Additional example for RTF, dose-dependency

arFramework3/Examples/ToyModels/TransientFunction/Example4_FitDoseDependentFunctionToData/Data/LDH_WT.def

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+DESCRIPTION
+
+PREDICTOR
+time        T   min time    0	10
+
+INPUTS
+
+OBSERVABLES
+
+ERRORS
+
+CONDITIONS
+isKO	"0"
+
+RANDOM
+

arFramework3/Examples/ToyModels/TransientFunction/Example4_FitDoseDependentFunctionToData/Models/TransientDoseFunction.def

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+DESCRIPTION
+
+PREDICTOR
+t               T   h     time	0	10
+
+COMPARTMENTS
+
+STATES
+
+INPUTS
+Signal_sus    C   au   conc  "signum_TF * amp_sus*(1-exp(-(log10(10^(10*t/maxt)+10^(toffset_TF_sus))-log10(1+10^(toffset_TF_sus)))/timescale_sus))"
+
+REACTIONS
+
+DERIVED
+
+
+OBSERVABLES
+Response                   C 	au     conc   0    0   "offset_TF + Signal_sus"
+
+ERRORS
+// the following error model assumes the same error for each expriment:
+Response           "sd_TF"
+
+
+SUBSTITUTIONS
+
+
+CONDITIONS
+timescale_sus 	"timescale_sus*timeUnitFactor/maxt"
+toffset_TF_sus 	"toffset_TF_sus*timeUnitFactor/maxt"
+signum_TF	"1"
+timeUnitFactor	"100"
+maxt		"10" 
+amp_sus		"(Max_amp_sus*dose^(hill_amp_sus))/(KD_amp_sus^(hill_amp_sus)+dose^(hill_amp_sus))*(1-isKO) + isKO*fold_as*(Max_amp_sus*dose^(hill_amp_sus))/(KD_amp_sus^(hill_amp_sus)+dose^(hill_amp_sus))"
+timescale_sus	"(Max_timescale_sus*KD_timescale_sus^(hill_timescale_sus))/(KD_timescale_sus^(hill_timescale_sus)+dose^(hill_timescale_sus))*(1-isKO) + isKO*fold_ts*(Max_timescale_sus*KD_timescale_sus^(hill_timescale_sus))/(KD_timescale_sus^(hill_timescale_sus)+dose^(hill_timescale_sus))"
+toffset_TF_sus	"(Max_toffset_TF_sus*KD_toffset_TF_sus^(hill_toffset_TF_sus))/(KD_toffset_TF_sus^(hill_toffset_TF_sus)+dose^(hill_toffset_TF_sus))*(1-isKO) + isKO*fold_to*(Max_toffset_TF_sus*KD_toffset_TF_sus^(hill_toffset_TF_sus))/(KD_toffset_TF_sus^(hill_toffset_TF_sus)+dose^(hill_toffset_TF_sus))"
+
+
+PARAMETERS
+//name		value	qFit	dolog	lb	ub
+//offset	 0	 1	 0	 -100	 100
+//signum	 1	 0	 0	 -1	 1
+
+

arFramework3/Examples/ToyModels/TransientFunction/Example4_FitDoseDependentFunctionToData/Setup.m

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+% addpath('../TransientFunction_library/') % functions for fitting the transient model (e.g. fitting both signums)
+
+nLHS = 500;
+
+%% LDH
+arInit
+arLoadModel('TransientDoseFunction')
+% arLoadData('LDH',1)
+arLoadData('LDH_WT',1)
+arLoadData('LDH_KO',1)
+arCompileAll(true)
+
+% Initialize_FitTransient % setting bounds, identification of parameter-types from name
+
+% arLoadPars(1)
+
+arSetPars('KD_toffset_TF_sus',log10(2), 1,1,-5,3);
+arSetPars('Max_toffset_TF_sus',10, 1,0,-1,100); % unlog
+arSetPars('hill_toffset_TF_sus',1, 1,0,1,5);
+arSetPars('hill_timescale_sus',1, 1,0,1,5);
+arSetPars('hill_amp_sus',1, 1,0,1,5);
+
+arFitLHS(nLHS) % multi-start fitting
+% arFitTransient % single fit
+arQplot('y')
+arPlot
+arPrint
+
+%% 
+arSave('LDH')
+
+arPLEInit
+ple
+pleExtend
+pleSmooth
+arSave('current')
+
+%%
+% arLoad('20220815T133125_PLEs_Gut')
+PlotHillCurves(2)
+print -dpng HillCurves_LDH
+
+PlotHillCurves(3)
+print -dpng HillCurves2_LDH
+
+PlotHillCurves_3D
+PrintAllToPng(1:2,'HillCurves_LDH_3D')
+
+% PLE 
+PlotProfile('fold_as','max. amplitude ratio KO/WT')
+title('LDH')
+print -dpng Profile_fold_Amax_LDH
+
+PlotProfile('fold_ts','velocity ratio KO/WT')
+title('LDH')
+print -dpng Profile_fold_timescale_LDH
+
+PlotProfile('fold_to','delay ratio KO/WT')
+title('LDH')
+print -dpng Profile_fold_toffset_LDH
+
+PlotFits
+suptitle('LDH')
+print -dpng PlotFits_LDH
+
+
+Plot3D
+print -dpng 3D_LDH
+% arSave('LDH_foldAufHill_LHS500_gut')
+
+%% IL1b
+arInit
+arLoadModel('TransientDoseFunction')
+% arLoadData('LDH',1)
+arLoadData('IL1b_WT',1)
+arLoadData('IL1b_KO',1)
+arCompileAll(true)
+
+% Initialize_FitTransient % setting bounds, identification of parameter-types from name
+
+% arLoadPars(1)
+
+arSetPars('KD_toffset_TF_sus',log10(2), 1,1,-5,3);
+arSetPars('Max_toffset_TF_sus',10, 1,0,-1,100); % unlog
+arSetPars('hill_toffset_TF_sus',1, 1,0,1,5);
+arSetPars('hill_timescale_sus',1, 1,0,1,5);
+arSetPars('hill_amp_sus',1, 1,0,1,5);
+
+arFitLHS(nLHS) % multi-start fitting
+% arFitTransient % single fit
+arQplot('y')
+arPlot
+arPrint
+
+%%
+arSave('IL1b')
+
+arPLEInit
+ple
+pleExtend
+arSave('current')
+
+
+%% without t_offset
+% indFix = [arPrint('fold_to'),arPrint('_toffset_')]
+% ar.qFit(indFix) = 0;
+
+arFit
+arSave('IL1b_toffsetFixed')
+
+arPLEInit
+ple
+pleExtend
+pleSmooth
+arSave('current')
+
+%% Fits IL1b
+% arLoad('20220815T150340_IL1b_toffsetFixed')
+
+PlotFits
+suptitle('IL1b')
+print -dpng PlotFits_IL1b
+
+PlotProfile('fold_as','max. amplitude ratio KO/WT')
+title('IL1b')
+print -dpng Profile_fold_Amax_IL1b
+
+PlotProfile('fold_ts','velocity ratio KO/WT')
+title('IL1b')
+print -dpng Profile_fold_timescale_IL1b
+
+PlotProfile('fold_to','delay ratio KO/WT')
+title('IL1b')
+print -dpng Profile_fold_toffset_IL1b
+
+
+PlotHillCurves(2)
+print -dpng HillCurves_IL1b
+
+PlotHillCurves(3)
+print -dpng HillCurves2_IL1b
+
+PlotHillCurves_3D
+PrintAllToPng(1:2,'HillCurves_IL1b_3D')
+
+PlotHillCurves_3D('1./((Max_timescale_sus*KD_timescale_sus^(hill_timescale_sus))./(KD_timescale_sus^(hill_timescale_sus)+dosesFine.^(hill_timescale_sus))*(1-isKO) + isKO*fold_ts*(Max_timescale_sus*KD_timescale_sus^(hill_timescale_sus))./(KD_timescale_sus^(hill_timescale_sus)+dosesFine.^(hill_timescale_sus)));',...
+    'Velocity');
+PlotHillCurves_3D('((Max_toffset_TF_sus*KD_toffset_TF_sus^(hill_toffset_TF_sus))./(KD_toffset_TF_sus^(hill_toffset_TF_sus)+dosesFine.^(hill_toffset_TF_sus))*(1-isKO) + isKO*fold_to*(Max_toffset_TF_sus*KD_toffset_TF_sus^(hill_toffset_TF_sus))./(KD_toffset_TF_sus^(hill_toffset_TF_sus)+dosesFine.^(hill_toffset_TF_sus)));',...
+    'Max. Delay');
+
+Plot3D
+print -dpng 3D_IL1b
+
+% arSave('IL1b_foldAufHill_LHS500_gut')