscale] lipolysis-opt(100.000), 210611-085808-NaN.mat
rename to Scripts and data/Parameter sets (with alternative epi data)/PL/[max, isoscale] lipolysis-opt(100.000), 211011-135042-NaN.mat
index f6eb189cb2a53c5a1ad8ae14cc8e104ccd0f3d1c..0c6f3fe71158cf45618f6d5f14b719fc5e0a769e 100644
Binary files a/Scripts and data/Parameter sets/PL/[max, isoscale] lipolysis-opt(100.000), 210611-085808-NaN.mat and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, isoscale] lipolysis-opt(100.000), 211011-135042-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1a2] lipolysis-opt(2.177), 211011-135042-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1a2] lipolysis-opt(2.177), 211011-135042-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..babbe2726724070a5a940600d76de27ef5ca26c3
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1a2] lipolysis-opt(2.177), 211011-135042-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1a] lipolysis-opt(4.125), 211011-135042-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1a] lipolysis-opt(4.125), 211011-135042-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..ba544453575a55062476e4ba6e9e45c437474591
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1a] lipolysis-opt(4.125), 211011-135042-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1b] lipolysis-opt(6.235), 211011-135042-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1b] lipolysis-opt(6.235), 211011-135042-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..482d39131bc18af7dab8ec1868881ba3271074ca
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k1b] lipolysis-opt(6.235), 211011-135042-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k2a] lipolysis-opt(14.001), 211011-135042-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k2a] lipolysis-opt(14.001), 211011-135042-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..061dccd1a9bb886762e242214340d6fad5a63ebe
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k2a] lipolysis-opt(14.001), 211011-135042-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k2b] lipolysis-opt(14.151), 211011-135043-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k2b] lipolysis-opt(14.151), 211011-135043-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..f4819da7c4c4910618a8e8095179a442d87f5c8a
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k2b] lipolysis-opt(14.151), 211011-135043-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3a2] lipolysis-opt(7.571), 211011-135043-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3a2] lipolysis-opt(7.571), 211011-135043-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..cc6eab8cf3316ace8bccbbbc8bcd704b93dcdc88
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3a2] lipolysis-opt(7.571), 211011-135043-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3a] lipolysis-opt(20.723), 211011-135043-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3a] lipolysis-opt(20.723), 211011-135043-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..8d230e0e7e4c930664b1e92befe315944e741cd1
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3a] lipolysis-opt(20.723), 211011-135043-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3b] lipolysis-opt(12.578), 211011-135043-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3b] lipolysis-opt(12.578), 211011-135043-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..b6f9a5ae552563e7b02e251fa310237f13dd2da6
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k3b] lipolysis-opt(12.578), 211011-135043-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4a2] lipolysis-opt(1.264), 211011-135043-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4a2] lipolysis-opt(1.264), 211011-135043-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..6115c2074ac649250d88bfcf86a9c6eb252ba902
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4a2] lipolysis-opt(1.264), 211011-135043-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4a] lipolysis-opt(5.186), 211011-135043-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4a] lipolysis-opt(5.186), 211011-135043-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..9e6e2f79c02f3bb8e209281a0eab17bf8d94b380
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4a] lipolysis-opt(5.186), 211011-135043-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4b] lipolysis-opt(13.242), 211011-135044-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4b] lipolysis-opt(13.242), 211011-135044-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2e96cfea40e9d8ebc51ca98c6b93fa5a57932d7e
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k4b] lipolysis-opt(13.242), 211011-135044-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k5a] lipolysis-opt(11.985), 211011-135044-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k5a] lipolysis-opt(11.985), 211011-135044-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..855fb92b8afc7037f0fee502e769d42880c3a170
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k5a] lipolysis-opt(11.985), 211011-135044-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k5b] lipolysis-opt(8.354), 211011-135044-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k5b] lipolysis-opt(8.354), 211011-135044-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..dadc7551fd2ac286255aacef071958755d756637
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k5b] lipolysis-opt(8.354), 211011-135044-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k6a] lipolysis-opt(13.216), 211011-135044-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k6a] lipolysis-opt(13.216), 211011-135044-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..5fde86a342d4c4dbb07ad2310a99f4be1f572294
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k6a] lipolysis-opt(13.216), 211011-135044-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k6b] lipolysis-opt(13.549), 211011-135044-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k6b] lipolysis-opt(13.549), 211011-135044-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..558a422656396e9e79656898c51805d9395564d1
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k6b] lipolysis-opt(13.549), 211011-135044-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k7a] lipolysis-opt(8.930), 211011-135044-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k7a] lipolysis-opt(8.930), 211011-135044-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..4b6d32fd999dae9050b38d194b53f29856529823
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k7a] lipolysis-opt(8.930), 211011-135044-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k7b] lipolysis-opt(13.436), 211011-135045-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k7b] lipolysis-opt(13.436), 211011-135045-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..7919cf8529a32e7b30415cf3dfeaded71523c36a
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k7b] lipolysis-opt(13.436), 211011-135045-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8a] lipolysis-opt(9.707), 211011-135045-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8a] lipolysis-opt(9.707), 211011-135045-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..85fb2c1b14f0b574121d5760c999372c55b6e327
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8a] lipolysis-opt(9.707), 211011-135045-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8b] lipolysis-opt(1.387), 211011-135045-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8b] lipolysis-opt(1.387), 211011-135045-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..0b3fe754ca2d3400f6f3a0ec4be61c55d3a74f44
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8b] lipolysis-opt(1.387), 211011-135045-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8c] lipolysis-opt(-3.535), 211011-135045-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8c] lipolysis-opt(-3.535), 211011-135045-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..8648151ab297cb647996a740772f071df534ea86
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, k8c] lipolysis-opt(-3.535), 211011-135045-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, kdrift] lipolysis-opt(4.748), 211011-135045-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, kdrift] lipolysis-opt(4.748), 211011-135045-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..8e26c0d926eaa96da4bfc94d0f6977c0db3d49a2
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, kdrift] lipolysis-opt(4.748), 211011-135045-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min1] lipolysis-opt(14.109), 211011-135045-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min1] lipolysis-opt(14.109), 211011-135045-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..86d281b3af1a652618bfd87a5ff703a3a34939a1
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min1] lipolysis-opt(14.109), 211011-135045-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min2] lipolysis-opt(35.324), 211011-135046-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min2] lipolysis-opt(35.324), 211011-135046-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..542c8c747d59a912802b1576c6b8d02c23370eca
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min2] lipolysis-opt(35.324), 211011-135046-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min3] lipolysis-opt(20.000), 211011-135046-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min3] lipolysis-opt(20.000), 211011-135046-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..77ed1a332f3589c426b30c5dbc003fccab0452bc
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, min3] lipolysis-opt(20.000), 211011-135046-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n1] lipolysis-opt(1.109), 211011-135046-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n1] lipolysis-opt(1.109), 211011-135046-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..27d33e9b8cf47bacb391a85ff782a8f44678f29f
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n1] lipolysis-opt(1.109), 211011-135046-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n2] lipolysis-opt(4.000), 211011-135046-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n2] lipolysis-opt(4.000), 211011-135046-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..a1a4baf17e41e8b808006d4d5138040abf24f009
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n2] lipolysis-opt(4.000), 211011-135046-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n3] lipolysis-opt(4.000), 211011-135046-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n3] lipolysis-opt(4.000), 211011-135046-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..6cd96a1b53d03ca0ac1bd22f94639c5887c5bf5f
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, n3] lipolysis-opt(4.000), 211011-135046-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, phe_effect] lipolysis-opt(1.000), 211011-135046-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, phe_effect] lipolysis-opt(1.000), 211011-135046-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..a2333f49ecfccc46b063f3e6f86a90a6aaf8cf13
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[max, phe_effect] lipolysis-opt(1.000), 211011-135046-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC501] lipolysis-opt(-1.362), 211011-135046-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC501] lipolysis-opt(-1.362), 211011-135046-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..849a827cc334cbf73ebd1b3f44133073d7fd1ebc
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC501] lipolysis-opt(-1.362), 211011-135046-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC502] lipolysis-opt(0.372), 211011-135047-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC502] lipolysis-opt(0.372), 211011-135047-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..d2fc3d9c2fd83fe055c95cbe6636aec88ce01aa6
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC502] lipolysis-opt(0.372), 211011-135047-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC503] lipolysis-opt(-6.000), 211011-135047-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC503] lipolysis-opt(-6.000), 211011-135047-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2d6c2aa79f61ed8ffa8f773989e4fac0a4d1f09f
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, EC503] lipolysis-opt(-6.000), 211011-135047-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, isoscale] lipolysis-opt(0.062), 211011-135047-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, isoscale] lipolysis-opt(0.062), 211011-135047-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..c86d9a6efcddf3d5f5b793934b23e0220266b825
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, isoscale] lipolysis-opt(0.062), 211011-135047-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1a2] lipolysis-opt(-9.875), 211011-135047-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1a2] lipolysis-opt(-9.875), 211011-135047-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..93b2c8fd5ba79483caa34827f8263e0ebefe4820
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1a2] lipolysis-opt(-9.875), 211011-135047-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1a] lipolysis-opt(-15.850), 211011-135047-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1a] lipolysis-opt(-15.850), 211011-135047-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..fb43f0b0d2c9b91153b4124ed1e7a867f02bd20e
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1a] lipolysis-opt(-15.850), 211011-135047-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1b] lipolysis-opt(-4.144), 211011-135047-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1b] lipolysis-opt(-4.144), 211011-135047-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..c5b056924d33e0ddc393bea83b962474b1bbf7cd
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k1b] lipolysis-opt(-4.144), 211011-135047-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k2a] lipolysis-opt(-11.550), 211011-135047-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k2a] lipolysis-opt(-11.550), 211011-135047-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..5985cc9894a1640ef241738aa64881654986db2f
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k2a] lipolysis-opt(-11.550), 211011-135047-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k2b] lipolysis-opt(-7.076), 211011-135048-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k2b] lipolysis-opt(-7.076), 211011-135048-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..5fe5e50624cf06121b3fa01d4b2704dc3541b090
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k2b] lipolysis-opt(-7.076), 211011-135048-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3a2] lipolysis-opt(-4.139), 211011-135048-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3a2] lipolysis-opt(-4.139), 211011-135048-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..e9676b0ea03b5ddfc73302bce7edc8b04f15cf3c
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3a2] lipolysis-opt(-4.139), 211011-135048-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3a] lipolysis-opt(-8.295), 211011-135048-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3a] lipolysis-opt(-8.295), 211011-135048-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..6ced60ef191df03d0596179c6091fcf2f0926c4a
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3a] lipolysis-opt(-8.295), 211011-135048-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3b] lipolysis-opt(-1.062), 211011-135048-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3b] lipolysis-opt(-1.062), 211011-135048-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..d250293393402c263c0d53e501a3846eca1c0558
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k3b] lipolysis-opt(-1.062), 211011-135048-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4a2] lipolysis-opt(-13.032), 211011-135048-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4a2] lipolysis-opt(-13.032), 211011-135048-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..3024b96adfb0d3725e31936f19a80ddd186834b6
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4a2] lipolysis-opt(-13.032), 211011-135048-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4a] lipolysis-opt(-6.980), 211011-135048-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4a] lipolysis-opt(-6.980), 211011-135048-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..b7e97694a2a5c65360d2c951b5d99b3a540a42e7
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4a] lipolysis-opt(-6.980), 211011-135048-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4b] lipolysis-opt(-1.449), 211011-135049-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4b] lipolysis-opt(-1.449), 211011-135049-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..a7584e65bca55c037fc98e30bd4b83f33bc64f4c
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k4b] lipolysis-opt(-1.449), 211011-135049-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k5a] lipolysis-opt(-2.906), 211011-135049-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k5a] lipolysis-opt(-2.906), 211011-135049-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..f1dc633cb1cf86268cc1e12532f1dcfc49f992aa
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k5a] lipolysis-opt(-2.906), 211011-135049-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k5b] lipolysis-opt(-4.243), 211011-135049-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k5b] lipolysis-opt(-4.243), 211011-135049-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..a37a5dfb8fc4a4d7e7f0969f36e7f5434a9a5a45
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k5b] lipolysis-opt(-4.243), 211011-135049-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k6a] lipolysis-opt(-8.098), 211011-135049-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k6a] lipolysis-opt(-8.098), 211011-135049-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..d8675b4705b3d7d4dc079b42ed89f759197bfe36
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k6a] lipolysis-opt(-8.098), 211011-135049-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k6b] lipolysis-opt(-5.314), 211011-135049-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k6b] lipolysis-opt(-5.314), 211011-135049-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..be4cc20b1b70971ab9f1993691ae22ff6f470045
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k6b] lipolysis-opt(-5.314), 211011-135049-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k7a] lipolysis-opt(-20.011), 211011-135049-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k7a] lipolysis-opt(-20.011), 211011-135049-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..42c2c5873b0d423714f2260dc1c5a96c721e8531
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k7a] lipolysis-opt(-20.011), 211011-135049-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k7b] lipolysis-opt(-3.344), 211011-135049-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k7b] lipolysis-opt(-3.344), 211011-135049-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..65e2ded82e3e6a1c87d861bb89a85c45b9b111b5
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k7b] lipolysis-opt(-3.344), 211011-135049-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8a] lipolysis-opt(-8.663), 211011-135050-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8a] lipolysis-opt(-8.663), 211011-135050-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..6f74bc0548009ff0d4021a5c8f2429988fa0b554
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8a] lipolysis-opt(-8.663), 211011-135050-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8b] lipolysis-opt(-3.475), 211011-135050-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8b] lipolysis-opt(-3.475), 211011-135050-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..e8a0f4ddfebacd1da98b54145656afcb12bd4a36
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8b] lipolysis-opt(-3.475), 211011-135050-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8c] lipolysis-opt(-20.723), 211011-135050-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8c] lipolysis-opt(-20.723), 211011-135050-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..dea9e5a728bdd21c9f1daf501f208c5d12f47bec
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, k8c] lipolysis-opt(-20.723), 211011-135050-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, kdrift] lipolysis-opt(-10.305), 211011-135050-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, kdrift] lipolysis-opt(-10.305), 211011-135050-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..57e021f12b943395a15f32a634a74393a9c3ea8b
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, kdrift] lipolysis-opt(-10.305), 211011-135050-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min1] lipolysis-opt(0.119), 211011-135050-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min1] lipolysis-opt(0.119), 211011-135050-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2550cd53914395467da09aa5c21c631848326ca6
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min1] lipolysis-opt(0.119), 211011-135050-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min2] lipolysis-opt(14.902), 211011-135050-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min2] lipolysis-opt(14.902), 211011-135050-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..24667c72d5ed8b40e15089f19ebb9c05f5c0293d
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min2] lipolysis-opt(14.902), 211011-135050-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min3] lipolysis-opt(0.000), 211011-135050-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min3] lipolysis-opt(0.000), 211011-135050-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2bc6a636262510b2a833fbf248fa17d26de3d7dd
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, min3] lipolysis-opt(0.000), 211011-135050-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n1] lipolysis-opt(0.310), 211011-135051-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n1] lipolysis-opt(0.310), 211011-135051-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..21bc6f0ae954bc758f88878019b9cdc7e437df91
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n1] lipolysis-opt(0.310), 211011-135051-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n2] lipolysis-opt(0.405), 211011-135051-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n2] lipolysis-opt(0.405), 211011-135051-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..4cca79d5f232e32d809cbba424a07e190dd7d460
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n2] lipolysis-opt(0.405), 211011-135051-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n3] lipolysis-opt(0.000), 211011-135051-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n3] lipolysis-opt(0.000), 211011-135051-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..d4dfdee64cb6664fb14017562a776a454720f43b
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, n3] lipolysis-opt(0.000), 211011-135051-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, phe_effect] lipolysis-opt(0.000), 211011-135051-NaN.mat b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, phe_effect] lipolysis-opt(0.000), 211011-135051-NaN.mat
new file mode 100644
index 0000000000000000000000000000000000000000..979a34b9b9a0be24ba227e43826fbb40e766e9f1
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/PL/[min, phe_effect] lipolysis-opt(0.000), 211011-135051-NaN.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/[HSL, cost, min, nan] lipolysis-opt(6.487), 211008-134757-2074222607.mat b/Scripts and data/Parameter sets (with alternative epi data)/[HSL, cost, min, nan] lipolysis-opt(6.487), 211008-134757-2074222607.mat
new file mode 100644
index 0000000000000000000000000000000000000000..f76c93e843ebd8d3abfd772cae673f93828b9f8f
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/[HSL, cost, min, nan] lipolysis-opt(6.487), 211008-134757-2074222607.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/lipolysis, opt-eSS(128.04), 20211006-100107 2055492541.mat b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis, opt-eSS(128.04), 20211006-100107 2055492541.mat
new file mode 100644
index 0000000000000000000000000000000000000000..6b3fd4a9311f8fea485e9de425c79a2bffe5da90
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis, opt-eSS(128.04), 20211006-100107 2055492541.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns1, opt-eSS(496.92), 20211006-091215 2055219633.mat b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns1, opt-eSS(496.92), 20211006-091215 2055219633.mat
new file mode 100644
index 0000000000000000000000000000000000000000..683fa05c8f18ad807c36b0ef9344854becb49b9b
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns1, opt-eSS(496.92), 20211006-091215 2055219633.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns2, opt-eSS(179.54), 20211006-095432 2055472920.mat b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns2, opt-eSS(179.54), 20211006-095432 2055472920.mat
new file mode 100644
index 0000000000000000000000000000000000000000..2eabed6f9b9ab5f9d6426f2423e3cbafd8571e04
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns2, opt-eSS(179.54), 20211006-095432 2055472920.mat differ
diff --git a/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns3, opt-eSS(120.39), 20211006-091218 2055219976.mat b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns3, opt-eSS(120.39), 20211006-091218 2055219976.mat
new file mode 100644
index 0000000000000000000000000000000000000000..99738b9e8f812e9a9de1e97e2055a40684d5f7d6
Binary files /dev/null and b/Scripts and data/Parameter sets (with alternative epi data)/lipolysis_noIns3, opt-eSS(120.39), 20211006-091218 2055219976.mat differ
diff --git a/Scripts and data/Parameter sets/PL/[max, EC501] lipolysis-opt(1.085), 210611-085808-NaN.mat b/Scripts and data/Parameter sets/PL/[max, EC501] lipolysis-opt(1.085), 210611-085808-NaN.mat
deleted file mode 100644
index f4a6e7509a40836aeb17ce1f6013d6adb162e758..0000000000000000000000000000000000000000
Binary files a/Scripts and data/Parameter sets/PL/[max, EC501] lipolysis-opt(1.085), 210611-085808-NaN.mat and /dev/null differ
diff --git a/Scripts and data/PlotInVivo.m b/Scripts and data/PlotInVivo.m
index b48dd8f5d6e4ffded37a49e3823fc50ebe083279..a0ad1c18f990e63f76406166e14df3d629d223b0 100644
--- a/Scripts and data/PlotInVivo.m
+++ b/Scripts and data/PlotInVivo.m
@@ -14,11 +14,12 @@ if posOverride ~=0
m=3; n=2; pos=[nan, nan, nan, posOverride];
elseif any(contains(vars, 'Diab'))
m=2; n=2; pos=[1 2];
-elseif any(strcmp(vars, 'Fig3Epi'))
+elseif sum(ismember(vars, {'Fig2Epi', 'Fig3Epi'}))==2
m=3; n=2; pos=[1 3 3 5 5];
-else
+elseif any(strcmp(vars, 'Fig2Epi'))
m=4; n=2; pos=[1 3 5 nan 7];
-
+elseif any(strcmp(vars, 'Fig3Epi'))
+ m=4; n=2; pos=[1 nan 5 3 7];
end
for i=1:length(vars)
diff --git a/Scripts and data/PlotInsulinActions.m b/Scripts and data/PlotInsulinActions.m
index 365da2a428eb8f61ca129453ec098b61f776e75b..ea8780e47a1ac326a372256bc63ecadaf976e542 100644
--- a/Scripts and data/PlotInsulinActions.m
+++ b/Scripts and data/PlotInsulinActions.m
@@ -1,6 +1,12 @@
-function [] = PlotInsulinActions()
+function [] = PlotInsulinActions(useFig2EpiData)
+if nargin<1, useFig2EpiData=1; end
+
modelName = 'lipolysis';
-baseFolder = './Parameter sets' ;
+if useFig2EpiData
+ baseFolder='./Parameter sets';
+else
+ baseFolder='./Parameter sets (with alternative epi data)';
+end
[model,data, lb, ub, nParams, expInd, stimulus, dgf] = Init(modelName, 0, 0);
inVitroData.Normal=data.InVitro;
diff --git a/Scripts and data/PlotPL.m b/Scripts and data/PlotPL.m
index a2476757a7de6a5181cf722546c957098e4ddf7f..4d6242b09cad53222f9959f9fa1dd8c5605017a2 100644
--- a/Scripts and data/PlotPL.m
+++ b/Scripts and data/PlotPL.m
@@ -1,13 +1,18 @@
-function [] = PlotPL(modelName)
+function [] = PlotPL(modelName, useFig2EpiData)
if nargin<1; modelName='lipolysis'; end
-baseFolder='./Parameter sets';
+if nargin<2; useFig2EpiData=1; end
-folder= 'Parameter sets/PL/';
+ if useFig2EpiData
+ baseFolder='./Parameter sets';
+ else
+ baseFolder='./Parameter sets (with alternative epi data)';
+ end
[model, data, lb, ub, nParams, expInd, stimulus, dgf] = Init(modelName, 0);
pNames = IQMparameters(model);
+pNames(nParams+1:end)=[];
rejectlb = lb;
rejectub = ub;
for i = 1:nParams
@@ -15,13 +20,15 @@ for i = 1:nParams
rejectub(i) = NonIdentifiabilityBound(pNames{i}, ub(i), 'max');
end
-files=dir(sprintf('%s/**/*%s*.mat', folder, modelName));
+files=dir(sprintf('%s/PL/**/*%s*.mat', baseFolder, modelName));
optParams=[];
for i = fliplr(1:length(files))
load([files(i).folder '/' files(i).name],'optParam');
optParams(i,:)=optParam;
end
optParams=unique(optParams,'rows');
+
+sortIdx = [1 10:14 6 7 5 2:4 8 9 15:19 21 20 22 23 25 26 24 28 29 27 31 32 30];
%% Print bounds
maxP = max(optParams)';
maxP=[exp(maxP(1:expInd)); maxP(expInd+1:end)];
@@ -29,8 +36,23 @@ maxP(27:29) = 10.^maxP(27:29);
minP = min(optParams)';
minP=[exp(minP(1:expInd)); minP(expInd+1:end)];
minP(27:29) = 10.^minP(27:29);
-params=table(pNames(1:32),minP,maxP,'VariableNames',{'Parameters', 'Min','Max'});
-disp('Boundry for parameter uncertainty, presented in Table S1.')
+lowerThreshold =[exp(rejectlb(1:expInd)) rejectlb(expInd+1:end)]';
+upperThreshold =[exp(rejectub(1:expInd)) rejectub(expInd+1:end)]';
+
+pNames=pNames(sortIdx);
+lowerThreshold = lowerThreshold(sortIdx);
+upperThreshold = upperThreshold(sortIdx);
+minP = minP(sortIdx);
+maxP = maxP(sortIdx);
+optParams = optParams(:,sortIdx);
+rejectub = rejectub(sortIdx);
+rejectlb = rejectlb(sortIdx);
+lb = lb(sortIdx);
+ub = ub(sortIdx);
+
+params=table(pNames,lowerThreshold, upperThreshold, minP,maxP,'VariableNames',{'Parameters', 'Lower_threshold', 'Upper_threshold','Min','Max'});
+params{27:29, 2:3} = 10.^params{27:29, 2:3};
+disp('Boundry for parameter uncertainty.')
disp(params)
%%
x = 2*(optParams-rejectlb) ./ (rejectub-rejectlb)-1;
@@ -50,7 +72,7 @@ bound = (maxx-minx)/2;
h = errorbar(1:size(x,2),center, bound,'.','linewidth',3, 'color', 'k');
h.CapSize = 20;
xticks(1:size(x,2))
-xticklabels(IQMparameters(model))
+xticklabels(pNames)
set(gca,'TickLabelInterpreter','none', 'fontsize',30)
xtickangle(45)
ylim([-1.05 1.05])
@@ -69,7 +91,7 @@ end
%% Plot the best solution
load(FindBestParametersFile(baseFolder, 1, [modelName ', opt-eSS']), 'optParam')
x = 2*(optParam-rejectlb) ./ (rejectub-rejectlb)-1;
-plot(x,'x','MarkerSize',15, 'color',[0 0.4470 0.7410]);
+plot(x(sortIdx),'x','MarkerSize',15, 'color',[0 0.4470 0.7410]);
%% Set size and save figure
set(gcf, 'outerposition',[0 0 2560 1440], 'PaperType','a4')
diff --git a/Scripts and data/PlotUncertainty.m b/Scripts and data/PlotUncertainty.m
index 3e5f0852820f96cd2724265f9f8f95248565dd42..2e8ddf4f3769396a724a6ce05a377c87423d99f2 100644
--- a/Scripts and data/PlotUncertainty.m
+++ b/Scripts and data/PlotUncertainty.m
@@ -1,11 +1,14 @@
-function [] = PlotUncertainty(doDiabetes,res, modelName)
+function [] = PlotUncertainty(doDiabetes,res, modelName, useFig2EpiData)
clear mex
if nargin<1, doDiabetes=0; end
if nargin<2, res=0.01; end
if nargin<3, modelName='lipolysis'; end
+if nargin<4, useFig2EpiData=1; end
-if ~doDiabetes
+if ~useFig2EpiData
+ baseFolder = './Parameter sets (with alternative epi data)' ;
+elseif ~doDiabetes
baseFolder = './Parameter sets' ;
elseif doDiabetes
baseFolder = './Parameter sets (with diabetes)' ;
@@ -22,12 +25,10 @@ stimulusHighRes.Ins=[0 10.^(ins(2):res:ins(end)) 0]';
stimulusHighRes.Iso=[0.01*ones(height(stimulusHighRes)-1,1); 0]; %10 nM = 0.01 µM
load(FindBestParametersFile(baseFolder, 1, [modelName ', opt-eSS']), 'optParam')
-
if length(optParam)==length(IQMparameters(model))-5
optParam=[optParam 0];
end
-
-cost = costfunction(optParam,model, expInd, data, stimulus, doDiabetes);
+cost = costfunction(optParam,model, expInd, data, stimulus, doDiabetes, useFig2EpiData);
fprintf('Total cost: %.2f, chi2: %.2f. Pass: %d\n',cost, limit, cost<limit)
params=[exp(optParam(1:expInd)) optParam(expInd+1:end)];
@@ -35,6 +36,18 @@ diab=params(end);
params(end)=[];
Best=simulateInVitro(model, params, expInd, diab, stimulusHighRes, 0);
+if strcmp(modelName, 'lipolysis') && ~doDiabetes
+ load(FindBestParametersFile(baseFolder, 1, 'HSL, cost, min'), 'optParam')
+ if length(optParam)==length(IQMparameters(model))-5
+ optParam=[optParam 0];
+ end
+ HSLParams=[exp(optParam(1:expInd)) optParam(expInd+1:end)];
+ diab=HSLParams(end);
+ HSLParams(end)=[];
+ BestHSL=simulateInVitro(model, HSLParams, expInd, diab, stimulusHighRes, 0);
+ Best.Normal.HSL = BestHSL.Normal.HSL;
+end
+
InVitrotmp.high=Best.Normal;
InVitrotmp.low=Best.Normal;
@@ -72,7 +85,7 @@ if size(optParams,1)>0
end
for i = 1:size(optParams,1)
optParam=optParams(i,:);
- cost = costfunction(optParam,model, expInd, data, stimulus, doDiabetes);
+ cost = costfunction(optParam,model, expInd, data, stimulus, doDiabetes, useFig2EpiData);
if cost<limit+0.1
params=[exp(optParam(1:expInd)) optParam(expInd+1:end-1)];
diab=optParam(end);
@@ -111,6 +124,7 @@ for i = 1:size(optParams,1)
fprintf('|')
end
end
+fprintf('\n')
%% Do the plotting
%Setup simulations and data (in vitro)
@@ -157,14 +171,22 @@ elseif ~contains(baseFolder, 'with diabetes') % Plot validation simulation and d
PlotInVitro(InVitro, allInVitroData, {'Normal'}, 3)
InVitroHSL.Normal(:,~ismember(InVitroHSL.Normal.Properties.VariableNames,{'Ins','Iso','HSL'}))=[];
+ if useFig2EpiData
+ PlotInVitro(InVitroHSL, allInVitroData, {'Normal'}, 54)
+ end
+ InVitroHSL.Normal.HSL(:,2:end)=[];
PlotInVitro(InVitroHSL, allInVitroData, {'Normal'}, 4)
elseif contains(baseFolder, 'with diabetes') % Plot diabetes in vitro predictions.
PlotInVivo(data, TS.Gly.Normal, 53,'Glycerol')
PlotInVitro(InVitro, allInVitroData, {'Normal'}, 53)
-
- data.InVivo.Fig3Epi=[];
- TS.Gly.Normal.Fig3Epi=[];
+ if useFig2EpiData
+ data.InVivo.Fig3Epi=[];
+ TS.Gly.Normal.Fig3Epi=[];
+ else
+ data.InVivo.Fig2Epi=[];
+ TS.Gly.Normal.Fig2Epi=[];
+ end
PlotInVivo(data, TS.Gly.Normal, 54,'Glycerol')
PlotInVitro(InVitro, allInVitroData, {'Normal'}, 54)
diff --git a/Scripts and data/costfunction.m b/Scripts and data/costfunction.m
index dca1feb5d36ef28a7f7f896a7d1552b7ecb70c1f..b2c4dcc9bd542c2ba79b35792b4cd34d72f393ac 100644
--- a/Scripts and data/costfunction.m
+++ b/Scripts and data/costfunction.m
@@ -1,4 +1,4 @@
-function [cost] = costfunction(param_in,model, expInd, data, stimulus, doDiabetes)
+function [cost] = costfunction(param_in,model, expInd, data, stimulus, doDiabetes, useFig2EpiData)
if (nargin < 6), doDiabetes = 0; end
@@ -12,7 +12,7 @@ else
diabetes=0.66; % not used
end
-costInVivo = CostInVivo(params, model, data.InVivo, 0);%% InVivo data
+costInVivo = CostInVivo(params, model, data.InVivo, 0, useFig2EpiData );%% InVivo data
costInVitro = CostInVitro(model, params, expInd, stimulus, data,diabetes, doDiabetes);%% InVitro data
cost=costInVivo+costInVitro;