Add model updates for Eric's project.

MunskyGroup · Jul 3, 2024 · e28c71c · e28c71c
1 parent 6052113
commit e28c71c
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Showing 45 changed files with 254,579 additions and 10,645 deletions.
diff --git a/...23_2024/Complete_dataframe_Ron_010224.csv → ...ricData/Complete_dataframe_Ron_010224.csv b/...23_2024/Complete_dataframe_Ron_010224.csv → ...ricData/Complete_dataframe_Ron_010224.csv
diff --git a/WorkSpace/EricModel/EricData/DUSP1_fit_filtered_data_100nM_031224.csv b/WorkSpace/EricModel/EricData/DUSP1_fit_filtered_data_100nM_031224.csv
diff --git a/WorkSpace/EricModel/EricData/DUSP1_predict_data_DUSP1_TPL_031224.csv b/WorkSpace/EricModel/EricData/DUSP1_predict_data_DUSP1_TPL_031224.csv
diff --git a/WorkSpace/EricModel/EricData/DUSP1_predict_filtered_data_03nM_1nM_10nM_031224.csv b/WorkSpace/EricModel/EricData/DUSP1_predict_filtered_data_03nM_1nM_10nM_031224.csv
diff --git a/WorkSpace/EricModel/EricData/DUSP1_predict_filtered_data_75min_ConcSweep_031224.csv b/WorkSpace/EricModel/EricData/DUSP1_predict_filtered_data_75min_ConcSweep_031224.csv
diff --git a/WorkSpace/EricModel/EricData/Data010224_Gated_On_Nuc.csv b/WorkSpace/EricModel/EricData/Data010224_Gated_On_Nuc.csv
diff --git a/...EricDataJan23_2024/EricModelDataJan29.mat → ...EricModel/EricData/EricModelDataJan29.mat b/...EricDataJan23_2024/EricModelDataJan29.mat → ...EricModel/EricData/EricModelDataJan29.mat
diff --git a/WorkSpace/EricModel/EricData/Gated_dataframe_Ron_020224_NormalizedGR_bins.csv b/WorkSpace/EricModel/EricData/Gated_dataframe_Ron_020224_NormalizedGR_bins.csv
diff --git a/WorkSpace/EricModel/EricData/NormalizedGR_fit_filtered_data_050124.csv b/WorkSpace/EricModel/EricData/NormalizedGR_fit_filtered_data_050124.csv
diff --git a/...odel/EricDataJan23_2024/ProcessErciData.m → ...pace/EricModel/EricData/ProcessErciData.m b/...odel/EricDataJan23_2024/ProcessErciData.m → ...pace/EricModel/EricData/ProcessErciData.m
diff --git a/...icDataJan23_2024/ProcessErciData_020224.m → ...icModel/EricData/ProcessErciData_020224.m b/...icDataJan23_2024/ProcessErciData_020224.m → ...icModel/EricData/ProcessErciData_020224.m
diff --git a/...EricDataJan23_2024/ProcessEricData_Feb6.m → ...EricModel/EricData/ProcessEricData_Jul3.m b/...EricDataJan23_2024/ProcessEricData_Feb6.m → ...EricModel/EricData/ProcessEricData_Jul3.m
diff --git a/...DataJan23_2024/createPDOCalibrationData.m → ...Model/EricData/createPDOCalibrationData.m b/...DataJan23_2024/createPDOCalibrationData.m → ...Model/EricData/createPDOCalibrationData.m
@@ -29,6 +29,13 @@
 TMP.Nuc_DUSP1_avg_int_tot = TMP.Nuc_DUSP1_avg_int.*(TMP.Nuc_Area.^p);
 TMP.Nuc_DUSP1_avg_int_tot = TMP.Nuc_DUSP1_avg_int_tot/maxVal;
 TMP.Nuc_DUSP1_avg_int_tot = round(400*TMP.Nuc_DUSP1_avg_int_tot);
+
+totNucRNA = TMP.RNA_DUSP1_nuc;
+totNucRNA(~isnan(TMP.DUSP1_ts_size_0)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_0)) + TMP.DUSP1_ts_size_0(~isnan(TMP.DUSP1_ts_size_0));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_1)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_1)) + TMP.DUSP1_ts_size_1(~isnan(TMP.DUSP1_ts_size_1));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_2)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_2)) + TMP.DUSP1_ts_size_2(~isnan(TMP.DUSP1_ts_size_2));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_3)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_3)) + TMP.DUSP1_ts_size_3(~isnan(TMP.DUSP1_ts_size_3));
+TMP.totalNucRNA = totNucRNA;
 writetable(TMP,'pdoCalibrationData_EricIntensity_DexSweeps.csv')
 
 %%
@@ -38,6 +45,14 @@
 TMP.Nuc_DUSP1_avg_int_tot = TMP.Nuc_DUSP1_avg_int.*(TMP.Nuc_Area.^p);
 TMP.Nuc_DUSP1_avg_int_tot = TMP.Nuc_DUSP1_avg_int_tot/maxVal;
 TMP.Nuc_DUSP1_avg_int_tot = round(400*TMP.Nuc_DUSP1_avg_int_tot);
+
+totNucRNA = TMP.RNA_DUSP1_nuc;
+totNucRNA(~isnan(TMP.DUSP1_ts_size_0)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_0)) + TMP.DUSP1_ts_size_0(~isnan(TMP.DUSP1_ts_size_0));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_1)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_1)) + TMP.DUSP1_ts_size_1(~isnan(TMP.DUSP1_ts_size_1));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_2)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_2)) + TMP.DUSP1_ts_size_2(~isnan(TMP.DUSP1_ts_size_2));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_3)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_3)) + TMP.DUSP1_ts_size_3(~isnan(TMP.DUSP1_ts_size_3));
+TMP.totalNucRNA = totNucRNA;
+
 writetable(TMP,'pdoCalibrationData_EricIntensity_ConcSweeps.csv')
 
 %%
@@ -47,4 +62,12 @@
 TMP.Nuc_DUSP1_avg_int_tot = TMP.Nuc_DUSP1_avg_int.*(TMP.Nuc_Area.^p);
 TMP.Nuc_DUSP1_avg_int_tot = TMP.Nuc_DUSP1_avg_int_tot/maxVal;
 TMP.Nuc_DUSP1_avg_int_tot = round(400*TMP.Nuc_DUSP1_avg_int_tot);
+
+totNucRNA = TMP.RNA_DUSP1_nuc;
+totNucRNA(~isnan(TMP.DUSP1_ts_size_0)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_0)) + TMP.DUSP1_ts_size_0(~isnan(TMP.DUSP1_ts_size_0));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_1)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_1)) + TMP.DUSP1_ts_size_1(~isnan(TMP.DUSP1_ts_size_1));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_2)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_2)) + TMP.DUSP1_ts_size_2(~isnan(TMP.DUSP1_ts_size_2));
+totNucRNA(~isnan(TMP.DUSP1_ts_size_3)) = totNucRNA(~isnan(TMP.DUSP1_ts_size_3)) + TMP.DUSP1_ts_size_3(~isnan(TMP.DUSP1_ts_size_3));
+TMP.totalNucRNA = totNucRNA;
+
 writetable(TMP,'pdoCalibrationData_EricIntensity_ConcHigh.csv')
diff --git a/...ete_dataframe_Ron_020224_NormalizedGR.csv → ...ete_dataframe_Ron_020224_NormalizedGR.csv b/...ete_dataframe_Ron_020224_NormalizedGR.csv → ...ete_dataframe_Ron_020224_NormalizedGR.csv
diff --git a/...an23_2024/Complete_dataframe_Ron_2024.csv → ...ablyTrash/Complete_dataframe_Ron_2024.csv b/...an23_2024/Complete_dataframe_Ron_2024.csv → ...ablyTrash/Complete_dataframe_Ron_2024.csv
diff --git a/...plete_dataframe_Ron_2024_NormalizedGR.csv → ...plete_dataframe_Ron_2024_NormalizedGR.csv b/...plete_dataframe_Ron_2024_NormalizedGR.csv → ...plete_dataframe_Ron_2024_NormalizedGR.csv
diff --git a/...plete_dataframe_Ron_2024_NormalizedGR.txt → ...plete_dataframe_Ron_2024_NormalizedGR.txt b/...plete_dataframe_Ron_2024_NormalizedGR.txt → ...plete_dataframe_Ron_2024_NormalizedGR.txt
diff --git a/WorkSpace/EricModel/EricData/oldProbablyTrash/DUSP1_fit_flitered_data_100nM_030624.csv b/WorkSpace/EricModel/EricData/oldProbablyTrash/DUSP1_fit_flitered_data_100nM_030624.csv
diff --git a/...an23_2024/DUSP1_predict_data_TPL_SSIT.csv → ...ablyTrash/DUSP1_predict_data_TPL_SSIT.csv b/...an23_2024/DUSP1_predict_data_TPL_SSIT.csv → ...ablyTrash/DUSP1_predict_data_TPL_SSIT.csv
diff --git a/...ct_flitered_data_03nM_1nM_10nM_030624.csv → ...ct_flitered_data_03nM_1nM_10nM_030624.csv b/...ct_flitered_data_03nM_1nM_10nM_030624.csv → ...ct_flitered_data_03nM_1nM_10nM_030624.csv
diff --git a/..._flitered_data_75min_ConcSweep_030624.csv → ..._flitered_data_75min_ConcSweep_030624.csv b/..._flitered_data_75min_ConcSweep_030624.csv → ..._flitered_data_75min_ConcSweep_030624.csv
diff --git a/WorkSpace/EricModel/EricData/oldProbablyTrash/Data010224_Gated_On_Nuc.csv b/WorkSpace/EricModel/EricData/oldProbablyTrash/Data010224_Gated_On_Nuc.csv
diff --git a/...ted_dataframe_Ron_020224_NormalizedGR.csv → ...ted_dataframe_Ron_020224_NormalizedGR.csv b/...ted_dataframe_Ron_020224_NormalizedGR.csv → ...ted_dataframe_Ron_020224_NormalizedGR.csv
diff --git a/...ataframe_Ron_020224_NormalizedGR_bins.csv → ...ataframe_Ron_020224_NormalizedGR_bins.csv b/...ataframe_Ron_020224_NormalizedGR_bins.csv → ...ataframe_Ron_020224_NormalizedGR_bins.csv
diff --git a/...ataframe_Ron_030624_NormalizedGR_bins.csv → ...ataframe_Ron_030624_NormalizedGR_bins.csv b/...ataframe_Ron_030624_NormalizedGR_bins.csv → ...ataframe_Ron_030624_NormalizedGR_bins.csv
diff --git a/WorkSpace/EricModel/EricData/oldProbablyTrash/pdoCalibrationData_EricIntensity.csv b/WorkSpace/EricModel/EricData/oldProbablyTrash/pdoCalibrationData_EricIntensity.csv
diff --git a/WorkSpace/EricModel/EricData/oldProbablyTrash/pdoCalibrationData_EricIntensity_100nM.csv b/WorkSpace/EricModel/EricData/oldProbablyTrash/pdoCalibrationData_EricIntensity_100nM.csv
diff --git a/...alibrationData_EricIntensity_ConcHigh.csv → ...alibrationData_EricIntensity_ConcHigh.csv b/...alibrationData_EricIntensity_ConcHigh.csv → ...alibrationData_EricIntensity_ConcHigh.csv
diff --git a/...ibrationData_EricIntensity_ConcSweeps.csv → ...ibrationData_EricIntensity_ConcSweeps.csv b/...ibrationData_EricIntensity_ConcSweeps.csv → ...ibrationData_EricIntensity_ConcSweeps.csv
diff --git a/...librationData_EricIntensity_DexSweeps.csv → ...librationData_EricIntensity_DexSweeps.csv b/...librationData_EricIntensity_DexSweeps.csv → ...librationData_EricIntensity_DexSweeps.csv
diff --git a/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity.csv b/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity.csv
diff --git a/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity_ConcHigh.csv b/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity_ConcHigh.csv
diff --git a/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity_ConcSweeps.csv b/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity_ConcSweeps.csv
diff --git a/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv b/WorkSpace/EricModel/EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv
diff --git a/WorkSpace/EricModel/EricDataJan23_2024/DUSP1_fit_flitered_data_100nM_030624.csv b/WorkSpace/EricModel/EricDataJan23_2024/DUSP1_fit_flitered_data_100nM_030624.csv
diff --git a/WorkSpace/EricModel/EricModelDusp1_MMDex.mat b/WorkSpace/EricModel/EricModelDusp1_MMDex.mat
diff --git a/WorkSpace/EricModel/RonModelPipelineJune16_2024.m b/WorkSpace/EricModel/RonModelPipelineJune16_2024.m
@@ -53,7 +53,7 @@
 ModelGRfit = cell(1,size(GRfitCases,1));
 ModelGRODEfit = cell(1,size(GRfitCases,1));
 for i=1:3
-    ModelGRfit{i} = ModelGR.loadData("EricDataJan23_2024/Gated_dataframe_Ron_030624_NormalizedGR_bins.csv",...
+    ModelGRfit{i} = ModelGR.loadData("EricData/Gated_dataframe_Ron_020224_NormalizedGR_bins.csv",...
         {'nucGR','normgrnuc';'cytGR','normgrcyt'},...
         {'Condition','GR_timesweep';'Dex_Conc',GRfitCases{i,2}});
     ModelGRfit{i}.parameters{13,2} = str2num(GRfitCases{i,1});    
@@ -136,8 +136,8 @@
 ModelDusp1parameterMap = cell(1,size(GRfitCases,1));
 for i = 1:size(Dusp1FitCases,1)
     % TODo - Adjust for newly processed data.
-    ModelDusp1Fit{i} = ModelGRDusp.loadData('EricDataJan23_2024/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
-        {'rna','RNA_DUSP1_nuc'},...
+    ModelDusp1Fit{i} = ModelGRDusp.loadData('EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
+        {'rna','totalNucRNA'},...
         {'Dex_Conc','100'}); 
     ModelDusp1Fit{i}.inputExpressions = {'IDex','Dex0*exp(-gDex*t)'};
 
@@ -148,8 +148,8 @@
 end
 DUSP1pars = [ModelDusp1Fit{i}.parameters{ModelGRDusp.fittingOptions.modelVarsToFit,2}];
 
-ModelGRDusp100nM = ModelGRDusp.loadData('EricDataJan23_2024/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
-        {'rna','RNA_DUSP1_nuc'},{'Dex_Conc','100'}); 
+ModelGRDusp100nM = ModelGRDusp.loadData('EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
+        {'rna','totalNucRNA'},{'Dex_Conc','100'}); 
 %%    Fit DUSP1 model(s) with single parameter set.
 % Specify prior on parameters.
 for i = 1:5
@@ -162,7 +162,7 @@
 end
 
 %%    Plot predictions for other Dex concentrations.
-showCases = [1,0,0,0];
+showCases = [0,0,1,0];
 makePlotsDUSP1(ModelDusp1Fit,ModelGRDusp,DUSP1pars,Dusp1FitCases,showCases)
 %% Sample uncertainty for Dusp1 Parameters
 %%    Compute sensitivity of the FSP solution
@@ -277,7 +277,7 @@
 
 %%    Calibrate PDO from Eric's DUSP1 Intensity Data.
 ModelPDOIntensEric = ModelGRDusp100nM;
-ModelPDOIntensEric = ModelPDOIntensEric.calibratePDO('EricDataJan23_2024/pdoCalibrationData_EricIntensity_ConcHigh.csv',...
+ModelPDOIntensEric = ModelPDOIntensEric.calibratePDO('EricData/pdoCalibrationData_EricIntensity_ConcHigh.csv',...
     {'rna'},{'RNA_DUSP1_nuc'},{'Nuc_DUSP1_avg_int_tot'},'AffinePoiss',true,[1,230,0.5]);
 
 %%  With PDO for MCP/smFISH
@@ -381,7 +381,7 @@
 % attempt to identify the model from just that data and at just the times
 % selected by the FIM.
 ModelPDOIntensEric.dataSet = [];
-ModelPDOIntensEric = ModelPDOIntensEric.loadData('EricDataJan23_2024/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
+ModelPDOIntensEric = ModelPDOIntensEric.loadData('EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
         {'rna','Nuc_DUSP1_avg_int_tot'},...
         {'Dex_Conc','100'}); 
 load('EricModelDusp1_MMDex','DUSP1parsIntensity') 
@@ -401,7 +401,7 @@
 % selected by the FIM.
 ModelPDOIntensEricFIM = ModelPDOIntensEric;
 ModelPDOIntensEricFIM.dataSet = [];
-ModelPDOIntensEricFIM = ModelPDOIntensEricFIM.loadData('EricDataJan23_2024/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
+ModelPDOIntensEricFIM = ModelPDOIntensEricFIM.loadData('EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
         {'rna','Nuc_DUSP1_avg_int_tot'},...
         {'Dex_Conc','100'}); 
 % Set fitting routine only to consider the time points selected by the FIM.
@@ -473,15 +473,17 @@
 
 %% Extend model to include cytoplasmic mRNA
 SSAModelCytoDusp1 = SSAModel;
+SSAModelCytoDusp1.ssaOptions.nSimsPerExpt = 20;
 SSAModelCytoDusp1.species = {'offGene';'onGene';'cytGR';'nucGR';'rna';'rCyt'};
 SSAModelCytoDusp1.initialCondition = [2;0;24;1;5;50];
 SSAModelCytoDusp1.propensityFunctions = {'kon*offGene*nucGR';'koff*onGene';
     '(kcn0 + (t>0)*kcn1*IDex/(MDex+IDex)) * cytGR';'knc*nucGR';'kg1';'gg1*cytGR';'gg2*nucGR';...
-    'kr*onGene';'gnuc*rna';...
+    'kr*onGene';'gnuc*rna/(1+(rna/50)^3)';...
     'ktr*rna';'gcyt*rCyt'};
-SSAModelCytoDusp1.parameters(4,:) = {'gnuc',0.01}; % add parameter for cytoplasmic decay
-SSAModelCytoDusp1.parameters(14,:) = {'gcyt',0.005}; % add parameter for cytoplasmic decay
-SSAModelCytoDusp1.parameters(15,:) = {'ktr',0.01896}; % add parameter for cytoplasmic decay
+gnuc = 0.00;
+SSAModelCytoDusp1.parameters(4,:) = {'gnuc',gnuc}; % add parameter for cytoplasmic decay
+SSAModelCytoDusp1.parameters(14,:) = {'gcyt',0.01}; % add parameter for cytoplasmic decay
+SSAModelCytoDusp1.parameters(15,:) = {'ktr',DUSP1pars(4)}; % add parameter for cytoplasmic decay
 SSAModelCytoDusp1.stoichiometry = [-1,1,0,0,0,0,0,0,0,0,0;...
                          1,-1,0,0,0,0,0,0,0,0,0;...
                          0,0,-1,1,1,-1,0,0,0,0,0;...
@@ -491,12 +493,12 @@
 
 SSAModelCytoDusp1 = SSAModelCytoDusp1.formPropensitiesGeneral('SSAEricCyt');
 ssaSolnCyt = SSAModelCytoDusp1.solve;
-
+%
 SSAModelCytoDusp1.makePlot(ssaSolnCyt,'meansAndDevs')
 
 %% Make plots of cytoplasmic RNA.
 tempCytModel = ModelGRDusp100nM;
-tempCytModel = tempCytModel.loadData('EricDataJan23_2024/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
+tempCytModel = tempCytModel.loadData('EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
         {'rna','RNA_DUSP1_cyto'},...
         {'Dex_Conc','100'}); 
 tempCytModel.makeFitPlot

diff --git a/WorkSpace/EricModel/RonModelPipelineMar11.m b/WorkSpace/EricModel/RonModelPipelineMar11.m
@@ -25,8 +25,8 @@
     'gg1',1e-5;'gg2',1e-6;'MDex',5;'Dex0',100});
 
 log10PriorMean = [-1 -1 0 -2,...
-    -1 -3 -2 -1 -2 -2 -2 0.5];
-log10PriorStd = ones(1,12);
+    -1 -3 -2 -1 -2 -2 -2 0.5, 2];
+log10PriorStd = ones(1,13);
 
 ModelGR.fspOptions.initApproxSS = true;
 
@@ -168,28 +168,57 @@
 end
 DUSP1pars = [ModelDusp1Fit{i}.parameters{ModelGRDusp.fittingOptions.modelVarsToFit,2}];
 
+%%
+ModelGRDusp100nM = ModelGRDusp.loadData('EricDataJan23_2024/DUSP1_fit_flitered_data_100nM_030624.csv',...
+        {'rna','RNA_DUSP1_nuc'}); 
 %%    Fit DUSP1 model(s) with single parameter set.
-for i = 1:5
-    fitOptions = optimset('Display','iter','MaxIter',50);
+duspLogPrior = @(x)-sum((log10(x(:))'-log10PriorMean(1:4)).^2./(2*log10PriorStd(1:4).^2));
+ModelGRDusp100nM.fittingOptions.logPrior = duspLogPrior;
+for i = 1%:5
+    fitOptions = optimset('Display','iter','MaxIter',100);
     fitOptions.suppressFSPExpansion = true;
-    combinedDusp1Model = SSITMultiModel(ModelDusp1Fit,ModelDusp1parameterMap);
-    combinedDusp1Model = combinedDusp1Model.initializeStateSpaces({[0;0;0;2;2;400]});
-    DUSP1pars = combinedDusp1Model.maximizeLikelihood(...
+    % combinedDusp1Model = SSITMultiModel(ModelDusp1Fit,ModelDusp1parameterMap,duspLogPrior);
+    % combinedDusp1Model = combinedDusp1Model.initializeStateSpaces({[0;0;0;2;2;400]});
+    DUSP1pars = ModelGRDusp100nM.maximizeLikelihood(...
         DUSP1pars, fitOptions);
+    ModelGRDusp100nM.parameters(1:4,2) = num2cell(DUSP1pars);
     ModelGRDusp.parameters(1:4,2) = num2cell(DUSP1pars);
-    save('EricModelDusp1_MMDex','DUSP1pars') 
+    % save('EricModelDusp1_MMDex','DUSP1pars') 
 end
 
 %% Sample uncertainty for Dusp1 Parameters
-% MHFitOptions.thin=1;
-% MHFitOptions.numberOfSamples=100;
-% MHFitOptions.burnIn=0;
-% MHFitOptions.progress=true;
-% MHFitOptions.proposalDistribution=@(x)x+0.01*randn(size(x));
-% MHFitOptions.numChains = 1;
-% MHFitOptions.saveFile = 'TMPEricMHDusp1.mat';
-% [~,~,MHResultsDusp1] = combinedDusp1Model.maximizeLikelihood(...
-%     DUSP1pars, MHFitOptions, 'MetropolisHastings');
+% specify prior on parameter values
+
+%      Compute FIM
+% fignums = [211,221,201,231];
+% combinedDusp1Model = combinedDusp1Model.updateModels(DUSP1pars,false,fignums);
+fimResults = ModelGRDusp100nM.computeFIM([],'log');
+fimTotal = ModelGRDusp100nM.evaluateExperiment(fimResults,ModelGRDusp100nM.dataSet.nCells,...
+    diag(log10PriorStd))
+
+% Run Metropolis Hastings Search
+FIMfree = fimTotal{1}(1:4,1:4);
+if min(eig(FIMfree))<1
+    disp('Warning -- FIM has one or more small eigenvalues.  Reducing proposal width to 10x in those directions. MH Convergence may be slow.')
+    FIMfree = FIMfree + 1*eye(length(FIMfree));
+end
+covFree = FIMfree^-1;
+covFree = 0.5*(covFree+covFree');
+%%
+MHFitOptions.proposalDistribution=@(x)mvnrnd(x,covFree);
+MHFitOptions.thin=1;
+MHFitOptions.numberOfSamples=100;
+MHFitOptions.burnIn=0;
+MHFitOptions.progress=true;
+MHFitOptions.numChains = 1;
+MHFitOptions.saveFile = 'TMPEricMHDusp1.mat';
+[DUSP1pars,~,MHResultsDusp1] = ModelGRDusp100nM.maximizeLikelihood(...
+    [], MHFitOptions, 'MetropolisHastings');
+delete('TMPEricMHDusp1.mat')
+%
+ModelGRDusp100nM.parameters(1:4,2) = num2cell(DUSP1pars);
+figNew = figure;
+ModelGRDusp100nM.plotMHResults(MHResultsDusp1,[FIMfree],'log',[],figNew)
 
 %%    Make Plots of DUSP1 FIT Results
 fignums = [211,221,201,231];

diff --git a/WorkSpace/EricModel/makePlotsDUSP1.m b/WorkSpace/EricModel/makePlotsDUSP1.m
@@ -27,8 +27,8 @@ function makePlotsDUSP1(ModelDusp1Fit,ModelGRDusp,DUSP1pars,Dusp1FitCases,showCa
         313,323,303,333];
     ModelPred = cell(size(Dusp1FitCases,1),1);
     for i=1:size(PredictionCases,1)
-        ModelPred{i} = ModelGRDusp.loadData('EricDataJan23_2024/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
-            {'rna','RNA_DUSP1_nuc'},...
+        ModelPred{i} = ModelGRDusp.loadData('EricData/pdoCalibrationData_EricIntensity_DexSweeps.csv',...
+            {'rna','totalNucRNA'},...
             {'Dex_Conc',PredictionCases{i,2}});
 
         ModelPred{i}.tSpan = sort(unique([ModelPred{i}.tSpan,linspace(0,180,30)]));
@@ -57,8 +57,8 @@ function makePlotsDUSP1(ModelDusp1Fit,ModelGRDusp,DUSP1pars,Dusp1FitCases,showCa
     for i=1:length(DexConc)
         ModelPredDexTtr = ModelGRDusp;
         ModelPredDexTtr.dataSet = [];
-        ModelPredDexTtr = ModelPredDexTtr.loadData('EricDataJan23_2024/pdoCalibrationData_EricIntensity_ConcSweeps.csv',...
-            {'rna','RNA_DUSP1_nuc'},...
+        ModelPredDexTtr = ModelPredDexTtr.loadData('EricData/pdoCalibrationData_EricIntensity_ConcSweeps.csv',...
+            {'rna','totalNucRNA'},...
             {'Dex_Conc',DecConcStr{i}});
 
         % Set model parameters to those supplied
@@ -117,8 +117,8 @@ function makePlotsDUSP1(ModelDusp1Fit,ModelGRDusp,DUSP1pars,Dusp1FitCases,showCa
     ModelPredDexTplSoln = cell(size(PredictionCases,1),1);
     for i=1:size(PredictionCases,1)
         ModelPredDexTpl{i}.dataSet = [];
-        ModelPredDexTpl{i} = ModelGRDusp.loadData('EricDataJan23_2024/DUSP1_predict_data_TPL_SSIT.csv',...
-            {'rna','RNA_DUSP1_nuc'},...
+        ModelPredDexTpl{i} = ModelGRDusp.loadData('EricData/DUSP1_predict_data_TPL_SSIT.csv',...
+            {'rna','totalNucRNA'},...
             {['tryptCond',num2str(i)],num2str(i)});
 
         % Set model parameters to those supplied