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Add support for experiments (previously named timecourses) #263

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Add support for experiments (previously named timecourses) #263

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cca2cd7
add timecourse.py:* to __init__
dilpath May 20, 2024
7d63ff0
add timecourse_df to petab.Problem
dilpath May 20, 2024
2a5ccb2
add timecourse_files to yaml.py
dilpath May 20, 2024
56b5b9e
add timecourse constants to C.py
dilpath May 20, 2024
2d6dcbb
add timecourses.py
dilpath May 24, 2024
8714e7a
save timecourses in PEtab yaml; test `to_files_generic`; add timecour…
dilpath May 24, 2024
40921a3
add test_timecourses.py
dilpath May 24, 2024
d543f1f
update measurements for timecourses; add `core.time_is_at_steady_stat…
dilpath May 29, 2024
815a258
parameter_mapping.py: update and refactor for timecourses
dilpath May 29, 2024
61dea8a
add `Timecourse` and `Period` classes
dilpath May 29, 2024
dbc210a
add `Timecourse.to_series`
dilpath May 29, 2024
df2f6a9
test denesting of nesting from `restartEvery` and nested timecourses
dilpath May 29, 2024
f4aee10
rename to experiments
dilpath Jun 2, 2024
5cabb65
update measurements
dilpath Jun 2, 2024
c98195b
update test_parameter_mapping to new par_map structure
dilpath Jun 3, 2024
2e9efcf
update sbml `get_period_model` and fix tests
dilpath Jun 4, 2024
350a38c
update simplify and lint for experiments
dilpath Jun 4, 2024
a7272b5
fix remaining nonvis tests
dilpath Jun 4, 2024
e9ca0d0
fix vis example petabs
dilpath Jun 4, 2024
cb663c4
Merge branch 'develop' into tc
dilpath Jun 4, 2024
3fc55a9
merge develop
dilpath Jul 1, 2024
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2 changes: 2 additions & 0 deletions doc/example/example_Fujita/Fujita.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand Down
7 changes: 7 additions & 0 deletions doc/example/example_Fujita/Fujita_experiments.tsv
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Original file line number Diff line number Diff line change
@@ -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
290 changes: 145 additions & 145 deletions doc/example/example_Fujita/Fujita_measurementData.tsv
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290 changes: 145 additions & 145 deletions doc/example/example_Fujita/Fujita_measurementData_minimal.tsv
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Original file line number Diff line number Diff line change
@@ -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
34 changes: 17 additions & 17 deletions doc/example/example_Fujita/Fujita_measurementData_nanData.tsv
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@@ -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