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Merged
m-philipps merged 19 commits into from
Jan 4, 2025
Merged

add the reformulated version of Fiedler_BMCSystBiol2016 #258

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23ea3cf
fix Fiedler_BMCSystBiol2016 ID
m-philipps Oct 8, 2024
60bf58a
run bmp-create-overview
m-philipps Oct 8, 2024
463333c
add reformulated Fiedler model
m-philipps Oct 8, 2024
b0a1a36
Merge branch 'master' into fiedler_reparam
m-philipps Oct 25, 2024
d988b8b
add PEtab model for reformulated Fiedler_BMCSystBiol2016
m-philipps Oct 25, 2024
21e903f
try optimisation
m-philipps Oct 25, 2024
3abfb1d
remove PREEEQUILIBRATION column
m-philipps Dec 4, 2024
065f414
remove PREEQUILIBRATION column
m-philipps Dec 4, 2024
97be5bb
update calibration script
m-philipps Dec 4, 2024
4bd6b19
Merge branch 'master' into fiedler_reparam
m-philipps Dec 4, 2024
2a7d38c
add dataset id column for convenience
m-philipps Dec 4, 2024
66bc26a
update nominal parameters with estimated values
m-philipps Dec 4, 2024
3c17601
add simulated data
m-philipps Dec 4, 2024
18484dc
remove calibration files
m-philipps Dec 4, 2024
5f76b4a
remove visualisation file
m-philipps Dec 4, 2024
5a7909d
change ID
m-philipps Jan 4, 2025
e68524c
update simulated data
m-philipps Jan 4, 2025
908c3ef
fix ID in file names
m-philipps Jan 4, 2025
2abb225
add annotation with identifier
m-philipps Jan 4, 2025
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146 changes: 73 additions & 73 deletions Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv
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Original file line number Diff line number Diff line change
@@ -1,73 +1,73 @@
observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters
pErk model1_data1 0.037959 0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk
pErk model1_data1 0.042262 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk
pErk model1_data1 0.162628 1 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk
pErk model1_data1 0.052124 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk
pErk model1_data1 0.023196 7 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk
pErk model1_data1 0.037687 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk
pErk model1_data1 0.028724 10 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk
pErk model1_data1 0.297881 0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk
pErk model1_data1 3.043549 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk
pErk model1_data1 3.098459 1 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk
pErk model1_data1 0.224662 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk
pErk model1_data1 0.38254 7 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk
pErk model1_data1 0.123338 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk
pErk model1_data1 0.229486 10 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk
pErk model1_data2 0.039731 0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data2 0.03303482 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data2 0.019296634 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data2 0.017683446 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data2 0.020209467 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data2 0.02141076 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data2 0.301624 0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data2 0.54 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data2 0.27 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data2 0.25 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data2 0.18 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data2 0.15 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data3 0.004107653 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data3 0.011631788 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data3 0.012694322 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data3 0.003687738 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data3 0.002426131 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk
pErk model1_data3 0.176167582 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data3 0.069008927 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data3 0.074311261 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data3 0.073151837 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pErk model1_data3 0.048102336 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk
pMek model1_data1 0.116721 0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek
pMek model1_data1 0.232984 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek
pMek model1_data1 0.305171 1 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek
pMek model1_data1 0.125647 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek
pMek model1_data1 0.073706 7 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek
pMek model1_data1 0.058253 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek
pMek model1_data1 0.066667 10 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek
pMek model1_data1 0.22033 0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek
pMek model1_data1 1.683107 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek
pMek model1_data1 1.441176 1 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek
pMek model1_data1 0.225572 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek
pMek model1_data1 0.278346 7 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek
pMek model1_data1 0.137178 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek
pMek model1_data1 0.196426 10 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek
pMek model1_data2 0.121231 0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data2 0.086929466 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data2 0.054910478 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data2 0.048881617 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data2 0.052341248 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data2 0.052595374 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data2 0.155276 0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data2 0.24 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data2 0.12 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data2 0.12 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data2 0.07 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data2 0.07 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data3 1.724493879 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data3 1.683168571 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data3 1.470175735 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data3 1.557371739 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data3 1.559108205 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek
pMek model1_data3 5.857600733 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data3 2.857976654 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data3 4.607660706 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data3 2.789397964 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
pMek model1_data3 1.623004546 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek
observableId simulationConditionId measurement time observableParameters noiseParameters datasetId
pErk model1_data1 0.037959 0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control
pErk model1_data1 0.042262 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control
pErk model1_data1 0.162628 1 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control
pErk model1_data1 0.052124 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control
pErk model1_data1 0.023196 7 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control
pErk model1_data1 0.037687 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control
pErk model1_data1 0.028724 10 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control
pErk model1_data1 0.297881 0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control
pErk model1_data1 3.043549 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control
pErk model1_data1 3.098459 1 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control
pErk model1_data1 0.224662 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control
pErk model1_data1 0.38254 7 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control
pErk model1_data1 0.123338 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control
pErk model1_data1 0.229486 10 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control
pErk model1_data2 0.039731 0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.03303482 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.019296634 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.017683446 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.020209467 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.02141076 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.301624 0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.54 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.27 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.25 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.18 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib
pErk model1_data2 0.15 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib
pErk model1_data3 0.004107653 1 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126
pErk model1_data3 0.011631788 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126
pErk model1_data3 0.012694322 7 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126
pErk model1_data3 0.003687738 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126
pErk model1_data3 0.002426131 10 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126
pErk model1_data3 0.176167582 1 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126
pErk model1_data3 0.069008927 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126
pErk model1_data3 0.074311261 7 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126
pErk model1_data3 0.073151837 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126
pErk model1_data3 0.048102336 10 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126
pMek model1_data1 0.116721 0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control
pMek model1_data1 0.232984 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control
pMek model1_data1 0.305171 1 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control
pMek model1_data1 0.125647 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control
pMek model1_data1 0.073706 7 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control
pMek model1_data1 0.058253 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control
pMek model1_data1 0.066667 10 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control
pMek model1_data1 0.22033 0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control
pMek model1_data1 1.683107 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control
pMek model1_data1 1.441176 1 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control
pMek model1_data1 0.225572 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control
pMek model1_data1 0.278346 7 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control
pMek model1_data1 0.137178 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control
pMek model1_data1 0.196426 10 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control
pMek model1_data2 0.121231 0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.086929466 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.054910478 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.048881617 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.052341248 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.052595374 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.155276 0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.24 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.12 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.12 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.07 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib
pMek model1_data2 0.07 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib
pMek model1_data3 1.724493879 1 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126
pMek model1_data3 1.683168571 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126
pMek model1_data3 1.470175735 7 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126
pMek model1_data3 1.557371739 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126
pMek model1_data3 1.559108205 10 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126
pMek model1_data3 5.857600733 1 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126
pMek model1_data3 2.857976654 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126
pMek model1_data3 4.607660706 7 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126
pMek model1_data3 2.789397964 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126
pMek model1_data3 1.623004546 10 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126
11 changes: 11 additions & 0 deletions Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml
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format_version: 1
parameter_file: parameters_Fiedler_BMCSystBiol2016_rel.tsv
problems:
- condition_files:
- experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv
measurement_files:
- measurementData_Fiedler_BMCSystBiol2016_rel.tsv
observable_files:
- observables_Fiedler_BMCSystBiol2016_rel.tsv
sbml_files:
- model_Fiedler_BMCSystBiol2016_rel.xml
4 changes: 4 additions & 0 deletions ...iedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv
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conditionId conditionName Sorafenib UO126
model1_data1 0 0
model1_data2 5 0
model1_data3 0 30
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