update formats

hetalang · Jul 27, 2021 · b4bef0f · b4bef0f
1 parent bcdfd08
commit b4bef0f
Show file tree

Hide file tree

Showing 42 changed files with 123 additions and 117 deletions.
diff --git a/boehm/measurements.csv b/boehm/measurements.csv
@@ -1,4 +1,4 @@
-t,measurement,scope,parameters.mean,parameters.sigma,condition,distribution
+t,measurement,scope,prob.mean,prob.sigma,condition,prob.type
 0,7.901072999,start_,pSTAT5A_rel,sd_pSTAT5A_rel,first,normal
 2.5,66.36349397,ode_,pSTAT5A_rel,sd_pSTAT5A_rel,first,normal
 5,81.17132392,ode_,pSTAT5A_rel,sd_pSTAT5A_rel,first,normal

diff --git a/boehm/run.jl b/boehm/run.jl
@@ -37,5 +37,5 @@ fit1 = fit(p, fit_cons; alg = CVODE_BDF()) # default algorithm doesn't work
 ################################## plot fitted #################
 
 sim(p) |> plot # default
-sim(p, constants = fit2.optim) |> plot # best fit XXX: how to update!? constants
-sim(p, constants = [:k_phos=>1000.]) |> plot # modified plot
+sim(p, parameters_upd = fit1.optim) |> plot # best fit
+sim(p, parameters_upd = [:k_phos=>1000.]) |> plot # modified plot
diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_ActD0_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_ActD0_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.730879658,pJAK2_au,sd_JAK2EpoR_au,task4_0,normal
 ode_,5,0,pJAK2_au,sd_JAK2EpoR_au,task4_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_ActD1_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_ActD1_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.652707226,pJAK2_au,sd_JAK2EpoR_au,task4_1,normal
 ode_,5,-0.225855653,pJAK2_au,sd_JAK2EpoR_au,task4_1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_CISoe0_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_CISoe0_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.572311287,pJAK2_au,sd_JAK2EpoR_au,task6_0,normal
 ode_,10,0,pJAK2_au,sd_JAK2EpoR_au,task6_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_CISoe1_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_CISoe1_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.749347693,pJAK2_au,sd_JAK2EpoR_au,task6_1,normal
 ode_,10,-0.077804717,pJAK2_au,sd_JAK2EpoR_au,task6_1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_CISoe_pEpoR0_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_CISoe_pEpoR0_log10-mod.csv
@@ -1,7 +1,7 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
-start_,0,-0.889772501,pEpoR_au,sd_JAK2EpoR_au,task7_0,nornal
-ode_,5,0,pEpoR_au,sd_JAK2EpoR_au,task7_0,nornal
-ode_,10,-0.053336448,pEpoR_au,sd_JAK2EpoR_au,task7_0,nornal
-ode_,60,-0.502231975,pEpoR_au,sd_JAK2EpoR_au,task7_0,nornal
-ode_,120,-0.673914115,pEpoR_au,sd_JAK2EpoR_au,task7_0,nornal
+start_,0,-0.889772501,pEpoR_au,sd_JAK2EpoR_au,task7_0,normal
+ode_,5,0,pEpoR_au,sd_JAK2EpoR_au,task7_0,normal
+ode_,10,-0.053336448,pEpoR_au,sd_JAK2EpoR_au,task7_0,normal
+ode_,60,-0.502231975,pEpoR_au,sd_JAK2EpoR_au,task7_0,normal
+ode_,120,-0.673914115,pEpoR_au,sd_JAK2EpoR_au,task7_0,normal
diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_CISoe_pEpoR1_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_CISoe_pEpoR1_log10-mod.csv
@@ -1,7 +1,7 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
-start_,0,-0.938968891,pEpoR_au,sd_JAK2EpoR_au,task7_1,nornal
-ode_,5,-0.482734186,pEpoR_au,sd_JAK2EpoR_au,task7_1,nornal
-ode_,10,-0.574379959,pEpoR_au,sd_JAK2EpoR_au,task7_1,nornal
-ode_,60,-0.636125555,pEpoR_au,sd_JAK2EpoR_au,task7_1,nornal
-ode_,120,-0.753095362,pEpoR_au,sd_JAK2EpoR_au,task7_1,nornal
+start_,0,-0.938968891,pEpoR_au,sd_JAK2EpoR_au,task7_1,normal
+ode_,5,-0.482734186,pEpoR_au,sd_JAK2EpoR_au,task7_1,normal
+ode_,10,-0.574379959,pEpoR_au,sd_JAK2EpoR_au,task7_1,normal
+ode_,60,-0.636125555,pEpoR_au,sd_JAK2EpoR_au,task7_1,normal
+ode_,120,-0.753095362,pEpoR_au,sd_JAK2EpoR_au,task7_1,normal
diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_Concentrations_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_Concentrations_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,1.797151886,STAT5_abs,sd_STAT5_abs,task2,normal
 start_,0,2.069033885,STAT5_abs,sd_STAT5_abs,task2,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR101.25e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR101.25e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,10,-0.188797589,pSTAT5_au,sd_STAT5_au,task12_2,normal
 ode_,10,-0.224513141,pSTAT5_au,sd_STAT5_au,task12_2,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR101.25e-8_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR101.25e-8_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,10,-0.68939994,pSTAT5_au,sd_STAT5_au,task12_0,normal
 ode_,10,-1.196067027,pSTAT5_au,sd_STAT5_au,task12_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR101.75e-8_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR101.75e-8_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,10,-0.072964823,pSTAT5_au,sd_STAT5_au,task12_1,normal
 ode_,10,-0.154983281,pSTAT5_au,sd_STAT5_au,task12_1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR101.7675e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR101.7675e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,10,-0.083873893,pSTAT5_au,sd_STAT5_au,task12_3,normal
 ode_,10,-0.139014773,pSTAT5_au,sd_STAT5_au,task12_3,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR102.5e-6_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR102.5e-6_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,10,-0.405403283,pSTAT5_au,sd_STAT5_au,task12_5,normal
 ode_,10,-0.712262823,pSTAT5_au,sd_STAT5_au,task12_5,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR102.5e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR102.5e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,10,-2.029739669,pSTAT5_au,sd_STAT5_au,task12_4,normal
 ode_,10,-2.379006225,pSTAT5_au,sd_STAT5_au,task12_4,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR301.25e-6_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR301.25e-6_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,30,-0.08197578,pJAK2_au,sd_JAK2EpoR_au,task11_4,normal
 ode_,30,-0.120320772,pJAK2_au,sd_JAK2EpoR_au,task11_4,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR301.25e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR301.25e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,30,-0.113690193,pJAK2_au,sd_JAK2EpoR_au,task11_2,normal
 ode_,30,-0.175458638,pJAK2_au,sd_JAK2EpoR_au,task11_2,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-6_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-6_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,30,0,pJAK2_au,sd_JAK2EpoR_au,task11_5,normal
 ode_,30,-0.103930356,pJAK2_au,sd_JAK2EpoR_au,task11_5,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,30,-0.139094773,pJAK2_au,sd_JAK2EpoR_au,task11_3,normal
 ode_,30,-0.186989257,pJAK2_au,sd_JAK2EpoR_au,task11_3,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-8_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-8_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,30,-0.418022824,pJAK2_au,sd_JAK2EpoR_au,task11_1,normal
 ode_,30,-0.628420585,pJAK2_au,sd_JAK2EpoR_au,task11_1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-9_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR302.5e-9_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,30,-1.042533731,pJAK2_au,sd_JAK2EpoR_au,task11_0,normal
 ode_,30,-1.156896219,pJAK2_au,sd_JAK2EpoR_au,task11_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-5_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-5_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,7,-0.299430383,pJAK2_au,sd_JAK2EpoR_au,task10_4,normal
 ode_,7,-0.119102071,pJAK2_au,sd_JAK2EpoR_au,task10_4,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-6_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-6_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,7,-0.24827786,pJAK2_au,sd_JAK2EpoR_au,task10_3,normal
 ode_,7,-0.09851554,pJAK2_au,sd_JAK2EpoR_au,task10_3,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,7,-0.343064179,pJAK2_au,sd_JAK2EpoR_au,task10_2,normal
 ode_,7,-0.228849308,pJAK2_au,sd_JAK2EpoR_au,task10_2,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-8_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-8_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,7,-0.811793009,pJAK2_au,sd_JAK2EpoR_au,task10_1,normal
 ode_,7,-0.781691277,pJAK2_au,sd_JAK2EpoR_au,task10_1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-9_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR72.5e-9_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,7,-1.391576606,pJAK2_au,sd_JAK2EpoR_au,task10_0,normal
 ode_,7,-1.343064179,pJAK2_au,sd_JAK2EpoR_au,task10_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR901.25e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR901.25e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,90,-0.101189713,CIS_au1,sd_CIS_au,task13_2,normal
 ode_,90,-0.013162469,CIS_au1,sd_CIS_au,task13_2,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-6_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-6_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,90,-0.136728067,CIS_au1,sd_CIS_au,task13_4,normal
 ode_,90,-0.052566085,CIS_au1,sd_CIS_au,task13_4,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-7_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-7_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,90,-0.012820505,CIS_au1,sd_CIS_au,task13_3,normal
 ode_,90,-1.24E-05,CIS_au1,sd_CIS_au,task13_3,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-8_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-8_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,90,-0.289601874,CIS_au1,sd_CIS_au,task13_1,normal
 ode_,90,-0.325318154,CIS_au1,sd_CIS_au,task13_1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-9_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_DR902.5e-9_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,90,-1.380934033,CIS_au1,sd_CIS_au,task13_0,normal
 ode_,90,-1.422931419,CIS_au1,sd_CIS_au,task13_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_Fine_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_Fine_log10-mod.csv
@@ -1,63 +1,63 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
-start_,0,-1.674274777,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-start_,0,-1.582310457,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,0.5,-0.705956125,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,1,-0.421299842,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,1.5,-0.383923183,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,2,-0.43334733,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,3,-0.308799335,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,4,-0.042521777,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,5,0,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,6,-0.09713723,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,7.5,-0.118821812,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,9,-0.184913509,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,10.5,-0.081962223,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,12,-0.219164539,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,13.5,-0.31991534,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,15,-0.618350553,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,16.5,-0.397170665,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,18,-0.123583555,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,20,-0.452426028,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,22,-0.641832181,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,25,-0.730089805,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,28,-0.41086672,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,31,-0.762417049,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,35,-1.112909669,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,40,-0.785329912,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,45,-0.624628283,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,50,-0.896724098,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,60,-1.195097257,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,65,-0.945275598,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
-ode_,70,-0.65294001,pJAK2_au,sd_JAK2EpoR_au,task4,nornal
+start_,0,-1.674274777,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+start_,0,-1.582310457,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,0.5,-0.705956125,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,1,-0.421299842,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,1.5,-0.383923183,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,2,-0.43334733,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,3,-0.308799335,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,4,-0.042521777,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,5,0,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,6,-0.09713723,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,7.5,-0.118821812,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,9,-0.184913509,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,10.5,-0.081962223,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,12,-0.219164539,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,13.5,-0.31991534,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,15,-0.618350553,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,16.5,-0.397170665,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,18,-0.123583555,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,20,-0.452426028,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,22,-0.641832181,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,25,-0.730089805,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,28,-0.41086672,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,31,-0.762417049,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,35,-1.112909669,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,40,-0.785329912,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,45,-0.624628283,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,50,-0.896724098,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,60,-1.195097257,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,65,-0.945275598,pJAK2_au,sd_JAK2EpoR_au,task5,normal
+ode_,70,-0.65294001,pJAK2_au,sd_JAK2EpoR_au,task5,normal
 
-start_,0,-0.509010399,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-start_,0,-1.568778604,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,0.5,-0.675893656,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,1,-0.372670403,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,1.5,-0.040241219,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,2,-0.165182766,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,3,-0.000641025,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,4,-0.114236953,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,5,0,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,6,-0.280899813,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,7.5,-0.379443258,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,9,-0.042579905,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,10.5,-0.700895925,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,12,-0.289500719,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,13.5,-0.469501858,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,15,-0.11011269,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,16.5,-0.021669979,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,18,-0.548012165,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,20,-0.77815125,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,22,-0.663307132,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,25,-0.919007637,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,28,-0.843201668,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,31,-1.072976552,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,35,-1.096301914,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,40,-1.009866852,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,45,-0.915107515,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,50,-1.158015195,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,60,-0.829245166,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,65,-0.801845916,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
-ode_,70,-0.981049243,pEpoR_au,sd_JAK2EpoR_au,task4,nornal
+start_,0,-0.509010399,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+start_,0,-1.568778604,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,0.5,-0.675893656,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,1,-0.372670403,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,1.5,-0.040241219,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,2,-0.165182766,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,3,-0.000641025,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,4,-0.114236953,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,5,0,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,6,-0.280899813,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,7.5,-0.379443258,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,9,-0.042579905,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,10.5,-0.700895925,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,12,-0.289500719,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,13.5,-0.469501858,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,15,-0.11011269,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,16.5,-0.021669979,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,18,-0.548012165,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,20,-0.77815125,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,22,-0.663307132,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,25,-0.919007637,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,28,-0.843201668,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,31,-1.072976552,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,35,-1.096301914,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,40,-1.009866852,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,45,-0.915107515,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,50,-1.158015195,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,60,-0.829245166,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,65,-0.801845916,pEpoR_au,sd_JAK2EpoR_au,task5,normal
+ode_,70,-0.981049243,pEpoR_au,sd_JAK2EpoR_au,task5,normal
diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_Long_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_Long_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.955997626,pJAK2_au,sd_JAK2EpoR_au,task1,normal
 ode_,5,0,pJAK2_au,sd_JAK2EpoR_au,task1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_RNA_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_RNA_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 ode_,15,0.126391167,SOCS3RNA_foldA,sd_RNA_fold,task3,normal
 ode_,30,0.097316966,SOCS3RNA_foldA,sd_RNA_fold,task3,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_SHP1oe0_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_SHP1oe0_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.714827047,pJAK2_au,sd_JAK2EpoR_au,task9_0,normal
 ode_,5,0,pJAK2_au,sd_JAK2EpoR_au,task9_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_SHP1oe1_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_SHP1oe1_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.42714728,pJAK2_au,sd_JAK2EpoR_au,task9_1,normal
 ode_,5,-0.007119741,pJAK2_au,sd_JAK2EpoR_au,task9_1,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_SOCS3oe0_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_SOCS3oe0_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.12595226,pJAK2_au,sd_JAK2Epo_au,task8_0,normal
 ode_,10,0,pJAK2_au,sd_JAK2Epo_au,task8_0,normal

diff --git a/jak2stat5/Data/JAK2STAT5_CFUE_SOCS3oe1_log10-mod.csv b/jak2stat5/Data/JAK2STAT5_CFUE_SOCS3oe1_log10-mod.csv
@@ -1,4 +1,4 @@
-scope,t,measurement,parameters.mean,parameters.sigma,condition,distribution
+scope,t,measurement,prob.mean,prob.sigma,condition,prob.type
 
 start_,0,-1.064255568,pJAK2_au,sd_JAK2Epo_au,task8_1,normal
 ode_,10,-0.349156063,pJAK2_au,sd_JAK2Epo_au,task8_1,normal

diff --git a/jak2stat5/Data/conditions.csv b/jak2stat5/Data/conditions.csv
@@ -1,4 +1,4 @@
-id,model,tspan,constants.ActD,constants.CISoe,constants.SOCS3oe,constants.SHP1oe,constants.epo_level,observables[]
+id,model,tspan,parameter.ActD,parameter.CISoe,parameter.SOCS3oe,parameter.SHP1oe,parameter.epo_level,observables[]
 task1,nameless,300,0,0,0,0,1.25E-07,pJAK2_au;pEpoR_au;CIS_au;SOCS3_au;tSTAT5_au;pSTAT5_au
 task2,nameless,150,0,0,0,0,1.25E-07,STAT5_abs;SHP1_abs;CIS_abs;SOCS3_abs;pSTAT5B_rel
 task3,nameless,400,0,0,0,0,1.25E-07,SOCS3RNA_foldA;SOCS3RNA_foldB;SOCS3RNA_foldC;CISRNA_foldA;CISRNA_foldB;CISRNA_foldC

diff --git a/jak2stat5/run.jl b/jak2stat5/run.jl
@@ -8,8 +8,8 @@ sim(p.models[:nameless], tspan = (0., 100.), alg = CVODE_BDF()) |> plot
 
 ### Load conditions
 
-cond_csv = read_conditions("./jak2stat5/Data/conditions.csv")
-add_conditions!(p, cond_csv)
+cond_df = read_conditions("./jak2stat5/Data/conditions.csv")
+add_conditions!(p, cond_df)
 
 # chapter 2.3.1, page 21, figure S11 => task1
 dts1_csv = read_measurements("./jak2stat5/Data/JAK2STAT5_CFUE_Long_log10-mod.csv");
@@ -110,4 +110,4 @@ add_measurements!(p, dts13_3_csv)
 add_measurements!(p, dts13_4_csv)
 
 res = sim(p; alg = CVODE_BDF())
-plot(res)
+plot(res) # very bad picture
diff --git a/sbml_00375/run.jl b/sbml_00375/run.jl
@@ -3,6 +3,7 @@ using HetaSimulator, Plots
 p = load_platform("./sbml_00375"; source = "index.heta", type = "heta");
 m = p.models[:nameless]
 
-res0 = sim(m; saveat = 0:0.06:3.0, observables = [:S1, :S2, :S3])
+# res0 = sim(m; saveat = 0:0.06:3.0, observables = [:S1, :S2, :S3]) # XXX: wrong time sequence here
+res0 = sim(m; tspan = (0,3), observables = [:S1, :S2, :S3])
 plot(res0)
 DataFrame(res0)