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Commit f1e72144
authored
2020-09-21 17:42:02 +0200
by
Chiara Antonini
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update code
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8 changed files
with
126 additions
and
68 deletions
CRA_Updated_Version/CRA_Toolbox_GUI/cra_steps_gui.docx
CRA_Updated_Version/CRA_Toolbox_bash/Examples/parameters_EGFR_IGF1R_model.m
CRA_Updated_Version/CRA_Toolbox_bash/compute_MIRI.m
CRA_Updated_Version/CRA_Toolbox_bash/cra_steps_bash.docx
CRA_Updated_Version/CRA_Toolbox_bash/main_EGFRIGF1Rmodel.m
CRA_Updated_Version/CRA_Toolbox_bash/main_PulseGeneratorNetwork.m
CRA_Updated_Version/CRA_Toolbox_bash/main_modelPeng2016.m
CRA_Updated_Version/CRA_Toolbox_bash/plotpdf_param.m
CRA_Updated_Version/CRA_Toolbox_GUI/cra_steps_gui.docx
0 → 100644
View file @
f1e7214
No preview for this file type
CRA_Updated_Version/CRA_Toolbox_bash/Examples/parameters_EGFR_IGF1R_model.m
0 → 100644
View file @
f1e7214
% 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
View file @
f1e7214
...
...
@@ -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
;
%
num_parameters=length(nominal_parameters);
nominal_parameters_name
=
model
.
nominal_
parameters_name
;
num_parameters
=
length
(
nominal_parameters
);
parameters_name
=
model
.
parameters_name
;
if
(
isfield
(
model
,
'derived_parameters'
))
derived_parameters
=
model
.
derived_parameters
;
derived_parameters_name
=
model
.
derived_parameters_name
;
num_parameters
=
length
(
nominal_parameters
)
+
length
(
derived_parameters
);
parameters_name
=
[
nominal_parameters_name
derived_parameters_name
];
else
num_parameters
=
length
(
nominal_parameters
);
parameters_name
=
[
nominal_parameters_name
];
end
%
if(isfield(model,'derived_parameters'))
%
derived_parameters=model.derived_parameters;
%
derived_parameters_name=model.derived_parameters_name;
%
num_parameters=length(nominal_parameters)+length(derived_parameters);
%
parameters_name=[nominal_parameters_name derived_parameters_name];
%
else
%
num_parameters=length(nominal_parameters);
%
parameters_name=[nominal_parameters_name];
%
end
obs_name
=
model
.
observables_name
;
...
...
@@ -124,7 +124,7 @@ try
Results
.
currentTailMethod
=
current_tm
;
[
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);
NcloudMax
=
size
(
XiMax
,
1
);
...
...
@@ -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);
[
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'
))
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,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
=
[
MIRI_param
MIRI_param_d
];
CloudCondMax
=
[
CloudCondMax
CloudCondMax_d
];
CloudCondMin
=
[
CloudCondMin
CloudCondMin_d
];
end
%
if(isfield(model,'derived_parameters'))
%
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,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=[MIRI_param MIRI_param_d];
%
CloudCondMax=[CloudCondMax CloudCondMax_d];
%
CloudCondMin=[CloudCondMin CloudCondMin_d];
%
end
MIRIT
(
k
,:)
=
MIRI_param
;
...
...
@@ -164,14 +164,14 @@ try
ks_param
{
2
,
k
}(
ip
,:)
=
all_ks_min
(
ip
,:);
end
if
(
isfield
(
model
,
'derived_parameters'
))
for
ip
=
1
:
length
(
derived_parameters
)
xbin_param_d
{
1
,
k
}(
ip
,:)
=
all_xbin_max_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
{
2
,
k
}(
ip
,:)
=
all_ks_min_d
(
ip
,:);
end
end
%
if(isfield(model,'derived_parameters'))
%
for ip=1:length(derived_parameters)
%
xbin_param_d{1,k}(ip,:)=all_xbin_max_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{2,k}(ip,:)=all_ks_min_d(ip,:);
%
end
%
end
end
...
...
@@ -210,9 +210,9 @@ try
disp
(
'saving probability density functions of all parameters'
)
save
(
fullfile
(
folder
,
variable_name
,
'pdf_param.mat'
),
'xbin_param'
,
'ks_param'
);
if
(
isfield
(
model
,
'derived_parameters'
))
save
(
fullfile
(
folder
,
variable_name
,
'pdf_param_derived.mat'
),
'xbin_param_d'
,
'ks_param_d'
);
end
%
if(isfield(model,'derived_parameters'))
%
save(fullfile(folder,variable_name,'pdf_param_derived.mat'),'xbin_param_d','ks_param_d');
%
end
catch
ME
...
...
CRA_Updated_Version/CRA_Toolbox_bash/cra_steps_bash.docx
0 → 100644
View file @
f1e7214
No preview for this file type
CRA_Updated_Version/CRA_Toolbox_bash/main_EGFRIGF1Rmodel.m
View file @
f1e7214
...
...
@@ -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
);
Nr
=
100
;
Nr
=
3
;
LBpi
=
0.1
;
UBpi
=
10
;
Ns
=
1000
0
;
Ns
=
1000
;
variable_name
=
'Erk_active'
;
current_func
=
Area
();
%current evaluation function
tail_size
=
10
00
;
%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)
current_tm
=
tmp_sum
(
step_size
);
...
...
@@ -108,7 +108,7 @@ disp('Starting computation of the MIRI for each parameter...');
try
compute_MIRI
(
model
,
variable_name
,
current_func
,
tail_size
,
current_tm
,
Nr
,
Ns
,
AllResults
,
AllPerturbations
,
folder
)
catch
ME
break
return
end
%plot and save probability density function of the evaluation function
disp
(
'Plot of the probability density function of the chosen evaluation function'
);
...
...
CRA_Updated_Version/CRA_Toolbox_bash/main_PulseGeneratorNetwork.m
View file @
f1e7214
...
...
@@ -64,21 +64,21 @@ parameters_name={'k1','K1','lambda2','k12','K2','lambda'};
x0
=
[
0
0
];
u
=
470
;
num_observables
=
2
;
observables_name
=
{
'R
1
'
,
'Y'
};
observables_name
=
{
'R
2
'
,
'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'
;
LBpi
=
0.1
;
UBpi
=
10
;
Ns
=
3
000
;
Ns
=
1
000
;
variable_name
=
'Y'
;
current_func
=
Area
();
%current evaluation function
tail_size
=
100
0
;
%number of samples for the lower and upper tail
current_func
=
TimeOfMaximum
();
%current evaluation function
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)
%current_tm=tmp_sum(0.1);
current_tm
=
sorted
();
...
...
@@ -92,8 +92,7 @@ disp('All done! Model simulation completed!');
%variable
disp
(
'Starting computation of the MIRI for each parameter...'
);
try
AllDerivedParam
=
cell
(
Nr
,
1
);
compute_MIRI
(
model
,
variable_name
,
current_func
,
tail_size
,
current_tm
,
Nr
,
Ns
,
AllResults
,
AllPerturbations
,
AllDerivedParam
,
folder
)
compute_MIRI
(
model
,
variable_name
,
current_func
,
tail_size
,
current_tm
,
Nr
,
Ns
,
AllResults
,
AllPerturbations
,
folder
)
catch
ME
%break
return
...
...
CRA_Updated_Version/CRA_Toolbox_bash/main_modelPeng2016.m
View file @
f1e7214
...
...
@@ -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
);
Nr
=
10
0
;
Nr
=
10
;
LBpi
=
0.1
;
UBpi
=
10
;
Ns
=
100
00
;
Ns
=
100
;
variable_name
=
'C1'
;
current_func
=
Area
();
%current evaluation function
...
...
@@ -91,7 +91,7 @@ disp('Starting computation of the MIRI for each parameter...');
try
compute_MIRI
(
model
,
variable_name
,
current_func
,
tail_size
,
current_tm
,
Nr
,
Ns
,
AllResults
,
AllPerturbations
,
folder
)
catch
ME
break
return
end
%plot and save probability density function of the evaluation function
disp
(
'Plot of the probability density function of the chosen evaluation function'
);
...
...
CRA_Updated_Version/CRA_Toolbox_bash/plotpdf_param.m
View file @
f1e7214
...
...
@@ -7,10 +7,7 @@
function
plotpdf_param
(
folder
,
variable_name
,
model
,
Nr
)
nominal_parameters
=
model
.
nominal_parameters
;
nominal_parameters_name
=
model
.
nominal_parameters_name
;
derived_parameters
=
model
.
derived_parameters
;
derived_parameters_name
=
model
.
derived_parameters_name
;
nominal_parameters_name
=
model
.
parameters_name
;
try
load
(
fullfile
(
folder
,
variable_name
,
'pdf_param.mat'
));
...
...
@@ -26,20 +23,6 @@ derived_parameters_name=model.derived_parameters_name;
legend
(
'Conditional upper density'
,
'Conditional lower density'
);
savefig
(
fullfile
(
folder
,
variable_name
,
nominal_parameters_name
{
1
,
i
}));
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
errordlg
(
ME
.
message
)
end
...
...
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