Fix bug in model constraints for Dusp1 model.

Author: Munsky

WorkSpace/EricModel/a0_Fit_GR_and_DUSP1_models.m

@@ -9,8 +9,8 @@
 close all 
 addpath(genpath('../../src'));
 
-loadPrevious = true;
-savedWorkspace = 'workspaceJuly24';
+loadPrevious = false;
+savedWorkspace = 'workspaceOct22_2024';
 addpath('tmpPropensityFunctions');
 
 %% STEP 0 -- Preliminaries.
@@ -88,7 +88,7 @@
     for i=1:3
         ModelGRfit{i} = ModelGR.loadData("EricData/Gated_dataframe_Ron_020224_NormalizedGR_bins.csv",...
             {'nucGR','normgrnuc';'cytGR','normgrcyt'},...
-            {'Condition','GR_timesweep';'Dex_Conc',GRfitCases{i,2}});
+            {'Dex_Conc',GRfitCases{i,2}});
         ModelGRfit{i}.parameters(13,:) = {'Dex0', str2num(GRfitCases{i,1})};
         ModelGRparameterMap(i) = {(1:8)};
         % parameters 1 - 8 refer to the parameter set that is relevant to
@@ -180,6 +180,7 @@
     ModelGRDusp100nM.useHybrid = true;
     ModelGRDusp100nM.hybridOptions.upstreamODEs = {'cytGR','nucGR'};
     ModelGRDusp100nM.solutionScheme = 'FSP';
+    ModelGRDusp100nM.customConstraintFuns = [];
     ModelGRDusp100nM.fspOptions.bounds = [0;0;0;2;2;400];
     ModelGRDusp100nM.fittingOptions.modelVarsToFit = 1:4;
     ModelGRDusp100nM = ModelGRDusp100nM.formPropensitiesGeneral('EricModDusp1');
@@ -235,7 +236,6 @@
 %%      STEP 2.D.2. -- Compute FIM
 % define which species in model are not observed.
 ModelGRDusp100nM.pdoOptions.unobservedSpecies = {'offGene';'onGene'};
-% TODO - Make this automated when you load data.
 
 % compute the FIM
 fimResults = ModelGRDusp100nM.computeFIM(sensSoln.sens,'log');
@@ -262,7 +262,7 @@
 else
     MHFitOptions.proposalDistribution=@(x)mvnrnd(x,covFree);
     MHFitOptions.thin=1;
-    MHFitOptions.numberOfSamples=10000;
+    MHFitOptions.numberOfSamples=1000;
     MHFitOptions.burnIn=0;
     MHFitOptions.progress=true;
     MHFitOptions.numChains = 1;
@@ -545,7 +545,7 @@
     %'DUSP1parsIntensity'
     });
 
-save('workspaceJuly24',varNames{:})
+save('workspaceOct22_2024',varNames{:})
 
 %% Extra Function
 

WorkSpace/EricModel/a1_Apply_PDO_to_DUSP1_data_and_model.m

@@ -5,10 +5,10 @@
 addpath(genpath('../../src'));
 
 loadPrevious = true;
-savedWorkspace = 'workspaceJuly24';
+savedWorkspace = 'workspaceOct22_2024';
 addpath('tmpPropensityFunctions');
 
-load('workspaceJuly24.mat');
+load(savedWorkspace);
 
 figNew = figure;
 
@@ -168,7 +168,7 @@
     DUSP1parsFIMDesign = ModelGRDusp100nM_FIMDesign.maximizeLikelihood(...
         DUSP1parsFIMDesign, fitOptions);
     ModelGRDusp100nM_FIMDesign.parameters(1:4,2) = num2cell(DUSP1parsFIMDesign);
-    save('EricModelDusp1_MMDex','GRpars','DUSP1pars','DUSP1parsFIMDesign') 
+    save('EricModelDusp1_MMDex_PDO','GRpars','DUSP1pars','DUSP1parsFIMDesign') 
 end
 
 %%      STEP XX.D.2. -- Plot fit and predicitons using FIM suggested conditions.
@@ -183,15 +183,15 @@
 ModelPDOIntensEric = ModelPDOIntensEric.loadData('EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
         {'rna','Nuc_DUSP1_avg_int_tot'},...
         {'Dex_Conc','100'}); 
-load('EricModelDusp1_MMDex','DUSP1parsIntensity') 
+load('EricModelDusp1_MMDex_PDO','DUSP1parsIntensity') 
 
 ModelPDOIntensEric.parameters(1:4,2) = num2cell(DUSP1parsIntensity);
 
 for i = 1:fitIters
     DUSP1parsIntensity = ModelPDOIntensEric.maximizeLikelihood(...
         DUSP1parsIntensity, fitOptions);
     ModelPDOIntensEric.parameters(1:4,2) = num2cell(DUSP1parsIntensity);
-    save('EricModelDusp1_MMDex','GRpars','DUSP1pars','DUSP1parsFIMDesign','DUSP1parsIntensity','DUSP1parsFIMDesignIntensity') 
+    save('EricModelDusp1_MMDex_PDO','GRpars','DUSP1pars','DUSP1parsFIMDesign','DUSP1parsIntensity','DUSP1parsFIMDesignIntensity') 
 end
 %%        STEP XX.D.3.a. -- Plot predictions when fit to distorted data at ALL times.
 showCases = [1,1,1,1];
@@ -209,14 +209,14 @@
 % Set fitting routine only to consider the time points selected by the FIM.
 ModelPDOIntensEricFIM.fittingOptions.timesToFit = nCellsOpt>0;
 % Refit the model, but now with only those time points.
-load('EricModelDusp1_MMDex','DUSP1parsFIMDesignIntensity') 
+load('EricModelDusp1_MMDex_PDO','DUSP1parsFIMDesignIntensity') 
 ModelPDOIntensEricFIM.parameters(1:4,2) = num2cell(DUSP1parsFIMDesignIntensity);
 
 for i = 1:5
     DUSP1parsFIMDesignIntensity = ModelPDOIntensEricFIM.maximizeLikelihood(...
         DUSP1parsFIMDesignIntensity, fitOptions);
     ModelPDOIntensEricFIM.parameters(1:4,2) = num2cell(DUSP1parsFIMDesignIntensity);
-    save('EricModelDusp1_MMDex','GRpars','DUSP1pars','DUSP1parsFIMDesign','DUSP1parsFIMDesignIntensity') 
+    save('EricModelDusp1_MMDex_PDO','GRpars','DUSP1pars','DUSP1parsFIMDesign','DUSP1parsFIMDesignIntensity') 
 end
 %%        STEP XX.D.5.a. -- Plot predictions when fit to distorted data at FIM times.
 showCases = [1,1,1,1];