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Commit f1e72144 by Chiara Antonini
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update code

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Showing 8 changed files with 127 additions and 69 deletions
CRA_Updated_Version/CRA_Toolbox_bash/Examples/parameters_EGFR_IGF1R_model.m 0 → 100644
% Model parameters
gamma_EGFR=0.02;
gamma_IGF1R=0.02;
kd_PIK3_active=0.005;
k_p90Rsk_Erk=0.0213697;
KM_p90Rsk_Erk=763523;
k_SOS_EGFR=694.731;
KM_SOS_EGFR=6086070;
k_Ras_SOS=32.344;
KM_Ras_SOS=35954.3;
k_ERK_MEK=9.85367;
KM_ERK_MEK=1007340;
k_DSOS_p90Rsk=161197;
KM_DSOS_p90Rsk=896896;
k_SOS_IGF1R=500;
KM_SOS_IGF1R=100000;
k_PIK3_IGF1R=10.6737;
KM_PIK3_IGF1R=184912;
k_PIK3_EGFR=10.6737;
KM_PIK3_EGFR=184912;
k_Akt_PIK3=0.0566279;
KM_Akt_PIK3=653951;
kd_Akt=0.005;
k_Erk_PP2A=9.85367;
KM_Erk_PP2A=1007340;
k_PIK3_Ras=0.0771067;
KM_PIK3_Ras=272056;
k_Raf_Ras=0.884096;
KM_Raf_Ras=62464.6;
k_Mek_Raf=185.759;
KM_Mek_Raf=4768350;
k_Raf_Akt=15.1212;
KM_Raf_Akt=119355;
k_Ras_RasGab=1509.36;
KM_Ras_RasGab=1432410;
k_MEK_PP2A=2.83243;
KM_MEK_PP2A=518753;
k_Raf_RafPP=0.126329;
KM_Raf_RafPP=1061.71;
kd_P90Rsk=0.005;
% Input values
RafPP=120000;
PP2A=120000;
RasGapActive=120000;
% Total concentrations
DSOS_tot=120000.0;
Ras_tot=120000.0;
Raf_tot=120000.0;
Mek_tot=600000.0;
Erk_tot=600000.0;
p90Rsk_tot=120000.0;
PIK3_tot=120000.0;
Akt_tot=120000.0;
% Initial conditions for state variables
EGFR_active_0=8000.0;
IGF1R_active_0=650.0;
SOS_0=0.0;
Ras_active_0=0.0;
Raf_active_0=0.0;
Mek_active_0=0.0;
Erk_active_0=0.0;
p90Rsk_active_0=0.0;
PIK3_active_0=0.0;
Akt_active_0=0.0;
CRA_Updated_Version/CRA_Toolbox_bash/compute_MIRI.m
...@@ -29,21 +29,21 @@ ...@@ -29,21 +29,21 @@
function compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,AllDerivedParam,folder) function compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,folder)
nominal_parameters=model.nominal_parameters; nominal_parameters=model.nominal_parameters;
%num_parameters=length(nominal_parameters); num_parameters=length(nominal_parameters);
nominal_parameters_name=model.nominal_parameters_name; parameters_name=model.parameters_name;
if(isfield(model,'derived_parameters')) % if(isfield(model,'derived_parameters'))
derived_parameters=model.derived_parameters; % derived_parameters=model.derived_parameters;
derived_parameters_name=model.derived_parameters_name; % derived_parameters_name=model.derived_parameters_name;
num_parameters=length(nominal_parameters)+length(derived_parameters); % num_parameters=length(nominal_parameters)+length(derived_parameters);
parameters_name=[nominal_parameters_name derived_parameters_name]; % parameters_name=[nominal_parameters_name derived_parameters_name];
else % else
num_parameters=length(nominal_parameters); % num_parameters=length(nominal_parameters);
parameters_name=[nominal_parameters_name]; % parameters_name=[nominal_parameters_name];
end % end
obs_name=model.observables_name; obs_name=model.observables_name;
...@@ -124,7 +124,7 @@ try ...@@ -124,7 +124,7 @@ try
Results.currentTailMethod=current_tm; Results.currentTailMethod=current_tm;
[XiMax,XiMin]=Results.compute_tail(AllPerturbations{k,1},tail_size); [XiMax,XiMin]=Results.compute_tail(AllPerturbations{k,1},tail_size);
[XiMaxD,XiMinD]=Results.compute_tail(AllDerivedParam{k,1},tail_size); %[XiMaxD,XiMinD]=Results.compute_tail(AllDerivedParam{k,1},tail_size);
%[XiMax,XiMin]=handles.Results.compute_tail(handles1.perturbation,handles.tail_size); %[XiMax,XiMin]=handles.Results.compute_tail(handles1.perturbation,handles.tail_size);
NcloudMax=size(XiMax,1); NcloudMax=size(XiMax,1);
...@@ -138,17 +138,17 @@ try ...@@ -138,17 +138,17 @@ try
%[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin); %[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin);
[MIRI_param,CloudCondMin, CloudCondMax]=obj_MIRI.MIRI_computation(all_ks_max,all_ks_min,all_xbin_max,all_xbin_min); [MIRI_param,CloudCondMin, CloudCondMax]=obj_MIRI.MIRI_computation(all_ks_max,all_ks_min,all_xbin_max,all_xbin_min);
if(isfield(model,'derived_parameters')) % if(isfield(model,'derived_parameters'))
obj_MIRI_derived=MIRI(); % obj_MIRI_derived=MIRI();
[all_xbin_max_d,all_xbin_min_d,all_ks_max_d,all_ks_min_d]=obj_MIRI_derived.estimate_parampdfs(derived_parameters, AllDerivedParam{k,1}, XiMaxD, XiMinD); % [all_xbin_max_d,all_xbin_min_d,all_ks_max_d,all_ks_min_d]=obj_MIRI_derived.estimate_parampdfs(derived_parameters, AllDerivedParam{k,1}, XiMaxD, XiMinD);
%[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin); % %[all_xbin_max,all_xbin_min,all_ks_max,all_ks_min]=obj_MIRI.estimate_parampdfs(handles1.nominal_p, handles1.perturbation, Ncloud, handles.XiMax, handles.XiMin);
[MIRI_param_d,CloudCondMin_d, CloudCondMax_d]=obj_MIRI_derived.MIRI_computation(all_ks_max_d,all_ks_min_d,all_xbin_max_d,all_xbin_min_d); % [MIRI_param_d,CloudCondMin_d, CloudCondMax_d]=obj_MIRI_derived.MIRI_computation(all_ks_max_d,all_ks_min_d,all_xbin_max_d,all_xbin_min_d);
%
%
MIRI_param=[MIRI_param MIRI_param_d]; % MIRI_param=[MIRI_param MIRI_param_d];
CloudCondMax=[CloudCondMax CloudCondMax_d]; % CloudCondMax=[CloudCondMax CloudCondMax_d];
CloudCondMin=[CloudCondMin CloudCondMin_d]; % CloudCondMin=[CloudCondMin CloudCondMin_d];
end % end
MIRIT(k,:)=MIRI_param; MIRIT(k,:)=MIRI_param;
...@@ -164,14 +164,14 @@ try ...@@ -164,14 +164,14 @@ try
ks_param{2,k}(ip,:)=all_ks_min(ip,:); ks_param{2,k}(ip,:)=all_ks_min(ip,:);
end end
if(isfield(model,'derived_parameters')) % if(isfield(model,'derived_parameters'))
for ip=1:length(derived_parameters) % for ip=1:length(derived_parameters)
xbin_param_d{1,k}(ip,:)=all_xbin_max_d(ip,:); % xbin_param_d{1,k}(ip,:)=all_xbin_max_d(ip,:);
xbin_param_d{2,k}(ip,:)=all_xbin_min_d(ip,:); % xbin_param_d{2,k}(ip,:)=all_xbin_min_d(ip,:);
ks_param_d{1,k}(ip,:)=all_ks_max_d(ip,:); % ks_param_d{1,k}(ip,:)=all_ks_max_d(ip,:);
ks_param_d{2,k}(ip,:)=all_ks_min_d(ip,:); % ks_param_d{2,k}(ip,:)=all_ks_min_d(ip,:);
end % end
end % end
end end
...@@ -210,9 +210,9 @@ try ...@@ -210,9 +210,9 @@ try
disp('saving probability density functions of all parameters') disp('saving probability density functions of all parameters')
save(fullfile(folder,variable_name,'pdf_param.mat'),'xbin_param','ks_param'); save(fullfile(folder,variable_name,'pdf_param.mat'),'xbin_param','ks_param');
if(isfield(model,'derived_parameters')) % if(isfield(model,'derived_parameters'))
save(fullfile(folder,variable_name,'pdf_param_derived.mat'),'xbin_param_d','ks_param_d'); % save(fullfile(folder,variable_name,'pdf_param_derived.mat'),'xbin_param_d','ks_param_d');
end % end
catch ME catch ME
......
CRA_Updated_Version/CRA_Toolbox_bash/main_EGFRIGF1Rmodel.m
...@@ -83,15 +83,15 @@ xT=[DSOS_tot Ras_tot Raf_tot Mek_tot Erk_tot p90Rsk_tot PIK3_tot Akt_tot]; ...@@ -83,15 +83,15 @@ xT=[DSOS_tot Ras_tot Raf_tot Mek_tot Erk_tot p90Rsk_tot PIK3_tot Akt_tot];
model=struct('name',model_name,'odesolver',ode_solver,'time',time_axis,'stop',stop_time,'step',step_size,'nominal_parameters',nominal_parameters,'parameters_name',{parameters_name},'num_observables',num_observables,'observables_name',{observables_name},'initial_conditions',x0,'input',u,'total_proteins',xT); model=struct('name',model_name,'odesolver',ode_solver,'time',time_axis,'stop',stop_time,'step',step_size,'nominal_parameters',nominal_parameters,'parameters_name',{parameters_name},'num_observables',num_observables,'observables_name',{observables_name},'initial_conditions',x0,'input',u,'total_proteins',xT);
Nr=100; Nr=3;
LBpi=0.1; LBpi=0.1;
UBpi=10; UBpi=10;
Ns=10000; Ns=1000;
variable_name='Erk_active'; variable_name='Erk_active';
current_func=Area(); %current evaluation function current_func=Area(); %current evaluation function
tail_size=1000; %number of samples for the lower and upper tail tail_size=10; %number of samples for the lower and upper tail
step_size=0.01; %this parameter needs to be defined only when current_tm=tmp_sum(step_size) step_size=0.01; %this parameter needs to be defined only when current_tm=tmp_sum(step_size)
current_tm=tmp_sum(step_size); current_tm=tmp_sum(step_size);
...@@ -108,7 +108,7 @@ disp('Starting computation of the MIRI for each parameter...'); ...@@ -108,7 +108,7 @@ disp('Starting computation of the MIRI for each parameter...');
try try
compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,folder) compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,folder)
catch ME catch ME
break return
end end
%plot and save probability density function of the evaluation function %plot and save probability density function of the evaluation function
disp('Plot of the probability density function of the chosen evaluation function'); disp('Plot of the probability density function of the chosen evaluation function');
......
CRA_Updated_Version/CRA_Toolbox_bash/main_PulseGeneratorNetwork.m
...@@ -64,21 +64,21 @@ parameters_name={'k1','K1','lambda2','k12','K2','lambda'}; ...@@ -64,21 +64,21 @@ parameters_name={'k1','K1','lambda2','k12','K2','lambda'};
x0=[0 0]; x0=[0 0];
u=470; u=470;
num_observables=2; num_observables=2;
observables_name={'R1','Y'}; observables_name={'R2','Y'};
model=struct('name',model_name,'odesolver',ode_solver,'time',time_axis,'stop',stop_time,'step',step_size,'nominal_parameters',nominal_parameters,'nominal_parameters_name',{parameters_name},'num_observables',num_observables,'observables_name',{observables_name},'initial_conditions',x0,'input',u,'total_proteins',0); model=struct('name',model_name,'odesolver',ode_solver,'time',time_axis,'stop',stop_time,'step',step_size,'nominal_parameters',nominal_parameters,'parameters_name',{parameters_name},'num_observables',num_observables,'observables_name',{observables_name},'initial_conditions',x0,'input',u,'total_proteins',0);
Nr=2; Nr=10;
folder='2014sortedprovaparfor_PulseGeneratorNetwork_results'; folder='2014sortedprovaparfor_PulseGeneratorNetwork_results';
LBpi=0.1; LBpi=0.1;
UBpi=10; UBpi=10;
Ns=3000; Ns=1000;
variable_name='Y'; variable_name='Y';
current_func=Area(); %current evaluation function current_func=TimeOfMaximum(); %current evaluation function
tail_size=1000; %number of samples for the lower and upper tail tail_size=100; %number of samples for the lower and upper tail
step_size=0.1; %this parameter needs to be defined only when current_tm=tmp_sum(step_size) step_size=0.1; %this parameter needs to be defined only when current_tm=tmp_sum(step_size)
%current_tm=tmp_sum(0.1); %current_tm=tmp_sum(0.1);
current_tm=sorted(); current_tm=sorted();
...@@ -92,8 +92,7 @@ disp('All done! Model simulation completed!'); ...@@ -92,8 +92,7 @@ disp('All done! Model simulation completed!');
%variable %variable
disp('Starting computation of the MIRI for each parameter...'); disp('Starting computation of the MIRI for each parameter...');
try try
AllDerivedParam=cell(Nr,1); compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,folder)
compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,AllDerivedParam,folder)
catch ME catch ME
%break %break
return return
......
CRA_Updated_Version/CRA_Toolbox_bash/main_modelPeng2016.m
...@@ -66,11 +66,11 @@ observables_name={'A','X1','X2','D_m','C2','R2','I2','D_C','D_R','C1','R1','I1'} ...@@ -66,11 +66,11 @@ observables_name={'A','X1','X2','D_m','C2','R2','I2','D_C','D_R','C1','R1','I1'}
model=struct('name',model_name,'odesolver',ode_solver,'time',time_axis,'stop',stop_time,'step',step_size,'nominal_parameters',nominal_parameters,'parameters_name',{parameters_name},'num_observables',num_observables,'observables_name',{observables_name},'initial_conditions',x0,'input',0,'total_proteins',0); model=struct('name',model_name,'odesolver',ode_solver,'time',time_axis,'stop',stop_time,'step',step_size,'nominal_parameters',nominal_parameters,'parameters_name',{parameters_name},'num_observables',num_observables,'observables_name',{observables_name},'initial_conditions',x0,'input',0,'total_proteins',0);
Nr=100; Nr=10;
LBpi=0.1; LBpi=0.1;
UBpi=10; UBpi=10;
Ns=10000; Ns=100;
variable_name='C1'; variable_name='C1';
current_func=Area(); %current evaluation function current_func=Area(); %current evaluation function
...@@ -91,7 +91,7 @@ disp('Starting computation of the MIRI for each parameter...'); ...@@ -91,7 +91,7 @@ disp('Starting computation of the MIRI for each parameter...');
try try
compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,folder) compute_MIRI(model,variable_name,current_func,tail_size,current_tm,Nr,Ns,AllResults,AllPerturbations,folder)
catch ME catch ME
break return
end end
%plot and save probability density function of the evaluation function %plot and save probability density function of the evaluation function
disp('Plot of the probability density function of the chosen evaluation function'); disp('Plot of the probability density function of the chosen evaluation function');
......
CRA_Updated_Version/CRA_Toolbox_bash/plotpdf_param.m
...@@ -7,10 +7,7 @@ ...@@ -7,10 +7,7 @@
function plotpdf_param(folder,variable_name,model,Nr) function plotpdf_param(folder,variable_name,model,Nr)
nominal_parameters=model.nominal_parameters; nominal_parameters=model.nominal_parameters;
nominal_parameters_name=model.nominal_parameters_name; nominal_parameters_name=model.parameters_name;
derived_parameters=model.derived_parameters;
derived_parameters_name=model.derived_parameters_name;
try try
load(fullfile(folder,variable_name,'pdf_param.mat')); load(fullfile(folder,variable_name,'pdf_param.mat'));
...@@ -26,20 +23,6 @@ derived_parameters_name=model.derived_parameters_name; ...@@ -26,20 +23,6 @@ derived_parameters_name=model.derived_parameters_name;
legend('Conditional upper density','Conditional lower density'); legend('Conditional upper density','Conditional lower density');
savefig(fullfile(folder,variable_name,nominal_parameters_name{1,i})); savefig(fullfile(folder,variable_name,nominal_parameters_name{1,i}));
end end
load(fullfile(folder,variable_name,'pdf_param_derived.mat'));
for i=1:length(derived_parameters)
figure
for k=1:Nr
plot(xbin_param_d{1,k}(i,:),ks_param_d{1,k}(i,:),'b',xbin_param_d{2,k}(i,:),ks_param_d{2,k}(i,:),'r');
hold on
end
xlabel(derived_parameters_name{1,i},'Interpreter','none');
ylabel('pdf');
legend('Conditional upper density','Conditional lower density');
savefig(fullfile(folder,variable_name,derived_parameters_name{1,i}));
end
catch ME catch ME
errordlg(ME.message) errordlg(ME.message)
end end
......
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