From 131ef9db2a30229bdea4786389e3ae9c4b5d9e7a Mon Sep 17 00:00:00 2001 From: dilpath Date: Wed, 28 Apr 2021 21:27:39 +0200 Subject: [PATCH 1/2] add test data; input function to model --- .../Fujita_SciSignal2010.yaml | 2 +- ...rimentalCondition_Fujita_SciSignal2010.tsv | 24 ++- .../measurementData_Fujita_SciSignal2010.tsv | 145 ------------------ ...surementData_step_Fujita_SciSignal2010.tsv | 145 ++++++++++++++++++ .../model_Fujita_SciSignal2010.xml | 32 +++- .../input_all_Fujita_SciSignal2010.yaml | 15 ++ .../input_pulse_Fujita_SciSignal2010.yaml | 13 ++ .../input_ramp_Fujita_SciSignal2010.yaml | 13 ++ .../input_test_Fujita_SciSignal2010.yaml | 14 ++ ...urementData_pulse_Fujita_SciSignal2010.tsv | 145 ++++++++++++++++++ ...surementData_ramp_Fujita_SciSignal2010.tsv | 133 ++++++++++++++++ 11 files changed, 527 insertions(+), 154 deletions(-) delete mode 100644 Benchmark-Models/Fujita_SciSignal2010/measurementData_Fujita_SciSignal2010.tsv create mode 100644 Benchmark-Models/Fujita_SciSignal2010/measurementData_step_Fujita_SciSignal2010.tsv create mode 100644 Benchmark-Models/Fujita_SciSignal2010/test_data/input_all_Fujita_SciSignal2010.yaml create mode 100644 Benchmark-Models/Fujita_SciSignal2010/test_data/input_pulse_Fujita_SciSignal2010.yaml create mode 100644 Benchmark-Models/Fujita_SciSignal2010/test_data/input_ramp_Fujita_SciSignal2010.yaml create mode 100644 Benchmark-Models/Fujita_SciSignal2010/test_data/input_test_Fujita_SciSignal2010.yaml create mode 100644 Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_pulse_Fujita_SciSignal2010.tsv create mode 100644 Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_ramp_Fujita_SciSignal2010.tsv diff --git a/Benchmark-Models/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml b/Benchmark-Models/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml index 321b045..2b573ec 100644 --- a/Benchmark-Models/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml +++ b/Benchmark-Models/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml @@ -4,7 +4,7 @@ problems: - condition_files: - experimentalCondition_Fujita_SciSignal2010.tsv measurement_files: - - measurementData_Fujita_SciSignal2010.tsv + - measurementData_step_Fujita_SciSignal2010.tsv observable_files: - observables_Fujita_SciSignal2010.tsv sbml_files: diff --git a/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv b/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv index d0fe6c8..8a95a0f 100644 --- a/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv +++ b/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv @@ -1,7 +1,17 @@ -conditionId conditionName EGF -model1_data1 EGF 0.1 ng/ml 0.1 -model1_data2 EGF 0.3 ng/ml 0.3 -model1_data3 EGF 1 ng/ml 1 -model1_data4 EGF 3 ng/ml 3 -model1_data5 EGF 10 ng/ml 10 -model1_data6 EGF 30 ng/ml 30 +conditionId conditionName EGF_0 EGF_rate EGF_end +condition_step_00_1 EGF 00.1 ng/mL 0.1 0.0 3600 +condition_step_00_3 EGF 00.3 ng/mL 0.3 0.0 3600 +condition_step_01_0 EGF 01.0 ng/mL 1.0 0.0 3600 +condition_step_03_0 EGF 03.0 ng/mL 3.0 0.0 3600 +condition_step_10_0 EGF 10.0 ng/mL 10.0 0.0 3600 +condition_step_30_0 EGF 30.0 ng/mL 30.0 0.0 3600 +condition_pulse_00_1 EGF 00.1 ng/mL 0.1 0.0 60 +condition_pulse_00_3 EGF 00.3 ng/mL 0.3 0.0 60 +condition_pulse_01_0 EGF 01.0 ng/mL 1.0 0.0 60 +condition_pulse_03_0 EGF 03.0 ng/mL 3.0 0.0 60 +condition_pulse_10_0 EGF 10.0 ng/mL 10.0 0.0 60 +condition_pulse_30_0 EGF 30.0 ng/mL 30.0 0.0 60 +condition_ramp_8_3Enegative06 EGF 8.3E-06 ng/mL/s 0.0 8.333333333333334e-06 3600 +condition_ramp_8_3Enegative05 EGF 8.3E-05 ng/mL/s 0.0 8.333333333333333e-05 3600 +condition_ramp_8_3Enegative04 EGF 8.3E-04 ng/mL/s 0.0 0.0008333333333333333 3600 +condition_ramp_8_3Enegative03 EGF 8.3E-03 ng/mL/s 0.0 0.008333333333333333 3600 diff --git a/Benchmark-Models/Fujita_SciSignal2010/measurementData_Fujita_SciSignal2010.tsv b/Benchmark-Models/Fujita_SciSignal2010/measurementData_Fujita_SciSignal2010.tsv deleted file mode 100644 index b294bcf..0000000 --- a/Benchmark-Models/Fujita_SciSignal2010/measurementData_Fujita_SciSignal2010.tsv +++ /dev/null @@ -1,145 +0,0 @@ -observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters datasetId -pEGFR_tot model1_data1 0 0 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pEGFR_tot model1_data1 0.004955 60 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pEGFR_tot model1_data1 0.004034 120 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pEGFR_tot model1_data1 0.0063674 300 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pEGFR_tot model1_data1 0.010859 600 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pEGFR_tot model1_data1 0.0071353 900 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pEGFR_tot model1_data1 0.0037103 1800 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pEGFR_tot model1_data1 0.0067693 3600 scaling_pEGFR_tot 0.01 model1_data1_pEGFR_tot -pAkt_tot model1_data1 0 0 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pAkt_tot model1_data1 0.031232 60 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pAkt_tot model1_data1 0.093444 120 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pAkt_tot model1_data1 0.23689 300 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pAkt_tot model1_data1 0.14973 600 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pAkt_tot model1_data1 0.093097 900 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pAkt_tot model1_data1 0.065764 1800 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pAkt_tot model1_data1 0.045765 3600 scaling_pAkt_tot 0.01 model1_data1_pAkt_tot -pS6_tot model1_data1 0 0 scaling_pS6_tot 0.01 model1_data1_pS6_tot -pS6_tot model1_data1 0.0018563 60 scaling_pS6_tot 0.01 model1_data1_pS6_tot -pS6_tot model1_data1 0.0033416 120 scaling_pS6_tot 0.01 model1_data1_pS6_tot -pS6_tot model1_data1 0.012632 300 scaling_pS6_tot 0.01 model1_data1_pS6_tot -pS6_tot model1_data1 0.078914 600 scaling_pS6_tot 0.02 model1_data1_pS6_tot -pS6_tot model1_data1 0.25521 900 scaling_pS6_tot 0.02 model1_data1_pS6_tot -pS6_tot model1_data1 0.44745 1800 scaling_pS6_tot 0.035 model1_data1_pS6_tot -pS6_tot model1_data1 0.29547 3600 scaling_pS6_tot 0.035 model1_data1_pS6_tot -pEGFR_tot model1_data2 0 0 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pEGFR_tot model1_data2 0.0249 60 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pEGFR_tot model1_data2 0.022994 120 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pEGFR_tot model1_data2 0.028904 300 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pEGFR_tot model1_data2 0.027942 600 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pEGFR_tot model1_data2 0.035465 900 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pEGFR_tot model1_data2 0.021229 1800 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pEGFR_tot model1_data2 0.02063 3600 scaling_pEGFR_tot 0.01 model1_data2_pEGFR_tot -pAkt_tot model1_data2 0 0 scaling_pAkt_tot 0.01 model1_data2_pAkt_tot -pAkt_tot model1_data2 0.062207 60 scaling_pAkt_tot 0.01 model1_data2_pAkt_tot -pAkt_tot model1_data2 0.40715 120 scaling_pAkt_tot 0.03 model1_data2_pAkt_tot -pAkt_tot model1_data2 0.319 300 scaling_pAkt_tot 0.01 model1_data2_pAkt_tot -pAkt_tot model1_data2 0.20592 600 scaling_pAkt_tot 0.02 model1_data2_pAkt_tot -pAkt_tot model1_data2 0.14706 900 scaling_pAkt_tot 0.02 model1_data2_pAkt_tot -pAkt_tot model1_data2 0.12542 1800 scaling_pAkt_tot 0.02 model1_data2_pAkt_tot -pAkt_tot model1_data2 0.067827 3600 scaling_pAkt_tot 0.01 model1_data2_pAkt_tot -pS6_tot model1_data2 0 0 scaling_pS6_tot 0.01 model1_data2_pS6_tot -pS6_tot model1_data2 0.0019654 60 scaling_pS6_tot 0.01 model1_data2_pS6_tot -pS6_tot model1_data2 0.0021975 120 scaling_pS6_tot 0.01 model1_data2_pS6_tot -pS6_tot model1_data2 0.020119 300 scaling_pS6_tot 0.01 model1_data2_pS6_tot -pS6_tot model1_data2 0.22158 600 scaling_pS6_tot 0.02 model1_data2_pS6_tot -pS6_tot model1_data2 0.52331 900 scaling_pS6_tot 0.03 model1_data2_pS6_tot -pS6_tot model1_data2 0.85846 1800 scaling_pS6_tot 0.1 model1_data2_pS6_tot -pS6_tot model1_data2 0.6598 3600 scaling_pS6_tot 0.025 model1_data2_pS6_tot -pEGFR_tot model1_data3 0 0 scaling_pEGFR_tot 0.01 model1_data3_pEGFR_tot -pEGFR_tot model1_data3 0.12816 60 scaling_pEGFR_tot 0.05 model1_data3_pEGFR_tot -pEGFR_tot model1_data3 0.13179 120 scaling_pEGFR_tot 0.025 model1_data3_pEGFR_tot -pEGFR_tot model1_data3 0.12123 300 scaling_pEGFR_tot 0.065 model1_data3_pEGFR_tot -pEGFR_tot model1_data3 0.09165 600 scaling_pEGFR_tot 0.025 model1_data3_pEGFR_tot -pEGFR_tot model1_data3 0.11645 900 scaling_pEGFR_tot 0.02 model1_data3_pEGFR_tot -pEGFR_tot model1_data3 0.049997 1800 scaling_pEGFR_tot 0.01 model1_data3_pEGFR_tot -pEGFR_tot model1_data3 0.017926 3600 scaling_pEGFR_tot 0.01 model1_data3_pEGFR_tot -pAkt_tot model1_data3 0 0 scaling_pAkt_tot 0.01 model1_data3_pAkt_tot -pAkt_tot model1_data3 0.38989 60 scaling_pAkt_tot 0.1 model1_data3_pAkt_tot -pAkt_tot model1_data3 0.82306 120 scaling_pAkt_tot 0.07 model1_data3_pAkt_tot -pAkt_tot model1_data3 0.49708 300 scaling_pAkt_tot 0.03 model1_data3_pAkt_tot -pAkt_tot model1_data3 0.2549 600 scaling_pAkt_tot 0.03 model1_data3_pAkt_tot -pAkt_tot model1_data3 0.19377 900 scaling_pAkt_tot 0.03 model1_data3_pAkt_tot -pAkt_tot model1_data3 0.12942 1800 scaling_pAkt_tot 0.02 model1_data3_pAkt_tot -pAkt_tot model1_data3 0.061242 3600 scaling_pAkt_tot 0.01 model1_data3_pAkt_tot -pS6_tot model1_data3 0 0 scaling_pS6_tot 0.01 model1_data3_pS6_tot -pS6_tot model1_data3 0.0020839 60 scaling_pS6_tot 0.01 model1_data3_pS6_tot -pS6_tot model1_data3 0.0047955 120 scaling_pS6_tot 0.01 model1_data3_pS6_tot -pS6_tot model1_data3 0.047495 300 scaling_pS6_tot 0.01 model1_data3_pS6_tot -pS6_tot model1_data3 0.39197 600 scaling_pS6_tot 0.01 model1_data3_pS6_tot -pS6_tot model1_data3 0.68142 900 scaling_pS6_tot 0.025 model1_data3_pS6_tot -pS6_tot model1_data3 1.0001 1800 scaling_pS6_tot 0.07 model1_data3_pS6_tot -pS6_tot model1_data3 0.75108 3600 scaling_pS6_tot 0.075 model1_data3_pS6_tot -pEGFR_tot model1_data4 0 0 scaling_pEGFR_tot 0.01 model1_data4_pEGFR_tot -pEGFR_tot model1_data4 0.48781 60 scaling_pEGFR_tot 0.15 model1_data4_pEGFR_tot -pEGFR_tot model1_data4 0.28974 120 scaling_pEGFR_tot 0.12 model1_data4_pEGFR_tot -pEGFR_tot model1_data4 0.24074 300 scaling_pEGFR_tot 0.15 model1_data4_pEGFR_tot -pEGFR_tot model1_data4 0.13851 600 scaling_pEGFR_tot 0.065 model1_data4_pEGFR_tot -pEGFR_tot model1_data4 0.11025 900 scaling_pEGFR_tot 0.03 model1_data4_pEGFR_tot -pEGFR_tot model1_data4 0.047644 1800 scaling_pEGFR_tot 0.02 model1_data4_pEGFR_tot -pEGFR_tot model1_data4 0.017833 3600 scaling_pEGFR_tot 0.01 model1_data4_pEGFR_tot -pAkt_tot model1_data4 0 0 scaling_pAkt_tot 0.01 model1_data4_pAkt_tot -pAkt_tot model1_data4 0.71187 60 scaling_pAkt_tot 0.05 model1_data4_pAkt_tot -pAkt_tot model1_data4 0.89633 120 scaling_pAkt_tot 0.05 model1_data4_pAkt_tot -pAkt_tot model1_data4 0.49719 300 scaling_pAkt_tot 0.02 model1_data4_pAkt_tot -pAkt_tot model1_data4 0.2397 600 scaling_pAkt_tot 0.03 model1_data4_pAkt_tot -pAkt_tot model1_data4 0.18333 900 scaling_pAkt_tot 0.02 model1_data4_pAkt_tot -pAkt_tot model1_data4 0.089574 1800 scaling_pAkt_tot 0.02 model1_data4_pAkt_tot -pAkt_tot model1_data4 0.037055 3600 scaling_pAkt_tot 0.02 model1_data4_pAkt_tot -pS6_tot model1_data4 0 0 scaling_pS6_tot 0.01 model1_data4_pS6_tot -pS6_tot model1_data4 0.0057189 60 scaling_pS6_tot 0.01 model1_data4_pS6_tot -pS6_tot model1_data4 0.013126 120 scaling_pS6_tot 0.01 model1_data4_pS6_tot -pS6_tot model1_data4 0.062408 300 scaling_pS6_tot 0.01 model1_data4_pS6_tot -pS6_tot model1_data4 0.41154 600 scaling_pS6_tot 0.01 model1_data4_pS6_tot -pS6_tot model1_data4 0.71428 900 scaling_pS6_tot 0.035 model1_data4_pS6_tot -pS6_tot model1_data4 0.92784 1800 scaling_pS6_tot 0.08 model1_data4_pS6_tot -pS6_tot model1_data4 0.55064 3600 scaling_pS6_tot 0.08 model1_data4_pS6_tot -pEGFR_tot model1_data5 0 0 scaling_pEGFR_tot 0.01 model1_data5_pEGFR_tot -pEGFR_tot model1_data5 0.90952 60 scaling_pEGFR_tot 0.3 model1_data5_pEGFR_tot -pEGFR_tot model1_data5 0.3891 120 scaling_pEGFR_tot 0.15 model1_data5_pEGFR_tot -pEGFR_tot model1_data5 0.30117 300 scaling_pEGFR_tot 0.15 model1_data5_pEGFR_tot -pEGFR_tot model1_data5 0.10321 600 scaling_pEGFR_tot 0.05 model1_data5_pEGFR_tot -pEGFR_tot model1_data5 0.10615 900 scaling_pEGFR_tot 0.02 model1_data5_pEGFR_tot -pEGFR_tot model1_data5 0.039496 1800 scaling_pEGFR_tot 0.02 model1_data5_pEGFR_tot -pEGFR_tot model1_data5 0.011403 3600 scaling_pEGFR_tot 0.01 model1_data5_pEGFR_tot -pAkt_tot model1_data5 0 0 scaling_pAkt_tot 0.01 model1_data5_pAkt_tot -pAkt_tot model1_data5 0.87147 60 scaling_pAkt_tot 0.1 model1_data5_pAkt_tot -pAkt_tot model1_data5 0.96118 120 scaling_pAkt_tot 0.025 model1_data5_pAkt_tot -pAkt_tot model1_data5 0.37349 300 scaling_pAkt_tot 0.02 model1_data5_pAkt_tot -pAkt_tot model1_data5 0.15548 600 scaling_pAkt_tot 0.02 model1_data5_pAkt_tot -pAkt_tot model1_data5 0.11922 900 scaling_pAkt_tot 0.02 model1_data5_pAkt_tot -pAkt_tot model1_data5 0.062311 1800 scaling_pAkt_tot 0.02 model1_data5_pAkt_tot -pAkt_tot model1_data5 0.03678 3600 scaling_pAkt_tot 0.01 model1_data5_pAkt_tot -pS6_tot model1_data5 0 0 scaling_pS6_tot 0.01 model1_data5_pS6_tot -pS6_tot model1_data5 0.0073292 60 scaling_pS6_tot 0.01 model1_data5_pS6_tot -pS6_tot model1_data5 0.014418 120 scaling_pS6_tot 0.01 model1_data5_pS6_tot -pS6_tot model1_data5 0.079732 300 scaling_pS6_tot 0.01 model1_data5_pS6_tot -pS6_tot model1_data5 0.4562 600 scaling_pS6_tot 0.01 model1_data5_pS6_tot -pS6_tot model1_data5 0.65294 900 scaling_pS6_tot 0.02 model1_data5_pS6_tot -pS6_tot model1_data5 0.75189 1800 scaling_pS6_tot 0.04 model1_data5_pS6_tot -pS6_tot model1_data5 0.37446 3600 scaling_pS6_tot 0.08 model1_data5_pS6_tot -pEGFR_tot model1_data6 0 0 scaling_pEGFR_tot 0.01 model1_data6_pEGFR_tot -pEGFR_tot model1_data6 0.95674 60 scaling_pEGFR_tot 0.1 model1_data6_pEGFR_tot -pEGFR_tot model1_data6 0.26888 120 scaling_pEGFR_tot 0.1 model1_data6_pEGFR_tot -pEGFR_tot model1_data6 0.34087 300 scaling_pEGFR_tot 0.2 model1_data6_pEGFR_tot -pEGFR_tot model1_data6 0.10018 600 scaling_pEGFR_tot 0.05 model1_data6_pEGFR_tot -pEGFR_tot model1_data6 0.097799 900 scaling_pEGFR_tot 0.02 model1_data6_pEGFR_tot -pEGFR_tot model1_data6 0.025369 1800 scaling_pEGFR_tot 0.01 model1_data6_pEGFR_tot -pEGFR_tot model1_data6 0.0081957 3600 scaling_pEGFR_tot 0.01 model1_data6_pEGFR_tot -pAkt_tot model1_data6 0 0 scaling_pAkt_tot 0.01 model1_data6_pAkt_tot -pAkt_tot model1_data6 0.99726 60 scaling_pAkt_tot 0.05 model1_data6_pAkt_tot -pAkt_tot model1_data6 0.8819 120 scaling_pAkt_tot 0.02 model1_data6_pAkt_tot -pAkt_tot model1_data6 0.27373 300 scaling_pAkt_tot 0.02 model1_data6_pAkt_tot -pAkt_tot model1_data6 0.11182 600 scaling_pAkt_tot 0.02 model1_data6_pAkt_tot -pAkt_tot model1_data6 0.073731 900 scaling_pAkt_tot 0.02 model1_data6_pAkt_tot -pAkt_tot model1_data6 0.053436 1800 scaling_pAkt_tot 0.02 model1_data6_pAkt_tot -pAkt_tot model1_data6 0.038275 3600 scaling_pAkt_tot 0.01 model1_data6_pAkt_tot -pS6_tot model1_data6 0 0 scaling_pS6_tot 0.01 model1_data6_pS6_tot -pS6_tot model1_data6 0.0086144 60 scaling_pS6_tot 0.01 model1_data6_pS6_tot -pS6_tot model1_data6 0.013062 120 scaling_pS6_tot 0.01 model1_data6_pS6_tot -pS6_tot model1_data6 0.07993 300 scaling_pS6_tot 0.01 model1_data6_pS6_tot -pS6_tot model1_data6 0.42868 600 scaling_pS6_tot 0.02 model1_data6_pS6_tot -pS6_tot model1_data6 0.60508 900 scaling_pS6_tot 0.03 model1_data6_pS6_tot -pS6_tot model1_data6 0.62088 1800 scaling_pS6_tot 0.035 model1_data6_pS6_tot -pS6_tot model1_data6 0.32084 3600 scaling_pS6_tot 0.07 model1_data6_pS6_tot diff --git a/Benchmark-Models/Fujita_SciSignal2010/measurementData_step_Fujita_SciSignal2010.tsv b/Benchmark-Models/Fujita_SciSignal2010/measurementData_step_Fujita_SciSignal2010.tsv new file mode 100644 index 0000000..bc786e3 --- /dev/null +++ b/Benchmark-Models/Fujita_SciSignal2010/measurementData_step_Fujita_SciSignal2010.tsv @@ -0,0 +1,145 @@ +observableId simulationConditionId measurement time observableParameters noiseParameters datasetId +pEGFR_tot condition_step_00_1 0.0 0 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pEGFR_tot condition_step_00_1 0.00495502124323188 60 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pEGFR_tot condition_step_00_1 0.00403395805839657 120 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pEGFR_tot condition_step_00_1 0.00636740948965264 300 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pEGFR_tot condition_step_00_1 0.0108590905848178 600 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pEGFR_tot condition_step_00_1 0.00713529112795963 900 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pEGFR_tot condition_step_00_1 0.00371026458752022 1800 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pEGFR_tot condition_step_00_1 0.0067693198844283 3600 scaling_pEGFR_tot 0.01 condition_step_00_1_pEGFR_tot +pAkt_tot condition_step_00_1 0.0 0 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pAkt_tot condition_step_00_1 0.0312319063363424 60 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pAkt_tot condition_step_00_1 0.0934440605778122 120 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pAkt_tot condition_step_00_1 0.23689070684454 300 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pAkt_tot condition_step_00_1 0.149728787111733 600 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pAkt_tot condition_step_00_1 0.0930965638279408 900 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pAkt_tot condition_step_00_1 0.0657639903037222 1800 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pAkt_tot condition_step_00_1 0.0457654161255516 3600 scaling_pAkt_tot 0.01 condition_step_00_1_pAkt_tot +pS6_tot condition_step_00_1 0.0 0 scaling_pS6_tot 0.01 condition_step_00_1_pS6_tot +pS6_tot condition_step_00_1 0.00185626116271975 60 scaling_pS6_tot 0.01 condition_step_00_1_pS6_tot +pS6_tot condition_step_00_1 0.00334156724852441 120 scaling_pS6_tot 0.01 condition_step_00_1_pS6_tot +pS6_tot condition_step_00_1 0.0126322041194513 300 scaling_pS6_tot 0.01 condition_step_00_1_pS6_tot +pS6_tot condition_step_00_1 0.0789139948464721 600 scaling_pS6_tot 0.02 condition_step_00_1_pS6_tot +pS6_tot condition_step_00_1 0.255205694905064 900 scaling_pS6_tot 0.02 condition_step_00_1_pS6_tot +pS6_tot condition_step_00_1 0.447448267625208 1800 scaling_pS6_tot 0.035 condition_step_00_1_pS6_tot +pS6_tot condition_step_00_1 0.295468093040643 3600 scaling_pS6_tot 0.035 condition_step_00_1_pS6_tot +pEGFR_tot condition_step_00_3 0.0 0 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pEGFR_tot condition_step_00_3 0.0249003157231882 60 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pEGFR_tot condition_step_00_3 0.0229942298045425 120 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pEGFR_tot condition_step_00_3 0.0289040665442497 300 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pEGFR_tot condition_step_00_3 0.0279424909146837 600 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pEGFR_tot condition_step_00_3 0.0354646350814716 900 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pEGFR_tot condition_step_00_3 0.0212290758591334 1800 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pEGFR_tot condition_step_00_3 0.020630311420762 3600 scaling_pEGFR_tot 0.01 condition_step_00_3_pEGFR_tot +pAkt_tot condition_step_00_3 0.0 0 scaling_pAkt_tot 0.01 condition_step_00_3_pAkt_tot +pAkt_tot condition_step_00_3 0.0622065435525321 60 scaling_pAkt_tot 0.01 condition_step_00_3_pAkt_tot +pAkt_tot condition_step_00_3 0.407149521942874 120 scaling_pAkt_tot 0.03 condition_step_00_3_pAkt_tot +pAkt_tot condition_step_00_3 0.318995883749882 300 scaling_pAkt_tot 0.01 condition_step_00_3_pAkt_tot +pAkt_tot condition_step_00_3 0.205915257434171 600 scaling_pAkt_tot 0.02 condition_step_00_3_pAkt_tot +pAkt_tot condition_step_00_3 0.147058695832823 900 scaling_pAkt_tot 0.02 condition_step_00_3_pAkt_tot +pAkt_tot condition_step_00_3 0.125421345650406 1800 scaling_pAkt_tot 0.02 condition_step_00_3_pAkt_tot +pAkt_tot condition_step_00_3 0.0678265776127553 3600 scaling_pAkt_tot 0.01 condition_step_00_3_pAkt_tot +pS6_tot condition_step_00_3 0.0 0 scaling_pS6_tot 0.01 condition_step_00_3_pS6_tot +pS6_tot condition_step_00_3 0.00196541446755139 60 scaling_pS6_tot 0.01 condition_step_00_3_pS6_tot +pS6_tot condition_step_00_3 0.00219748165767664 120 scaling_pS6_tot 0.01 condition_step_00_3_pS6_tot +pS6_tot condition_step_00_3 0.0201194788851136 300 scaling_pS6_tot 0.01 condition_step_00_3_pS6_tot +pS6_tot condition_step_00_3 0.221584769298894 600 scaling_pS6_tot 0.02 condition_step_00_3_pS6_tot +pS6_tot condition_step_00_3 0.52331323911443 900 scaling_pS6_tot 0.03 condition_step_00_3_pS6_tot +pS6_tot condition_step_00_3 0.858460175894081 1800 scaling_pS6_tot 0.1 condition_step_00_3_pS6_tot +pS6_tot condition_step_00_3 0.659798980812272 3600 scaling_pS6_tot 0.025 condition_step_00_3_pS6_tot +pEGFR_tot condition_step_01_0 0.0 0 scaling_pEGFR_tot 0.01 condition_step_01_0_pEGFR_tot +pEGFR_tot condition_step_01_0 0.128159103 60 scaling_pEGFR_tot 0.05 condition_step_01_0_pEGFR_tot +pEGFR_tot condition_step_01_0 0.131793229 120 scaling_pEGFR_tot 0.025 condition_step_01_0_pEGFR_tot +pEGFR_tot condition_step_01_0 0.121231431 300 scaling_pEGFR_tot 0.065 condition_step_01_0_pEGFR_tot +pEGFR_tot condition_step_01_0 0.091650064 600 scaling_pEGFR_tot 0.025 condition_step_01_0_pEGFR_tot +pEGFR_tot condition_step_01_0 0.11645289 900 scaling_pEGFR_tot 0.02 condition_step_01_0_pEGFR_tot +pEGFR_tot condition_step_01_0 0.049997195 1800 scaling_pEGFR_tot 0.01 condition_step_01_0_pEGFR_tot +pEGFR_tot condition_step_01_0 0.017926288 3600 scaling_pEGFR_tot 0.01 condition_step_01_0_pEGFR_tot +pAkt_tot condition_step_01_0 0.0 0 scaling_pAkt_tot 0.01 condition_step_01_0_pAkt_tot +pAkt_tot condition_step_01_0 0.389886810328942 60 scaling_pAkt_tot 0.1 condition_step_01_0_pAkt_tot +pAkt_tot condition_step_01_0 0.823063169218381 120 scaling_pAkt_tot 0.07 condition_step_01_0_pAkt_tot +pAkt_tot condition_step_01_0 0.497078823862592 300 scaling_pAkt_tot 0.03 condition_step_01_0_pAkt_tot +pAkt_tot condition_step_01_0 0.254895348825743 600 scaling_pAkt_tot 0.03 condition_step_01_0_pAkt_tot +pAkt_tot condition_step_01_0 0.19377122723629 900 scaling_pAkt_tot 0.03 condition_step_01_0_pAkt_tot +pAkt_tot condition_step_01_0 0.129424783804315 1800 scaling_pAkt_tot 0.02 condition_step_01_0_pAkt_tot +pAkt_tot condition_step_01_0 0.0612417422136091 3600 scaling_pAkt_tot 0.01 condition_step_01_0_pAkt_tot +pS6_tot condition_step_01_0 0.0 0 scaling_pS6_tot 0.01 condition_step_01_0_pS6_tot +pS6_tot condition_step_01_0 0.00208394430584247 60 scaling_pS6_tot 0.01 condition_step_01_0_pS6_tot +pS6_tot condition_step_01_0 0.0047955268536628 120 scaling_pS6_tot 0.01 condition_step_01_0_pS6_tot +pS6_tot condition_step_01_0 0.0474948933605197 300 scaling_pS6_tot 0.01 condition_step_01_0_pS6_tot +pS6_tot condition_step_01_0 0.391968194089809 600 scaling_pS6_tot 0.01 condition_step_01_0_pS6_tot +pS6_tot condition_step_01_0 0.681417613180559 900 scaling_pS6_tot 0.025 condition_step_01_0_pS6_tot +pS6_tot condition_step_01_0 1.00014908339555 1800 scaling_pS6_tot 0.07 condition_step_01_0_pS6_tot +pS6_tot condition_step_01_0 0.751079341654748 3600 scaling_pS6_tot 0.075 condition_step_01_0_pS6_tot +pEGFR_tot condition_step_03_0 0.0 0 scaling_pEGFR_tot 0.01 condition_step_03_0_pEGFR_tot +pEGFR_tot condition_step_03_0 0.487808945488218 60 scaling_pEGFR_tot 0.15 condition_step_03_0_pEGFR_tot +pEGFR_tot condition_step_03_0 0.289743435542168 120 scaling_pEGFR_tot 0.12 condition_step_03_0_pEGFR_tot +pEGFR_tot condition_step_03_0 0.240736208928082 300 scaling_pEGFR_tot 0.15 condition_step_03_0_pEGFR_tot +pEGFR_tot condition_step_03_0 0.138514322853164 600 scaling_pEGFR_tot 0.065 condition_step_03_0_pEGFR_tot +pEGFR_tot condition_step_03_0 0.11025315008007 900 scaling_pEGFR_tot 0.03 condition_step_03_0_pEGFR_tot +pEGFR_tot condition_step_03_0 0.0476441503471867 1800 scaling_pEGFR_tot 0.02 condition_step_03_0_pEGFR_tot +pEGFR_tot condition_step_03_0 0.0178330035015746 3600 scaling_pEGFR_tot 0.01 condition_step_03_0_pEGFR_tot +pAkt_tot condition_step_03_0 0.0 0 scaling_pAkt_tot 0.01 condition_step_03_0_pAkt_tot +pAkt_tot condition_step_03_0 0.711868893977242 60 scaling_pAkt_tot 0.05 condition_step_03_0_pAkt_tot +pAkt_tot condition_step_03_0 0.896330977743735 120 scaling_pAkt_tot 0.05 condition_step_03_0_pAkt_tot +pAkt_tot condition_step_03_0 0.497187290467514 300 scaling_pAkt_tot 0.02 condition_step_03_0_pAkt_tot +pAkt_tot condition_step_03_0 0.239696393039484 600 scaling_pAkt_tot 0.03 condition_step_03_0_pAkt_tot +pAkt_tot condition_step_03_0 0.183327392791122 900 scaling_pAkt_tot 0.02 condition_step_03_0_pAkt_tot +pAkt_tot condition_step_03_0 0.0895735671008284 1800 scaling_pAkt_tot 0.02 condition_step_03_0_pAkt_tot +pAkt_tot condition_step_03_0 0.0370549094182817 3600 scaling_pAkt_tot 0.02 condition_step_03_0_pAkt_tot +pS6_tot condition_step_03_0 0.0 0 scaling_pS6_tot 0.01 condition_step_03_0_pS6_tot +pS6_tot condition_step_03_0 0.00571887346522448 60 scaling_pS6_tot 0.01 condition_step_03_0_pS6_tot +pS6_tot condition_step_03_0 0.0131263723775163 120 scaling_pS6_tot 0.01 condition_step_03_0_pS6_tot +pS6_tot condition_step_03_0 0.0624084329138648 300 scaling_pS6_tot 0.01 condition_step_03_0_pS6_tot +pS6_tot condition_step_03_0 0.411539752790082 600 scaling_pS6_tot 0.01 condition_step_03_0_pS6_tot +pS6_tot condition_step_03_0 0.714282332014208 900 scaling_pS6_tot 0.035 condition_step_03_0_pS6_tot +pS6_tot condition_step_03_0 0.927841062568102 1800 scaling_pS6_tot 0.08 condition_step_03_0_pS6_tot +pS6_tot condition_step_03_0 0.550639986283507 3600 scaling_pS6_tot 0.08 condition_step_03_0_pS6_tot +pEGFR_tot condition_step_10_0 0.0 0 scaling_pEGFR_tot 0.01 condition_step_10_0_pEGFR_tot +pEGFR_tot condition_step_10_0 0.909519635914505 60 scaling_pEGFR_tot 0.3 condition_step_10_0_pEGFR_tot +pEGFR_tot condition_step_10_0 0.389104930862414 120 scaling_pEGFR_tot 0.15 condition_step_10_0_pEGFR_tot +pEGFR_tot condition_step_10_0 0.30116919323453 300 scaling_pEGFR_tot 0.15 condition_step_10_0_pEGFR_tot +pEGFR_tot condition_step_10_0 0.103206977395624 600 scaling_pEGFR_tot 0.05 condition_step_10_0_pEGFR_tot +pEGFR_tot condition_step_10_0 0.106151933606013 900 scaling_pEGFR_tot 0.02 condition_step_10_0_pEGFR_tot +pEGFR_tot condition_step_10_0 0.0394963635767962 1800 scaling_pEGFR_tot 0.02 condition_step_10_0_pEGFR_tot +pEGFR_tot condition_step_10_0 0.0114034978937496 3600 scaling_pEGFR_tot 0.01 condition_step_10_0_pEGFR_tot +pAkt_tot condition_step_10_0 0.0 0 scaling_pAkt_tot 0.01 condition_step_10_0_pAkt_tot +pAkt_tot condition_step_10_0 0.871467734953423 60 scaling_pAkt_tot 0.1 condition_step_10_0_pAkt_tot +pAkt_tot condition_step_10_0 0.961175155634732 120 scaling_pAkt_tot 0.025 condition_step_10_0_pAkt_tot +pAkt_tot condition_step_10_0 0.373485785381097 300 scaling_pAkt_tot 0.02 condition_step_10_0_pAkt_tot +pAkt_tot condition_step_10_0 0.155480498541231 600 scaling_pAkt_tot 0.02 condition_step_10_0_pAkt_tot +pAkt_tot condition_step_10_0 0.119220797400196 900 scaling_pAkt_tot 0.02 condition_step_10_0_pAkt_tot +pAkt_tot condition_step_10_0 0.0623112588964791 1800 scaling_pAkt_tot 0.02 condition_step_10_0_pAkt_tot +pAkt_tot condition_step_10_0 0.0367804100732703 3600 scaling_pAkt_tot 0.01 condition_step_10_0_pAkt_tot +pS6_tot condition_step_10_0 0.0 0 scaling_pS6_tot 0.01 condition_step_10_0_pS6_tot +pS6_tot condition_step_10_0 0.00732922711299566 60 scaling_pS6_tot 0.01 condition_step_10_0_pS6_tot +pS6_tot condition_step_10_0 0.0144181307467439 120 scaling_pS6_tot 0.01 condition_step_10_0_pS6_tot +pS6_tot condition_step_10_0 0.079732441516859 300 scaling_pS6_tot 0.01 condition_step_10_0_pS6_tot +pS6_tot condition_step_10_0 0.456199664080073 600 scaling_pS6_tot 0.01 condition_step_10_0_pS6_tot +pS6_tot condition_step_10_0 0.652939475356473 900 scaling_pS6_tot 0.02 condition_step_10_0_pS6_tot +pS6_tot condition_step_10_0 0.751891451625626 1800 scaling_pS6_tot 0.04 condition_step_10_0_pS6_tot +pS6_tot condition_step_10_0 0.374455161641499 3600 scaling_pS6_tot 0.08 condition_step_10_0_pS6_tot +pEGFR_tot condition_step_30_0 0.0 0 scaling_pEGFR_tot 0.01 condition_step_30_0_pEGFR_tot +pEGFR_tot condition_step_30_0 0.956742072851792 60 scaling_pEGFR_tot 0.1 condition_step_30_0_pEGFR_tot +pEGFR_tot condition_step_30_0 0.268884645531158 120 scaling_pEGFR_tot 0.1 condition_step_30_0_pEGFR_tot +pEGFR_tot condition_step_30_0 0.340873694692337 300 scaling_pEGFR_tot 0.2 condition_step_30_0_pEGFR_tot +pEGFR_tot condition_step_30_0 0.100179678812072 600 scaling_pEGFR_tot 0.05 condition_step_30_0_pEGFR_tot +pEGFR_tot condition_step_30_0 0.09779872600827 900 scaling_pEGFR_tot 0.02 condition_step_30_0_pEGFR_tot +pEGFR_tot condition_step_30_0 0.0253694502237385 1800 scaling_pEGFR_tot 0.01 condition_step_30_0_pEGFR_tot +pEGFR_tot condition_step_30_0 0.00819570411203463 3600 scaling_pEGFR_tot 0.01 condition_step_30_0_pEGFR_tot +pAkt_tot condition_step_30_0 0.0 0 scaling_pAkt_tot 0.01 condition_step_30_0_pAkt_tot +pAkt_tot condition_step_30_0 0.997262492478515 60 scaling_pAkt_tot 0.05 condition_step_30_0_pAkt_tot +pAkt_tot condition_step_30_0 0.881898613324219 120 scaling_pAkt_tot 0.02 condition_step_30_0_pAkt_tot +pAkt_tot condition_step_30_0 0.273730504572033 300 scaling_pAkt_tot 0.02 condition_step_30_0_pAkt_tot +pAkt_tot condition_step_30_0 0.111818664622823 600 scaling_pAkt_tot 0.02 condition_step_30_0_pAkt_tot +pAkt_tot condition_step_30_0 0.0737306301883729 900 scaling_pAkt_tot 0.02 condition_step_30_0_pAkt_tot +pAkt_tot condition_step_30_0 0.0534355172175516 1800 scaling_pAkt_tot 0.02 condition_step_30_0_pAkt_tot +pAkt_tot condition_step_30_0 0.0382751174255833 3600 scaling_pAkt_tot 0.01 condition_step_30_0_pAkt_tot +pS6_tot condition_step_30_0 0.0 0 scaling_pS6_tot 0.01 condition_step_30_0_pS6_tot +pS6_tot condition_step_30_0 0.00861438046558738 60 scaling_pS6_tot 0.01 condition_step_30_0_pS6_tot +pS6_tot condition_step_30_0 0.0130624764575662 120 scaling_pS6_tot 0.01 condition_step_30_0_pS6_tot +pS6_tot condition_step_30_0 0.0799298041116208 300 scaling_pS6_tot 0.01 condition_step_30_0_pS6_tot +pS6_tot condition_step_30_0 0.42868014153471 600 scaling_pS6_tot 0.02 condition_step_30_0_pS6_tot +pS6_tot condition_step_30_0 0.605075827703608 900 scaling_pS6_tot 0.03 condition_step_30_0_pS6_tot +pS6_tot condition_step_30_0 0.620879461942708 1800 scaling_pS6_tot 0.035 condition_step_30_0_pS6_tot +pS6_tot condition_step_30_0 0.320844147774031 3600 scaling_pS6_tot 0.07 condition_step_30_0_pS6_tot diff --git a/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml b/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml index 9d46dbd..008fd6e 100644 --- a/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml +++ b/Benchmark-Models/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml @@ -39,7 +39,10 @@ - + + + + @@ -58,6 +61,33 @@ + + + + + + + + + + EGF_rate + time + + EGF_0 + + + + time + EGF_end + + + + 0 + + + + + diff --git a/Benchmark-Models/Fujita_SciSignal2010/test_data/input_all_Fujita_SciSignal2010.yaml b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_all_Fujita_SciSignal2010.yaml new file mode 100644 index 0000000..8ff7960 --- /dev/null +++ b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_all_Fujita_SciSignal2010.yaml @@ -0,0 +1,15 @@ +format_version: 1 +parameter_file: ../parameters_Fujita_SciSignal2010.tsv +problems: +- condition_files: + - ../experimentalCondition_Fujita_SciSignal2010.tsv + measurement_files: + - ../measurementData_step_Fujita_SciSignal2010.tsv + - measurementData_pulse_Fujita_SciSignal2010.tsv + - measurementData_ramp_Fujita_SciSignal2010.tsv + observable_files: + - ../observables_Fujita_SciSignal2010.tsv + sbml_files: + - ../model_Fujita_SciSignal2010.xml + visualization_files: + - ../visualizationSpecification_Fujita_SciSignal2010.tsv diff --git a/Benchmark-Models/Fujita_SciSignal2010/test_data/input_pulse_Fujita_SciSignal2010.yaml b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_pulse_Fujita_SciSignal2010.yaml new file mode 100644 index 0000000..16a92cc --- /dev/null +++ b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_pulse_Fujita_SciSignal2010.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: ../parameters_Fujita_SciSignal2010.tsv +problems: +- condition_files: + - ../experimentalCondition_Fujita_SciSignal2010.tsv + measurement_files: + - measurementData_pulse_Fujita_SciSignal2010.tsv + observable_files: + - ../observables_Fujita_SciSignal2010.tsv + sbml_files: + - ../model_Fujita_SciSignal2010.xml + visualization_files: + - ../visualizationSpecification_Fujita_SciSignal2010.tsv diff --git a/Benchmark-Models/Fujita_SciSignal2010/test_data/input_ramp_Fujita_SciSignal2010.yaml b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_ramp_Fujita_SciSignal2010.yaml new file mode 100644 index 0000000..f0a1fe9 --- /dev/null +++ b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_ramp_Fujita_SciSignal2010.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: ../parameters_Fujita_SciSignal2010.tsv +problems: +- condition_files: + - ../experimentalCondition_Fujita_SciSignal2010.tsv + measurement_files: + - measurementData_ramp_Fujita_SciSignal2010.tsv + observable_files: + - ../observables_Fujita_SciSignal2010.tsv + sbml_files: + - ../model_Fujita_SciSignal2010.xml + visualization_files: + - ../visualizationSpecification_Fujita_SciSignal2010.tsv diff --git a/Benchmark-Models/Fujita_SciSignal2010/test_data/input_test_Fujita_SciSignal2010.yaml b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_test_Fujita_SciSignal2010.yaml new file mode 100644 index 0000000..ff79354 --- /dev/null +++ b/Benchmark-Models/Fujita_SciSignal2010/test_data/input_test_Fujita_SciSignal2010.yaml @@ -0,0 +1,14 @@ +format_version: 1 +parameter_file: ../parameters_Fujita_SciSignal2010.tsv +problems: +- condition_files: + - ../experimentalCondition_Fujita_SciSignal2010.tsv + measurement_files: + - measurementData_pulse_Fujita_SciSignal2010.tsv + - measurementData_ramp_Fujita_SciSignal2010.tsv + observable_files: + - ../observables_Fujita_SciSignal2010.tsv + sbml_files: + - ../model_Fujita_SciSignal2010.xml + visualization_files: + - ../visualizationSpecification_Fujita_SciSignal2010.tsv diff --git a/Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_pulse_Fujita_SciSignal2010.tsv b/Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_pulse_Fujita_SciSignal2010.tsv new file mode 100644 index 0000000..113a495 --- /dev/null +++ b/Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_pulse_Fujita_SciSignal2010.tsv @@ -0,0 +1,145 @@ +observableId simulationConditionId measurement time observableParameters noiseParameters datasetId +pEGFR_tot condition_pulse_00_1 0.0 0 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pEGFR_tot condition_pulse_00_1 0.0266074989390743 60 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pEGFR_tot condition_pulse_00_1 0.0187472761236052 120 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pEGFR_tot condition_pulse_00_1 0.0044578443109673 300 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pEGFR_tot condition_pulse_00_1 0.00287189514527486 600 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pEGFR_tot condition_pulse_00_1 0.00287189514527486 900 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pEGFR_tot condition_pulse_00_1 0.00287189514527464 1800 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pEGFR_tot condition_pulse_00_1 0.000687587995760408 3600 scaling_pEGFR_tot 0.01 condition_pulse_00_1_pEGFR_tot +pAkt_tot condition_pulse_00_1 0.0 0 scaling_pAkt_tot 0.01 condition_pulse_00_1_pAkt_tot +pAkt_tot condition_pulse_00_1 0.0182920536802764 60 scaling_pAkt_tot 0.02 condition_pulse_00_1_pAkt_tot +pAkt_tot condition_pulse_00_1 0.038759236057474 120 scaling_pAkt_tot 0.01 condition_pulse_00_1_pAkt_tot +pAkt_tot condition_pulse_00_1 0.0333975743777475 300 scaling_pAkt_tot 0.01 condition_pulse_00_1_pAkt_tot +pAkt_tot condition_pulse_00_1 0.00344154316644074 600 scaling_pAkt_tot 0.01 condition_pulse_00_1_pAkt_tot +pAkt_tot condition_pulse_00_1 0.00344154316631373 900 scaling_pAkt_tot 0.01 condition_pulse_00_1_pAkt_tot +pAkt_tot condition_pulse_00_1 0.00344154316631373 1800 scaling_pAkt_tot 0.01 condition_pulse_00_1_pAkt_tot +pAkt_tot condition_pulse_00_1 0.00529395855421799 3600 scaling_pAkt_tot 0.01 condition_pulse_00_1_pAkt_tot +pS6_tot condition_pulse_00_1 0.0 0 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pS6_tot condition_pulse_00_1 0.00853448983378446 60 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pS6_tot condition_pulse_00_1 0.00669554149737328 120 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pS6_tot condition_pulse_00_1 0.00547262982003827 300 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pS6_tot condition_pulse_00_1 0.00991611544446358 600 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pS6_tot condition_pulse_00_1 0.00904072880902995 900 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pS6_tot condition_pulse_00_1 0.00298815325311197 1800 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pS6_tot condition_pulse_00_1 0.000671625327261838 3600 scaling_pS6_tot 0.01 condition_pulse_00_1_pS6_tot +pEGFR_tot condition_pulse_00_3 0.0 0 scaling_pEGFR_tot 0.01 condition_pulse_00_3_pEGFR_tot +pEGFR_tot condition_pulse_00_3 0.0721427790588283 60 scaling_pEGFR_tot 0.02 condition_pulse_00_3_pEGFR_tot +pEGFR_tot condition_pulse_00_3 0.0282963827467968 120 scaling_pEGFR_tot 0.01 condition_pulse_00_3_pEGFR_tot +pEGFR_tot condition_pulse_00_3 0.0120364203529775 300 scaling_pEGFR_tot 0.01 condition_pulse_00_3_pEGFR_tot +pEGFR_tot condition_pulse_00_3 0.00639160114676773 600 scaling_pEGFR_tot 0.01 condition_pulse_00_3_pEGFR_tot +pEGFR_tot condition_pulse_00_3 0.0065770372103553 900 scaling_pEGFR_tot 0.01 condition_pulse_00_3_pEGFR_tot +pEGFR_tot condition_pulse_00_3 0.002463803698183 1800 scaling_pEGFR_tot 0.01 condition_pulse_00_3_pEGFR_tot +pEGFR_tot condition_pulse_00_3 0.00117370892018775 3600 scaling_pEGFR_tot 0.01 condition_pulse_00_3_pEGFR_tot +pAkt_tot condition_pulse_00_3 0.0 0 scaling_pAkt_tot 0.01 condition_pulse_00_3_pAkt_tot +pAkt_tot condition_pulse_00_3 0.0484076988767415 60 scaling_pAkt_tot 0.01 condition_pulse_00_3_pAkt_tot +pAkt_tot condition_pulse_00_3 0.218851256253394 120 scaling_pAkt_tot 0.04 condition_pulse_00_3_pAkt_tot +pAkt_tot condition_pulse_00_3 0.11153496239958 300 scaling_pAkt_tot 0.02 condition_pulse_00_3_pAkt_tot +pAkt_tot condition_pulse_00_3 0.0110405027805105 600 scaling_pAkt_tot 0.01 condition_pulse_00_3_pAkt_tot +pAkt_tot condition_pulse_00_3 0.0106488807000349 900 scaling_pAkt_tot 0.01 condition_pulse_00_3_pAkt_tot +pAkt_tot condition_pulse_00_3 0.00555664034250669 1800 scaling_pAkt_tot 0.01 condition_pulse_00_3_pAkt_tot +pAkt_tot condition_pulse_00_3 0.00486649307086529 3600 scaling_pAkt_tot 0.01 condition_pulse_00_3_pAkt_tot +pS6_tot condition_pulse_00_3 0.0 0 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pS6_tot condition_pulse_00_3 4.99955231925142e-06 60 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pS6_tot condition_pulse_00_3 2.77251938869405e-05 120 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pS6_tot condition_pulse_00_3 0.000347664545423898 300 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pS6_tot condition_pulse_00_3 0.0112098774706104 600 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pS6_tot condition_pulse_00_3 0.0326187830572067 900 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pS6_tot condition_pulse_00_3 0.00607534244199348 1800 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pS6_tot condition_pulse_00_3 -0.000749477581823754 3600 scaling_pS6_tot 0.01 condition_pulse_00_3_pS6_tot +pEGFR_tot condition_pulse_01_0 0.0 0 scaling_pEGFR_tot 0.01 condition_pulse_01_0_pEGFR_tot +pEGFR_tot condition_pulse_01_0 0.254348901309658 60 scaling_pEGFR_tot 0.05 condition_pulse_01_0_pEGFR_tot +pEGFR_tot condition_pulse_01_0 0.0860429615904363 120 scaling_pEGFR_tot 0.01 condition_pulse_01_0_pEGFR_tot +pEGFR_tot condition_pulse_01_0 0.0103074227798929 300 scaling_pEGFR_tot 0.01 condition_pulse_01_0_pEGFR_tot +pEGFR_tot condition_pulse_01_0 0.00287189514527086 600 scaling_pEGFR_tot 0.01 condition_pulse_01_0_pEGFR_tot +pEGFR_tot condition_pulse_01_0 0.00287189514527486 900 scaling_pEGFR_tot 0.01 condition_pulse_01_0_pEGFR_tot +pEGFR_tot condition_pulse_01_0 0.00287189514527464 1800 scaling_pEGFR_tot 0.01 condition_pulse_01_0_pEGFR_tot +pEGFR_tot condition_pulse_01_0 0.00233837292275996 3600 scaling_pEGFR_tot 0.01 condition_pulse_01_0_pEGFR_tot +pAkt_tot condition_pulse_01_0 0.0 0 scaling_pAkt_tot 0.01 condition_pulse_01_0_pAkt_tot +pAkt_tot condition_pulse_01_0 0.329087009376939 60 scaling_pAkt_tot 0.03 condition_pulse_01_0_pAkt_tot +pAkt_tot condition_pulse_01_0 0.450381869916895 120 scaling_pAkt_tot 0.1 condition_pulse_01_0_pAkt_tot +pAkt_tot condition_pulse_01_0 0.184387206521519 300 scaling_pAkt_tot 0.03 condition_pulse_01_0_pAkt_tot +pAkt_tot condition_pulse_01_0 0.0183509762411476 600 scaling_pAkt_tot 0.03 condition_pulse_01_0_pAkt_tot +pAkt_tot condition_pulse_01_0 0.00688308633262769 900 scaling_pAkt_tot 0.02 condition_pulse_01_0_pAkt_tot +pAkt_tot condition_pulse_01_0 0.00688308633262769 1800 scaling_pAkt_tot 0.01 condition_pulse_01_0_pAkt_tot +pAkt_tot condition_pulse_01_0 0.000926445865121028 3600 scaling_pAkt_tot 0.01 condition_pulse_01_0_pAkt_tot +pS6_tot condition_pulse_01_0 0.0 0 scaling_pS6_tot 0.01 condition_pulse_01_0_pS6_tot +pS6_tot condition_pulse_01_0 0.00614925064904681 60 scaling_pS6_tot 0.01 condition_pulse_01_0_pS6_tot +pS6_tot condition_pulse_01_0 0.0062248329011001 120 scaling_pS6_tot 0.01 condition_pulse_01_0_pS6_tot +pS6_tot condition_pulse_01_0 0.00828588300505317 300 scaling_pS6_tot 0.02 condition_pulse_01_0_pS6_tot +pS6_tot condition_pulse_01_0 0.0407327759694014 600 scaling_pS6_tot 0.01 condition_pulse_01_0_pS6_tot +pS6_tot condition_pulse_01_0 0.13314355925987 900 scaling_pS6_tot 0.01 condition_pulse_01_0_pS6_tot +pS6_tot condition_pulse_01_0 0.0194423479934303 1800 scaling_pS6_tot 0.01 condition_pulse_01_0_pS6_tot +pS6_tot condition_pulse_01_0 0.00598412883616439 3600 scaling_pS6_tot 0.01 condition_pulse_01_0_pS6_tot +pEGFR_tot condition_pulse_03_0 0.0 0 scaling_pEGFR_tot 0.01 condition_pulse_03_0_pEGFR_tot +pEGFR_tot condition_pulse_03_0 0.583564088860833 60 scaling_pEGFR_tot 0.1 condition_pulse_03_0_pEGFR_tot +pEGFR_tot condition_pulse_03_0 0.212776572736683 120 scaling_pEGFR_tot 0.04 condition_pulse_03_0_pEGFR_tot +pEGFR_tot condition_pulse_03_0 0.0246744933026408 300 scaling_pEGFR_tot 0.01 condition_pulse_03_0_pEGFR_tot +pEGFR_tot condition_pulse_03_0 0.0138496556300061 600 scaling_pEGFR_tot 0.01 condition_pulse_03_0_pEGFR_tot +pEGFR_tot condition_pulse_03_0 0.00784264627142939 900 scaling_pEGFR_tot 0.01 condition_pulse_03_0_pEGFR_tot +pEGFR_tot condition_pulse_03_0 0.00762949330916585 1800 scaling_pEGFR_tot 0.01 condition_pulse_03_0_pEGFR_tot +pEGFR_tot condition_pulse_03_0 0.00163725120018143 3600 scaling_pEGFR_tot 0.01 condition_pulse_03_0_pEGFR_tot +pAkt_tot condition_pulse_03_0 0.0 0 scaling_pAkt_tot 0.01 condition_pulse_03_0_pAkt_tot +pAkt_tot condition_pulse_03_0 0.814054262937915 60 scaling_pAkt_tot 0.1 condition_pulse_03_0_pAkt_tot +pAkt_tot condition_pulse_03_0 0.847955016487729 120 scaling_pAkt_tot 0.05 condition_pulse_03_0_pAkt_tot +pAkt_tot condition_pulse_03_0 0.31184710938064 300 scaling_pAkt_tot 0.05 condition_pulse_03_0_pAkt_tot +pAkt_tot condition_pulse_03_0 0.0364732963092587 600 scaling_pAkt_tot 0.03 condition_pulse_03_0_pAkt_tot +pAkt_tot condition_pulse_03_0 0.0160656315157377 900 scaling_pAkt_tot 0.03 condition_pulse_03_0_pAkt_tot +pAkt_tot condition_pulse_03_0 0.0180310987000241 1800 scaling_pAkt_tot 0.01 condition_pulse_03_0_pAkt_tot +pAkt_tot condition_pulse_03_0 0.0139503484454673 3600 scaling_pAkt_tot 0.01 condition_pulse_03_0_pAkt_tot +pS6_tot condition_pulse_03_0 0.0 0 scaling_pS6_tot 0.01 condition_pulse_03_0_pS6_tot +pS6_tot condition_pulse_03_0 0.00870612431806506 60 scaling_pS6_tot 0.01 condition_pulse_03_0_pS6_tot +pS6_tot condition_pulse_03_0 0.00859236176985578 120 scaling_pS6_tot 0.01 condition_pulse_03_0_pS6_tot +pS6_tot condition_pulse_03_0 0.0137318417108931 300 scaling_pS6_tot 0.03 condition_pulse_03_0_pS6_tot +pS6_tot condition_pulse_03_0 0.101452776406798 600 scaling_pS6_tot 0.02 condition_pulse_03_0_pS6_tot +pS6_tot condition_pulse_03_0 0.220091042121007 900 scaling_pS6_tot 0.02 condition_pulse_03_0_pS6_tot +pS6_tot condition_pulse_03_0 0.0457821435810959 1800 scaling_pS6_tot 0.01 condition_pulse_03_0_pS6_tot +pS6_tot condition_pulse_03_0 0.00656943906426033 3600 scaling_pS6_tot 0.01 condition_pulse_03_0_pS6_tot +pEGFR_tot condition_pulse_10_0 0.0 0 scaling_pEGFR_tot 0.01 condition_pulse_10_0_pEGFR_tot +pEGFR_tot condition_pulse_10_0 1.06299578424802 60 scaling_pEGFR_tot 0.125 condition_pulse_10_0_pEGFR_tot +pEGFR_tot condition_pulse_10_0 0.395108782643842 120 scaling_pEGFR_tot 0.06 condition_pulse_10_0_pEGFR_tot +pEGFR_tot condition_pulse_10_0 0.0493818393825014 300 scaling_pEGFR_tot 0.05 condition_pulse_10_0_pEGFR_tot +pEGFR_tot condition_pulse_10_0 0.0420192874784715 600 scaling_pEGFR_tot 0.03 condition_pulse_10_0_pEGFR_tot +pEGFR_tot condition_pulse_10_0 0.0277957186324111 900 scaling_pEGFR_tot 0.01 condition_pulse_10_0_pEGFR_tot +pEGFR_tot condition_pulse_10_0 0.0103273306589873 1800 scaling_pEGFR_tot 0.01 condition_pulse_10_0_pEGFR_tot +pEGFR_tot condition_pulse_10_0 0.00298408908638348 3600 scaling_pEGFR_tot 0.01 condition_pulse_10_0_pEGFR_tot +pAkt_tot condition_pulse_10_0 0.0 0 scaling_pAkt_tot 0.01 condition_pulse_10_0_pAkt_tot +pAkt_tot condition_pulse_10_0 0.893073451116625 60 scaling_pAkt_tot 0.1 condition_pulse_10_0_pAkt_tot +pAkt_tot condition_pulse_10_0 0.996458107289377 120 scaling_pAkt_tot 0.1 condition_pulse_10_0_pAkt_tot +pAkt_tot condition_pulse_10_0 0.298206083603657 300 scaling_pAkt_tot 0.07 condition_pulse_10_0_pAkt_tot +pAkt_tot condition_pulse_10_0 0.0393576449272099 600 scaling_pAkt_tot 0.02 condition_pulse_10_0_pAkt_tot +pAkt_tot condition_pulse_10_0 0.0240931545787786 900 scaling_pAkt_tot 0.01 condition_pulse_10_0_pAkt_tot +pAkt_tot condition_pulse_10_0 0.0180310986998071 1800 scaling_pAkt_tot 0.01 condition_pulse_10_0_pAkt_tot +pAkt_tot condition_pulse_10_0 0.0105884245814862 3600 scaling_pAkt_tot 0.01 condition_pulse_10_0_pAkt_tot +pS6_tot condition_pulse_10_0 0.0 0 scaling_pS6_tot 0.01 condition_pulse_10_0_pS6_tot +pS6_tot condition_pulse_10_0 0.0137990075213035 60 scaling_pS6_tot 0.01 condition_pulse_10_0_pS6_tot +pS6_tot condition_pulse_10_0 0.0137990322665478 120 scaling_pS6_tot 0.01 condition_pulse_10_0_pS6_tot +pS6_tot condition_pulse_10_0 0.0137083595670415 300 scaling_pS6_tot 0.01 condition_pulse_10_0_pS6_tot +pS6_tot condition_pulse_10_0 0.141891405886819 600 scaling_pS6_tot 0.04 condition_pulse_10_0_pS6_tot +pS6_tot condition_pulse_10_0 0.284733273155458 900 scaling_pS6_tot 0.02 condition_pulse_10_0_pS6_tot +pS6_tot condition_pulse_10_0 0.113415474488028 1800 scaling_pS6_tot 0.03 condition_pulse_10_0_pS6_tot +pS6_tot condition_pulse_10_0 0.016032687371512 3600 scaling_pS6_tot 0.02 condition_pulse_10_0_pS6_tot +pEGFR_tot condition_pulse_30_0 0.0 0 scaling_pEGFR_tot 0.01 condition_pulse_30_0_pEGFR_tot +pEGFR_tot condition_pulse_30_0 1.01882457385384 60 scaling_pEGFR_tot 0.07 condition_pulse_30_0_pEGFR_tot +pEGFR_tot condition_pulse_30_0 0.450134026381059 120 scaling_pEGFR_tot 0.04 condition_pulse_30_0_pEGFR_tot +pEGFR_tot condition_pulse_30_0 0.103572636313968 300 scaling_pEGFR_tot 0.03 condition_pulse_30_0_pEGFR_tot +pEGFR_tot condition_pulse_30_0 0.0560011800750768 600 scaling_pEGFR_tot 0.01 condition_pulse_30_0_pEGFR_tot +pEGFR_tot condition_pulse_30_0 0.0206389183589482 900 scaling_pEGFR_tot 0.01 condition_pulse_30_0_pEGFR_tot +pEGFR_tot condition_pulse_30_0 0.0235001842165898 1800 scaling_pEGFR_tot 0.01 condition_pulse_30_0_pEGFR_tot +pEGFR_tot condition_pulse_30_0 0.00479584758313134 3600 scaling_pEGFR_tot 0.01 condition_pulse_30_0_pEGFR_tot +pAkt_tot condition_pulse_30_0 0.0 0 scaling_pAkt_tot 0.01 condition_pulse_30_0_pAkt_tot +pAkt_tot condition_pulse_30_0 1.00613137575667 60 scaling_pAkt_tot 0.05 condition_pulse_30_0_pAkt_tot +pAkt_tot condition_pulse_30_0 1.11278001380298 120 scaling_pAkt_tot 0.04 condition_pulse_30_0_pAkt_tot +pAkt_tot condition_pulse_30_0 0.304296586927262 300 scaling_pAkt_tot 0.05 condition_pulse_30_0_pAkt_tot +pAkt_tot condition_pulse_30_0 0.0402818457118217 600 scaling_pAkt_tot 0.01 condition_pulse_30_0_pAkt_tot +pAkt_tot condition_pulse_30_0 0.0147494706123468 900 scaling_pAkt_tot 0.01 condition_pulse_30_0_pAkt_tot +pAkt_tot condition_pulse_30_0 0.0147494707127835 1800 scaling_pAkt_tot 0.01 condition_pulse_30_0_pAkt_tot +pAkt_tot condition_pulse_30_0 0.00917431192660523 3600 scaling_pAkt_tot 0.01 condition_pulse_30_0_pAkt_tot +pS6_tot condition_pulse_30_0 0.0 0 scaling_pS6_tot 0.01 condition_pulse_30_0_pS6_tot +pS6_tot condition_pulse_30_0 0.00666158965199704 60 scaling_pS6_tot 0.01 condition_pulse_30_0_pS6_tot +pS6_tot condition_pulse_30_0 0.00666158965181807 120 scaling_pS6_tot 0.01 condition_pulse_30_0_pS6_tot +pS6_tot condition_pulse_30_0 0.0137341750608337 300 scaling_pS6_tot 0.01 condition_pulse_30_0_pS6_tot +pS6_tot condition_pulse_30_0 0.164160582107101 600 scaling_pS6_tot 0.04 condition_pulse_30_0_pS6_tot +pS6_tot condition_pulse_30_0 0.328797032098247 900 scaling_pS6_tot 0.015 condition_pulse_30_0_pS6_tot +pS6_tot condition_pulse_30_0 0.184621195655832 1800 scaling_pS6_tot 0.03 condition_pulse_30_0_pS6_tot +pS6_tot condition_pulse_30_0 0.0534979925867372 3600 scaling_pS6_tot 0.02 condition_pulse_30_0_pS6_tot diff --git a/Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_ramp_Fujita_SciSignal2010.tsv b/Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_ramp_Fujita_SciSignal2010.tsv new file mode 100644 index 0000000..3a14ae6 --- /dev/null +++ b/Benchmark-Models/Fujita_SciSignal2010/test_data/measurementData_ramp_Fujita_SciSignal2010.tsv @@ -0,0 +1,133 @@ +observableId simulationConditionId measurement time observableParameters noiseParameters datasetId +pEGFR_tot condition_ramp_8_3Enegative06 0.0 0 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.014067004435125 60 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.0342115684436839 120 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.0301691595679132 300 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.0228886084995557 600 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.027612007149564 900 scaling_pEGFR_tot 0.015 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.0249025041684694 1200 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.022124081515843 1800 scaling_pEGFR_tot 0.015 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.016665384734881 2400 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.0162291337050473 3000 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pEGFR_tot condition_ramp_8_3Enegative06 0.0216177882484525 3600 scaling_pEGFR_tot 0.01 condition_ramp_8_3Enegative06_pEGFR_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0 0 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.00275108410333202 60 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0153063620544882 120 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0466946159873562 300 scaling_pAkt_tot 0.03 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0294464884299228 600 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0394680292342149 900 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0443097954204217 1200 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0505631619705318 1800 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.060299097967536 2400 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0648466818008433 3000 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pAkt_tot condition_ramp_8_3Enegative06 0.0643371358063778 3600 scaling_pAkt_tot 0.01 condition_ramp_8_3Enegative06_pAkt_tot +pS6_tot condition_ramp_8_3Enegative06 0.0 0 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.00111313148589365 60 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.00101096534843226 120 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.00213494986155105 300 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.0130672432920407 600 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.0151725256387492 900 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.0178955964643865 1200 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.0283399111031666 1800 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.0470532091069193 2400 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative06_pS6_tot +pS6_tot condition_ramp_8_3Enegative06 0.063593954177781 3000 scaling_pS6_tot 0.02 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condition_ramp_8_3Enegative03 0.0647704686995025 3600 scaling_pAkt_tot 0.02 condition_ramp_8_3Enegative03_pAkt_tot +pS6_tot condition_ramp_8_3Enegative03 0.0 0 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.00734753357821072 60 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.00735758191584424 120 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.0406579993856047 300 scaling_pS6_tot 0.01 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.455624294352898 600 scaling_pS6_tot 0.03 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.69257607267951 900 scaling_pS6_tot 0.1 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.770840843870901 1200 scaling_pS6_tot 0.08 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.758059099313035 1800 scaling_pS6_tot 0.03 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.639529823613404 2400 scaling_pS6_tot 0.02 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.556562335813751 3000 scaling_pS6_tot 0.05 condition_ramp_8_3Enegative03_pS6_tot +pS6_tot condition_ramp_8_3Enegative03 0.47656113178634 3600 scaling_pS6_tot 0.07 condition_ramp_8_3Enegative03_pS6_tot From b777c7c51a061e4bfd7873256b9c6252134c8d6c Mon Sep 17 00:00:00 2001 From: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> Date: Fri, 22 Oct 2021 16:03:06 +0200 Subject: [PATCH 2/2] remove zero padding from condition names --- ...xperimentalCondition_Fujita_SciSignal2010.tsv | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv b/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv index 8a95a0f..2115794 100644 --- a/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv +++ b/Benchmark-Models/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv @@ -1,14 +1,14 @@ conditionId conditionName EGF_0 EGF_rate EGF_end -condition_step_00_1 EGF 00.1 ng/mL 0.1 0.0 3600 -condition_step_00_3 EGF 00.3 ng/mL 0.3 0.0 3600 -condition_step_01_0 EGF 01.0 ng/mL 1.0 0.0 3600 -condition_step_03_0 EGF 03.0 ng/mL 3.0 0.0 3600 +condition_step_00_1 EGF 0.1 ng/mL 0.1 0.0 3600 +condition_step_00_3 EGF 0.3 ng/mL 0.3 0.0 3600 +condition_step_01_0 EGF 1.0 ng/mL 1.0 0.0 3600 +condition_step_03_0 EGF 3.0 ng/mL 3.0 0.0 3600 condition_step_10_0 EGF 10.0 ng/mL 10.0 0.0 3600 condition_step_30_0 EGF 30.0 ng/mL 30.0 0.0 3600 -condition_pulse_00_1 EGF 00.1 ng/mL 0.1 0.0 60 -condition_pulse_00_3 EGF 00.3 ng/mL 0.3 0.0 60 -condition_pulse_01_0 EGF 01.0 ng/mL 1.0 0.0 60 -condition_pulse_03_0 EGF 03.0 ng/mL 3.0 0.0 60 +condition_pulse_00_1 EGF 0.1 ng/mL 0.1 0.0 60 +condition_pulse_00_3 EGF 0.3 ng/mL 0.3 0.0 60 +condition_pulse_01_0 EGF 1.0 ng/mL 1.0 0.0 60 +condition_pulse_03_0 EGF 3.0 ng/mL 3.0 0.0 60 condition_pulse_10_0 EGF 10.0 ng/mL 10.0 0.0 60 condition_pulse_30_0 EGF 30.0 ng/mL 30.0 0.0 60 condition_ramp_8_3Enegative06 EGF 8.3E-06 ng/mL/s 0.0 8.333333333333334e-06 3600