Add support for experiments (previously named timecourses)

doc/example/example_Fujita/Fujita.yaml

@@ -3,6 +3,8 @@ format_version: 1
 problems:
 - condition_files:
   - Fujita_experimentalCondition.tsv
+  experiment_files:
+  - Fujita_experiments.tsv
   measurement_files:
   - Fujita_measurementData.tsv
   sbml_files:

doc/example/example_Fujita/Fujita_experiments.tsv

@@ -0,0 +1,7 @@
+experimentId	experiment
+experiment1	0;model1_data1
+experiment2	0;model1_data2
+experiment3	0;model1_data3
+experiment4	0;model1_data4
+experiment5	0;model1_data5
+experiment6	0;model1_data6

doc/example/example_Fujita/Fujita_measurementData_minimal.tsv

@@ -1,145 +1,145 @@
-observableId	simulationConditionId	measurement	time
-pEGFR_tot	model1_data1	0	0
-pEGFR_tot	model1_data1	0.004955	60
-pEGFR_tot	model1_data1	0.004034	120
-pEGFR_tot	model1_data1	0.0063674	300
-pEGFR_tot	model1_data1	0.010859	600
-pEGFR_tot	model1_data1	0.0071353	900
-pEGFR_tot	model1_data1	0.0037103	1800
-pEGFR_tot	model1_data1	0.0067693	3600
-pAkt_tot	model1_data1	0	0
-pAkt_tot	model1_data1	0.031232	60
-pAkt_tot	model1_data1	0.093444	120
-pAkt_tot	model1_data1	0.23689	300
-pAkt_tot	model1_data1	0.14973	600
-pAkt_tot	model1_data1	0.093097	900
-pAkt_tot	model1_data1	0.065764	1800
-pAkt_tot	model1_data1	0.045765	3600
-pS6_tot	model1_data1	0	0
-pS6_tot	model1_data1	0.0018563	60
-pS6_tot	model1_data1	0.0033416	120
-pS6_tot	model1_data1	0.012632	300
-pS6_tot	model1_data1	0.078914	600
-pS6_tot	model1_data1	0.25521	900
-pS6_tot	model1_data1	0.44745	1800
-pS6_tot	model1_data1	0.29547	3600
-pEGFR_tot	model1_data2	0	0
-pEGFR_tot	model1_data2	0.0249	60
-pEGFR_tot	model1_data2	0.022994	120
-pEGFR_tot	model1_data2	0.028904	300
-pEGFR_tot	model1_data2	0.027942	600
-pEGFR_tot	model1_data2	0.035465	900
-pEGFR_tot	model1_data2	0.021229	1800
-pEGFR_tot	model1_data2	0.02063	3600
-pAkt_tot	model1_data2	0	0
-pAkt_tot	model1_data2	0.062207	60
-pAkt_tot	model1_data2	0.40715	120
-pAkt_tot	model1_data2	0.319	300
-pAkt_tot	model1_data2	0.20592	600
-pAkt_tot	model1_data2	0.14706	900
-pAkt_tot	model1_data2	0.12542	1800
-pAkt_tot	model1_data2	0.067827	3600
-pS6_tot	model1_data2	0	0
-pS6_tot	model1_data2	0.0019654	60
-pS6_tot	model1_data2	0.0021975	120
-pS6_tot	model1_data2	0.020119	300
-pS6_tot	model1_data2	0.22158	600
-pS6_tot	model1_data2	0.52331	900
-pS6_tot	model1_data2	0.85846	1800
-pS6_tot	model1_data2	0.6598	3600
-pEGFR_tot	model1_data3	0	0
-pEGFR_tot	model1_data3	0.12816	60
-pEGFR_tot	model1_data3	0.13179	120
-pEGFR_tot	model1_data3	0.12123	300
-pEGFR_tot	model1_data3	0.09165	600
-pEGFR_tot	model1_data3	0.11645	900
-pEGFR_tot	model1_data3	0.049997	1800
-pEGFR_tot	model1_data3	0.017926	3600
-pAkt_tot	model1_data3	0	0
-pAkt_tot	model1_data3	0.38989	60
-pAkt_tot	model1_data3	0.82306	120
-pAkt_tot	model1_data3	0.49708	300
-pAkt_tot	model1_data3	0.2549	600
-pAkt_tot	model1_data3	0.19377	900
-pAkt_tot	model1_data3	0.12942	1800
-pAkt_tot	model1_data3	0.061242	3600
-pS6_tot	model1_data3	0	0
-pS6_tot	model1_data3	0.0020839	60
-pS6_tot	model1_data3	0.0047955	120
-pS6_tot	model1_data3	0.047495	300
-pS6_tot	model1_data3	0.39197	600
-pS6_tot	model1_data3	0.68142	900
-pS6_tot	model1_data3	1.0001	1800
-pS6_tot	model1_data3	0.75108	3600
-pEGFR_tot	model1_data4	0	0
-pEGFR_tot	model1_data4	0.48781	60
-pEGFR_tot	model1_data4	0.28974	120
-pEGFR_tot	model1_data4	0.24074	300
-pEGFR_tot	model1_data4	0.13851	600
-pEGFR_tot	model1_data4	0.11025	900
-pEGFR_tot	model1_data4	0.047644	1800
-pEGFR_tot	model1_data4	0.017833	3600
-pAkt_tot	model1_data4	0	0
-pAkt_tot	model1_data4	0.71187	60
-pAkt_tot	model1_data4	0.89633	120
-pAkt_tot	model1_data4	0.49719	300
-pAkt_tot	model1_data4	0.2397	600
-pAkt_tot	model1_data4	0.18333	900
-pAkt_tot	model1_data4	0.089574	1800
-pAkt_tot	model1_data4	0.037055	3600
-pS6_tot	model1_data4	0	0
-pS6_tot	model1_data4	0.0057189	60
-pS6_tot	model1_data4	0.013126	120
-pS6_tot	model1_data4	0.062408	300
-pS6_tot	model1_data4	0.41154	600
-pS6_tot	model1_data4	0.71428	900
-pS6_tot	model1_data4	0.92784	1800
-pS6_tot	model1_data4	0.55064	3600
-pEGFR_tot	model1_data5	0	0
-pEGFR_tot	model1_data5	0.90952	60
-pEGFR_tot	model1_data5	0.3891	120
-pEGFR_tot	model1_data5	0.30117	300
-pEGFR_tot	model1_data5	0.10321	600
-pEGFR_tot	model1_data5	0.10615	900
-pEGFR_tot	model1_data5	0.039496	1800
-pEGFR_tot	model1_data5	0.011403	3600
-pAkt_tot	model1_data5	0	0
-pAkt_tot	model1_data5	0.87147	60
-pAkt_tot	model1_data5	0.96118	120
-pAkt_tot	model1_data5	0.37349	300
-pAkt_tot	model1_data5	0.15548	600
-pAkt_tot	model1_data5	0.11922	900
-pAkt_tot	model1_data5	0.062311	1800
-pAkt_tot	model1_data5	0.03678	3600
-pS6_tot	model1_data5	0	0
-pS6_tot	model1_data5	0.0073292	60
-pS6_tot	model1_data5	0.014418	120
-pS6_tot	model1_data5	0.079732	300
-pS6_tot	model1_data5	0.4562	600
-pS6_tot	model1_data5	0.65294	900
-pS6_tot	model1_data5	0.75189	1800
-pS6_tot	model1_data5	0.37446	3600
-pEGFR_tot	model1_data6	0	0
-pEGFR_tot	model1_data6	0.95674	60
-pEGFR_tot	model1_data6	0.26888	120
-pEGFR_tot	model1_data6	0.34087	300
-pEGFR_tot	model1_data6	0.10018	600
-pEGFR_tot	model1_data6	0.097799	900
-pEGFR_tot	model1_data6	0.025369	1800
-pEGFR_tot	model1_data6	0.0081957	3600
-pAkt_tot	model1_data6	0	0
-pAkt_tot	model1_data6	0.99726	60
-pAkt_tot	model1_data6	0.8819	120
-pAkt_tot	model1_data6	0.27373	300
-pAkt_tot	model1_data6	0.11182	600
-pAkt_tot	model1_data6	0.073731	900
-pAkt_tot	model1_data6	0.053436	1800
-pAkt_tot	model1_data6	0.038275	3600
-pS6_tot	model1_data6	0	0
-pS6_tot	model1_data6	0.0086144	60
-pS6_tot	model1_data6	0.013062	120
-pS6_tot	model1_data6	0.07993	300
-pS6_tot	model1_data6	0.42868	600
-pS6_tot	model1_data6	0.60508	900
-pS6_tot	model1_data6	0.62088	1800
-pS6_tot	model1_data6	0.32084	3600
+observableId	experimentId	measurement	time
+pEGFR_tot	experiment1	0	0
+pEGFR_tot	experiment1	0.004955	60
+pEGFR_tot	experiment1	0.004034	120
+pEGFR_tot	experiment1	0.0063674	300
+pEGFR_tot	experiment1	0.010859	600
+pEGFR_tot	experiment1	0.0071353	900
+pEGFR_tot	experiment1	0.0037103	1800
+pEGFR_tot	experiment1	0.0067693	3600
+pAkt_tot	experiment1	0	0
+pAkt_tot	experiment1	0.031232	60
+pAkt_tot	experiment1	0.093444	120
+pAkt_tot	experiment1	0.23689	300
+pAkt_tot	experiment1	0.14973	600
+pAkt_tot	experiment1	0.093097	900
+pAkt_tot	experiment1	0.065764	1800
+pAkt_tot	experiment1	0.045765	3600
+pS6_tot	experiment1	0	0
+pS6_tot	experiment1	0.0018563	60
+pS6_tot	experiment1	0.0033416	120
+pS6_tot	experiment1	0.012632	300
+pS6_tot	experiment1	0.078914	600
+pS6_tot	experiment1	0.25521	900
+pS6_tot	experiment1	0.44745	1800
+pS6_tot	experiment1	0.29547	3600
+pEGFR_tot	experiment2	0	0
+pEGFR_tot	experiment2	0.0249	60
+pEGFR_tot	experiment2	0.022994	120
+pEGFR_tot	experiment2	0.028904	300
+pEGFR_tot	experiment2	0.027942	600
+pEGFR_tot	experiment2	0.035465	900
+pEGFR_tot	experiment2	0.021229	1800
+pEGFR_tot	experiment2	0.02063	3600
+pAkt_tot	experiment2	0	0
+pAkt_tot	experiment2	0.062207	60
+pAkt_tot	experiment2	0.40715	120
+pAkt_tot	experiment2	0.319	300
+pAkt_tot	experiment2	0.20592	600
+pAkt_tot	experiment2	0.14706	900
+pAkt_tot	experiment2	0.12542	1800
+pAkt_tot	experiment2	0.067827	3600
+pS6_tot	experiment2	0	0
+pS6_tot	experiment2	0.0019654	60
+pS6_tot	experiment2	0.0021975	120
+pS6_tot	experiment2	0.020119	300
+pS6_tot	experiment2	0.22158	600
+pS6_tot	experiment2	0.52331	900
+pS6_tot	experiment2	0.85846	1800
+pS6_tot	experiment2	0.6598	3600
+pEGFR_tot	experiment3	0	0
+pEGFR_tot	experiment3	0.12816	60
+pEGFR_tot	experiment3	0.13179	120
+pEGFR_tot	experiment3	0.12123	300
+pEGFR_tot	experiment3	0.09165	600
+pEGFR_tot	experiment3	0.11645	900
+pEGFR_tot	experiment3	0.049997	1800
+pEGFR_tot	experiment3	0.017926	3600
+pAkt_tot	experiment3	0	0
+pAkt_tot	experiment3	0.38989	60
+pAkt_tot	experiment3	0.82306	120
+pAkt_tot	experiment3	0.49708	300
+pAkt_tot	experiment3	0.2549	600
+pAkt_tot	experiment3	0.19377	900
+pAkt_tot	experiment3	0.12942	1800
+pAkt_tot	experiment3	0.061242	3600
+pS6_tot	experiment3	0	0
+pS6_tot	experiment3	0.0020839	60
+pS6_tot	experiment3	0.0047955	120
+pS6_tot	experiment3	0.047495	300
+pS6_tot	experiment3	0.39197	600
+pS6_tot	experiment3	0.68142	900
+pS6_tot	experiment3	1.0001	1800
+pS6_tot	experiment3	0.75108	3600
+pEGFR_tot	experiment4	0	0
+pEGFR_tot	experiment4	0.48781	60
+pEGFR_tot	experiment4	0.28974	120
+pEGFR_tot	experiment4	0.24074	300
+pEGFR_tot	experiment4	0.13851	600
+pEGFR_tot	experiment4	0.11025	900
+pEGFR_tot	experiment4	0.047644	1800
+pEGFR_tot	experiment4	0.017833	3600
+pAkt_tot	experiment4	0	0
+pAkt_tot	experiment4	0.71187	60
+pAkt_tot	experiment4	0.89633	120
+pAkt_tot	experiment4	0.49719	300
+pAkt_tot	experiment4	0.2397	600
+pAkt_tot	experiment4	0.18333	900
+pAkt_tot	experiment4	0.089574	1800
+pAkt_tot	experiment4	0.037055	3600
+pS6_tot	experiment4	0	0
+pS6_tot	experiment4	0.0057189	60
+pS6_tot	experiment4	0.013126	120
+pS6_tot	experiment4	0.062408	300
+pS6_tot	experiment4	0.41154	600
+pS6_tot	experiment4	0.71428	900
+pS6_tot	experiment4	0.92784	1800
+pS6_tot	experiment4	0.55064	3600
+pEGFR_tot	experiment5	0	0
+pEGFR_tot	experiment5	0.90952	60
+pEGFR_tot	experiment5	0.3891	120
+pEGFR_tot	experiment5	0.30117	300
+pEGFR_tot	experiment5	0.10321	600
+pEGFR_tot	experiment5	0.10615	900
+pEGFR_tot	experiment5	0.039496	1800
+pEGFR_tot	experiment5	0.011403	3600
+pAkt_tot	experiment5	0	0
+pAkt_tot	experiment5	0.87147	60
+pAkt_tot	experiment5	0.96118	120
+pAkt_tot	experiment5	0.37349	300
+pAkt_tot	experiment5	0.15548	600
+pAkt_tot	experiment5	0.11922	900
+pAkt_tot	experiment5	0.062311	1800
+pAkt_tot	experiment5	0.03678	3600
+pS6_tot	experiment5	0	0
+pS6_tot	experiment5	0.0073292	60
+pS6_tot	experiment5	0.014418	120
+pS6_tot	experiment5	0.079732	300
+pS6_tot	experiment5	0.4562	600
+pS6_tot	experiment5	0.65294	900
+pS6_tot	experiment5	0.75189	1800
+pS6_tot	experiment5	0.37446	3600
+pEGFR_tot	experiment6	0	0
+pEGFR_tot	experiment6	0.95674	60
+pEGFR_tot	experiment6	0.26888	120
+pEGFR_tot	experiment6	0.34087	300
+pEGFR_tot	experiment6	0.10018	600
+pEGFR_tot	experiment6	0.097799	900
+pEGFR_tot	experiment6	0.025369	1800
+pEGFR_tot	experiment6	0.0081957	3600
+pAkt_tot	experiment6	0	0
+pAkt_tot	experiment6	0.99726	60
+pAkt_tot	experiment6	0.8819	120
+pAkt_tot	experiment6	0.27373	300
+pAkt_tot	experiment6	0.11182	600
+pAkt_tot	experiment6	0.073731	900
+pAkt_tot	experiment6	0.053436	1800
+pAkt_tot	experiment6	0.038275	3600
+pS6_tot	experiment6	0	0
+pS6_tot	experiment6	0.0086144	60
+pS6_tot	experiment6	0.013062	120
+pS6_tot	experiment6	0.07993	300
+pS6_tot	experiment6	0.42868	600
+pS6_tot	experiment6	0.60508	900
+pS6_tot	experiment6	0.62088	1800
+pS6_tot	experiment6	0.32084	3600

doc/example/example_Fujita/Fujita_measurementData_nanData.tsv

@@ -1,17 +1,17 @@
-observableId	preequilibrationConditionId	simulationConditionId	measurement	time	observableParameters	noiseParameters
-pEGFR_tot		model1_data1	0	0	scaling_pEGFR_tot	0.01
-pEGFR_tot		model1_data1	0.004955	60	scaling_pEGFR_tot	0.01
-pEGFR_tot		model1_data1	0.004034	120	scaling_pEGFR_tot	0.01
-pEGFR_tot		model1_data1	0.0063674	300	scaling_pEGFR_tot	0.01
-pEGFR_tot		model1_data1	0.010859	600	scaling_pEGFR_tot	0.01
-pEGFR_tot		model1_data1	0.0071353	900	scaling_pEGFR_tot	0.01
-pEGFR_tot		model1_data1	0.0037103	1800	scaling_pEGFR_tot	0.01
-pEGFR_tot		model1_data1	0.0067693	3600	scaling_pEGFR_tot	0.01
-pAkt_tot		model1_data1	nan	0	scaling_pAkt_tot	0.01
-pAkt_tot		model1_data1	nan	60	scaling_pAkt_tot	0.01
-pAkt_tot		model1_data1	nan	120	scaling_pAkt_tot	0.01
-pAkt_tot		model1_data1	nan	300	scaling_pAkt_tot	0.01
-pAkt_tot		model1_data1	nan	600	scaling_pAkt_tot	0.01
-pAkt_tot		model1_data1	nan	900	scaling_pAkt_tot	0.01
-pAkt_tot		model1_data1	nan	1800	scaling_pAkt_tot	0.01
-pAkt_tot		model1_data1	nan	3600	scaling_pAkt_tot	0.01
+observableId	experimentId	measurement	time	observableParameters	noiseParameters
+pEGFR_tot	experiment1	0	0	scaling_pEGFR_tot	0.01
+pEGFR_tot	experiment1	0.004955	60	scaling_pEGFR_tot	0.01
+pEGFR_tot	experiment1	0.004034	120	scaling_pEGFR_tot	0.01
+pEGFR_tot	experiment1	0.0063674	300	scaling_pEGFR_tot	0.01
+pEGFR_tot	experiment1	0.010859	600	scaling_pEGFR_tot	0.01
+pEGFR_tot	experiment1	0.0071353	900	scaling_pEGFR_tot	0.01
+pEGFR_tot	experiment1	0.0037103	1800	scaling_pEGFR_tot	0.01
+pEGFR_tot	experiment1	0.0067693	3600	scaling_pEGFR_tot	0.01
+pAkt_tot	experiment1	nan	0	scaling_pAkt_tot	0.01
+pAkt_tot	experiment1	nan	60	scaling_pAkt_tot	0.01
+pAkt_tot	experiment1	nan	120	scaling_pAkt_tot	0.01
+pAkt_tot	experiment1	nan	300	scaling_pAkt_tot	0.01
+pAkt_tot	experiment1	nan	600	scaling_pAkt_tot	0.01
+pAkt_tot	experiment1	nan	900	scaling_pAkt_tot	0.01
+pAkt_tot	experiment1	nan	1800	scaling_pAkt_tot	0.01
+pAkt_tot	experiment1	nan	3600	scaling_pAkt_tot	0.01