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add the reformulated version of Fiedler_BMCSystBiol2016 (#258)
* fix Fiedler_BMCSystBiol2016 ID * remove preequilibrationConditionId column from measurement table * add DatasetId column to measurement table * add reformulated model Fiedler_BMCSystBiol2016_rel
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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 |
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Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| 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 |
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...iedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| conditionId conditionName Sorafenib UO126 | ||
| model1_data1 0 0 | ||
| model1_data2 5 0 | ||
| model1_data3 0 30 |
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