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fix vis example petabs
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‎doc/example/example_Fujita/Fujita.yaml‎

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problems:
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- condition_files:
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- Fujita_experimentalCondition.tsv
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experiment_files:
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- Fujita_experiments.tsv
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measurement_files:
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- Fujita_measurementData.tsv
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sbml_files:

‎doc/example/example_Fujita/Fujita_experiments.tsv‎

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experimentId experiment
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experiment1 0;model1_data1
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experiment2 0;model1_data2
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experiment3 0;model1_data3
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experiment4 0;model1_data4
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experiment5 0;model1_data5
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experiment6 0;model1_data6

‎doc/example/example_Fujita/Fujita_measurementData.tsv‎

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‎doc/example/example_Fujita/Fujita_measurementData_minimal.tsv‎

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observableId simulationConditionId measurement time
2-
pEGFR_tot model1_data1 0 0
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pEGFR_tot model1_data1 0.004955 60
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pEGFR_tot model1_data1 0.004034 120
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pEGFR_tot model1_data1 0.0063674 300
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pEGFR_tot model1_data1 0.010859 600
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pEGFR_tot model1_data1 0.0071353 900
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pEGFR_tot model1_data1 0.0037103 1800
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pEGFR_tot model1_data1 0.0067693 3600
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pAkt_tot model1_data1 0 0
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pAkt_tot model1_data1 0.031232 60
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pAkt_tot model1_data1 0.093444 120
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pAkt_tot model1_data1 0.23689 300
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pAkt_tot model1_data1 0.14973 600
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pAkt_tot model1_data1 0.093097 900
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pAkt_tot model1_data1 0.065764 1800
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pAkt_tot model1_data1 0.045765 3600
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pS6_tot model1_data1 0 0
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pS6_tot model1_data1 0.0018563 60
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pS6_tot model1_data1 0.0033416 120
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pS6_tot model1_data1 0.012632 300
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pS6_tot model1_data1 0.078914 600
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pS6_tot model1_data1 0.25521 900
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pS6_tot model1_data1 0.44745 1800
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pS6_tot model1_data1 0.29547 3600
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pEGFR_tot model1_data2 0 0
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pEGFR_tot model1_data2 0.0249 60
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pEGFR_tot model1_data2 0.022994 120
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pEGFR_tot model1_data2 0.028904 300
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pEGFR_tot model1_data2 0.027942 600
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pEGFR_tot model1_data2 0.035465 900
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pEGFR_tot model1_data2 0.021229 1800
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pEGFR_tot model1_data2 0.02063 3600
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pAkt_tot model1_data2 0 0
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pAkt_tot model1_data2 0.062207 60
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pAkt_tot model1_data2 0.40715 120
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pAkt_tot model1_data2 0.319 300
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pAkt_tot model1_data2 0.20592 600
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pAkt_tot model1_data2 0.14706 900
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pAkt_tot model1_data2 0.12542 1800
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pAkt_tot model1_data2 0.067827 3600
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pS6_tot model1_data2 0 0
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pS6_tot model1_data2 0.0019654 60
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pS6_tot model1_data2 0.0021975 120
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pS6_tot model1_data2 0.020119 300
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pS6_tot model1_data2 0.22158 600
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pS6_tot model1_data2 0.52331 900
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pS6_tot model1_data2 0.85846 1800
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pS6_tot model1_data2 0.6598 3600
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pEGFR_tot model1_data3 0 0
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pEGFR_tot model1_data3 0.12816 60
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pEGFR_tot model1_data3 0.13179 120
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pEGFR_tot model1_data3 0.12123 300
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pEGFR_tot model1_data3 0.09165 600
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pEGFR_tot model1_data3 0.11645 900
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pEGFR_tot model1_data3 0.049997 1800
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pEGFR_tot model1_data3 0.017926 3600
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pAkt_tot model1_data3 0 0
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pAkt_tot model1_data3 0.38989 60
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pAkt_tot model1_data3 0.82306 120
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pAkt_tot model1_data3 0.49708 300
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pAkt_tot model1_data3 0.2549 600
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pAkt_tot model1_data3 0.19377 900
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pAkt_tot model1_data3 0.12942 1800
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pAkt_tot model1_data3 0.061242 3600
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pS6_tot model1_data3 0 0
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pS6_tot model1_data3 0.0020839 60
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pS6_tot model1_data3 0.0047955 120
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pS6_tot model1_data3 0.047495 300
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pS6_tot model1_data3 0.39197 600
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pS6_tot model1_data3 0.68142 900
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pS6_tot model1_data3 1.0001 1800
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pS6_tot model1_data3 0.75108 3600
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pEGFR_tot model1_data4 0 0
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pEGFR_tot model1_data4 0.48781 60
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pEGFR_tot model1_data4 0.28974 120
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pEGFR_tot model1_data4 0.24074 300
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pEGFR_tot model1_data4 0.13851 600
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pEGFR_tot model1_data4 0.11025 900
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pEGFR_tot model1_data4 0.047644 1800
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pEGFR_tot model1_data4 0.017833 3600
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pAkt_tot model1_data4 0 0
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pAkt_tot model1_data4 0.71187 60
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pAkt_tot model1_data4 0.89633 120
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pAkt_tot model1_data4 0.49719 300
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pAkt_tot model1_data4 0.2397 600
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pAkt_tot model1_data4 0.18333 900
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pAkt_tot model1_data4 0.089574 1800
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pAkt_tot model1_data4 0.037055 3600
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pS6_tot model1_data4 0 0
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pS6_tot model1_data4 0.0057189 60
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pS6_tot model1_data4 0.013126 120
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pS6_tot model1_data4 0.062408 300
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pS6_tot model1_data4 0.41154 600
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pS6_tot model1_data4 0.71428 900
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pS6_tot model1_data4 0.92784 1800
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pS6_tot model1_data4 0.55064 3600
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pEGFR_tot model1_data5 0 0
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pEGFR_tot model1_data5 0.90952 60
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pEGFR_tot model1_data5 0.3891 120
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pEGFR_tot model1_data5 0.30117 300
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pEGFR_tot model1_data5 0.10321 600
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pEGFR_tot model1_data5 0.10615 900
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pEGFR_tot model1_data5 0.039496 1800
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pEGFR_tot model1_data5 0.011403 3600
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pAkt_tot model1_data5 0 0
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pAkt_tot model1_data5 0.87147 60
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pAkt_tot model1_data5 0.96118 120
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pAkt_tot model1_data5 0.37349 300
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pAkt_tot model1_data5 0.15548 600
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pAkt_tot model1_data5 0.11922 900
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pAkt_tot model1_data5 0.062311 1800
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pAkt_tot model1_data5 0.03678 3600
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pS6_tot model1_data5 0 0
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pS6_tot model1_data5 0.0073292 60
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pS6_tot model1_data5 0.014418 120
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pS6_tot model1_data5 0.079732 300
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pS6_tot model1_data5 0.4562 600
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pS6_tot model1_data5 0.65294 900
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pS6_tot model1_data5 0.75189 1800
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pS6_tot model1_data5 0.37446 3600
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pEGFR_tot model1_data6 0 0
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pEGFR_tot model1_data6 0.95674 60
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pEGFR_tot model1_data6 0.26888 120
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pEGFR_tot model1_data6 0.34087 300
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pEGFR_tot model1_data6 0.10018 600
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pEGFR_tot model1_data6 0.097799 900
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pEGFR_tot model1_data6 0.025369 1800
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pEGFR_tot model1_data6 0.0081957 3600
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pAkt_tot model1_data6 0 0
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pAkt_tot model1_data6 0.99726 60
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pAkt_tot model1_data6 0.8819 120
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pAkt_tot model1_data6 0.27373 300
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pAkt_tot model1_data6 0.11182 600
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pAkt_tot model1_data6 0.073731 900
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pAkt_tot model1_data6 0.053436 1800
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pAkt_tot model1_data6 0.038275 3600
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pS6_tot model1_data6 0 0
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pS6_tot model1_data6 0.0086144 60
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pS6_tot model1_data6 0.013062 120
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pS6_tot model1_data6 0.07993 300
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pS6_tot model1_data6 0.42868 600
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pS6_tot model1_data6 0.60508 900
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pS6_tot model1_data6 0.62088 1800
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pS6_tot model1_data6 0.32084 3600
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observableId experimentId measurement time
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pEGFR_tot experiment1 0 0
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pEGFR_tot experiment1 0.004955 60
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pEGFR_tot experiment1 0.004034 120
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pEGFR_tot experiment1 0.0063674 300
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pEGFR_tot experiment1 0.010859 600
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pEGFR_tot experiment1 0.0071353 900
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pEGFR_tot experiment1 0.0037103 1800
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pEGFR_tot experiment1 0.0067693 3600
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pAkt_tot experiment1 0 0
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pAkt_tot experiment1 0.031232 60
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pAkt_tot experiment1 0.093444 120
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pAkt_tot experiment1 0.23689 300
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pAkt_tot experiment1 0.14973 600
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pAkt_tot experiment1 0.093097 900
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pAkt_tot experiment1 0.065764 1800
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pAkt_tot experiment1 0.045765 3600
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pS6_tot experiment1 0 0
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pS6_tot experiment1 0.0018563 60
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pS6_tot experiment1 0.0033416 120
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pS6_tot experiment1 0.012632 300
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pS6_tot experiment1 0.078914 600
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pS6_tot experiment1 0.25521 900
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pS6_tot experiment1 0.44745 1800
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pS6_tot experiment1 0.29547 3600
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pEGFR_tot experiment2 0 0
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pEGFR_tot experiment2 0.0249 60
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pEGFR_tot experiment2 0.022994 120
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pEGFR_tot experiment2 0.028904 300
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pEGFR_tot experiment2 0.027942 600
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pEGFR_tot experiment2 0.035465 900
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pEGFR_tot experiment2 0.021229 1800
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pEGFR_tot experiment2 0.02063 3600
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pAkt_tot experiment2 0 0
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pAkt_tot experiment2 0.062207 60
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pAkt_tot experiment2 0.40715 120
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pAkt_tot experiment2 0.319 300
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pAkt_tot experiment2 0.20592 600
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pAkt_tot experiment2 0.14706 900
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pAkt_tot experiment2 0.12542 1800
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pAkt_tot experiment2 0.067827 3600
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pS6_tot experiment2 0 0
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pS6_tot experiment2 0.0019654 60
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pS6_tot experiment2 0.0021975 120
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pS6_tot experiment2 0.020119 300
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pS6_tot experiment2 0.22158 600
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pS6_tot experiment2 0.52331 900
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pS6_tot experiment2 0.85846 1800
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pS6_tot experiment2 0.6598 3600
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pEGFR_tot experiment3 0 0
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pEGFR_tot experiment3 0.12816 60
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pEGFR_tot experiment3 0.13179 120
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pEGFR_tot experiment3 0.12123 300
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pEGFR_tot experiment3 0.09165 600
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pEGFR_tot experiment3 0.11645 900
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pEGFR_tot experiment3 0.049997 1800
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pEGFR_tot experiment3 0.017926 3600
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pAkt_tot experiment3 0 0
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pAkt_tot experiment3 0.38989 60
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pAkt_tot experiment3 0.82306 120
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pAkt_tot experiment3 0.49708 300
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pAkt_tot experiment3 0.2549 600
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pAkt_tot experiment3 0.19377 900
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pAkt_tot experiment3 0.12942 1800
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pAkt_tot experiment3 0.061242 3600
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pS6_tot experiment3 0 0
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pS6_tot experiment3 0.0020839 60
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pS6_tot experiment3 0.0047955 120
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pS6_tot experiment3 0.047495 300
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pS6_tot experiment3 0.39197 600
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pS6_tot experiment3 0.68142 900
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pS6_tot experiment3 1.0001 1800
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pS6_tot experiment3 0.75108 3600
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pEGFR_tot experiment4 0 0
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pEGFR_tot experiment4 0.48781 60
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pEGFR_tot experiment4 0.28974 120
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pEGFR_tot experiment4 0.24074 300
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pEGFR_tot experiment4 0.13851 600
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pEGFR_tot experiment4 0.11025 900
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pEGFR_tot experiment4 0.047644 1800
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pEGFR_tot experiment4 0.017833 3600
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pAkt_tot experiment4 0 0
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pAkt_tot experiment4 0.71187 60
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pAkt_tot experiment4 0.89633 120
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pAkt_tot experiment4 0.49719 300
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pAkt_tot experiment4 0.2397 600
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pAkt_tot experiment4 0.18333 900
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pAkt_tot experiment4 0.089574 1800
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pAkt_tot experiment4 0.037055 3600
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pS6_tot experiment4 0 0
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pS6_tot experiment4 0.0057189 60
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pS6_tot experiment4 0.013126 120
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pS6_tot experiment4 0.062408 300
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pS6_tot experiment4 0.41154 600
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pS6_tot experiment4 0.71428 900
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pS6_tot experiment4 0.92784 1800
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pS6_tot experiment4 0.55064 3600
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pEGFR_tot experiment5 0 0
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pEGFR_tot experiment5 0.90952 60
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pEGFR_tot experiment5 0.3891 120
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pEGFR_tot experiment5 0.30117 300
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pEGFR_tot experiment5 0.10321 600
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pEGFR_tot experiment5 0.10615 900
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pEGFR_tot experiment5 0.039496 1800
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pEGFR_tot experiment5 0.011403 3600
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pAkt_tot experiment5 0 0
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pAkt_tot experiment5 0.87147 60
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pAkt_tot experiment5 0.96118 120
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pAkt_tot experiment5 0.37349 300
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pAkt_tot experiment5 0.15548 600
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pAkt_tot experiment5 0.11922 900
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pAkt_tot experiment5 0.062311 1800
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pAkt_tot experiment5 0.03678 3600
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pS6_tot experiment5 0 0
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pS6_tot experiment5 0.0073292 60
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pS6_tot experiment5 0.014418 120
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pS6_tot experiment5 0.079732 300
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pS6_tot experiment5 0.4562 600
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pS6_tot experiment5 0.65294 900
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pS6_tot experiment5 0.75189 1800
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pS6_tot experiment5 0.37446 3600
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pEGFR_tot experiment6 0 0
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pEGFR_tot experiment6 0.95674 60
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pEGFR_tot experiment6 0.26888 120
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pEGFR_tot experiment6 0.34087 300
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pEGFR_tot experiment6 0.10018 600
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pEGFR_tot experiment6 0.097799 900
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pEGFR_tot experiment6 0.025369 1800
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pEGFR_tot experiment6 0.0081957 3600
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pAkt_tot experiment6 0 0
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pAkt_tot experiment6 0.99726 60
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pAkt_tot experiment6 0.8819 120
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pAkt_tot experiment6 0.27373 300
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pAkt_tot experiment6 0.11182 600
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pAkt_tot experiment6 0.073731 900
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pAkt_tot experiment6 0.053436 1800
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pAkt_tot experiment6 0.038275 3600
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pS6_tot experiment6 0 0
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pS6_tot experiment6 0.0086144 60
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pS6_tot experiment6 0.013062 120
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pS6_tot experiment6 0.07993 300
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pS6_tot experiment6 0.42868 600
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pS6_tot experiment6 0.60508 900
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pS6_tot experiment6 0.62088 1800
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pS6_tot experiment6 0.32084 3600

‎doc/example/example_Fujita/Fujita_measurementData_nanData.tsv‎

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

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