diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv index df0578f..9d1adc7 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/measurementData_Fiedler_BMCSystBiol2016.tsv @@ -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 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml new file mode 100644 index 0000000..3b4e7e2 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/Fiedler_BMCSystBiol2016_rel.yaml @@ -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 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv new file mode 100644 index 0000000..2d18519 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/experimentalCondition_Fiedler_BMCSystBiol2016_rel.tsv @@ -0,0 +1,4 @@ +conditionId conditionName Sorafenib UO126 +model1_data1 0 0 +model1_data2 5 0 +model1_data3 0 30 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016_rel.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016_rel.tsv new file mode 100644 index 0000000..0c8c060 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/measurementData_Fiedler_BMCSystBiol2016_rel.tsv @@ -0,0 +1,73 @@ +observableId simulationConditionId measurement time observableParameters noiseParameters datasetId +pMek_rel model1_data1 0.116721 0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.232984 0.25 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.305171 1 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.125647 5.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.073706 7 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.058253 8.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.066667 10 s_pMek_rel_20140430_gel1 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a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv new file mode 100644 index 0000000..da0359b --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/observables_Fiedler_BMCSystBiol2016_rel.tsv @@ -0,0 +1,3 @@ +observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution +pMek_rel [pMEK]/MEK_0 x2 * observableParameter1_pMek_rel noiseParameter1_pMek_rel*noiseParameter2_pMek_rel lin normal +pErk_rel [pERK]/ERK_0 x3 * observableParameter1_pErk_rel noiseParameter1_pErk_rel*noiseParameter2_pErk_rel lin normal \ No newline at end of file diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016_rel.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016_rel.tsv new file mode 100644 index 0000000..88e1f7e --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/parameters_Fiedler_BMCSystBiol2016_rel.tsv @@ -0,0 +1,23 @@ +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate +k11_k10 k_{1,1}/k{1,0} log10 1E-04 1E02 99.99999999999484 1 +tau1 \tau_{1} log10 1E-04 1E02 0.00010000000000000521 1 +tau2 \tau_{2} log10 1E-04 1E02 0.09288918225167495 1 +K1_ERK0 K_1/[ERK]_0 log10 1E-04 1E02 0.00010000000000012946 1 +k11 k_{1,1} log10 1E-04 1E02 26.142114172396994 1 +k2 k_2 log10 1E-04 1E02 1.757125014844015 1 +K2 K_2 log10 1E-04 1E02 1.6238964133341307 1 +k3_Raf0 k_3[Raf]_0 log10 1E-04 1E02 99.99999999999488 1 +k4 k_4 log10 1E-04 1E02 2.8508244620658574 1 +K3 K_3 log10 1E-04 1E02 0.8147224203594344 1 +k5_MEK0 k_5[MEK]_0 log10 1E-04 1E02 50.6208607696601 1 +k6 k_6 log10 1E-04 1E02 3.0464232664775106 1 +s_pMek_rel_20140430_gel1 s_{pMek_rel,20140430,gel1} log10 1E-04 1E02 9.113038276921857 1 +s_pMek_rel_20140430_gel2 s_{pMek_rel,20140430,gel2} log10 1E-04 1E02 40.51627466624935 1 +s_pMek_rel_20140505_gel1 s_{pMek_rel,20140505,gel1} log10 1E-04 1E02 46.07048727325895 1 +s_pMek_rel_20140505_gel2 s_{pMek_rel,20140505,gel2} log10 1E-04 1E02 99.99999999999484 1 +s_pErk_rel_20140430_gel1 s_{pErk_rel,20140430,gel1} log10 1E-04 1E02 0.4021713054528761 1 +s_pErk_rel_20140430_gel2 s_{pErk_rel,20140430,gel2} log10 1E-04 1E02 0.2576150559169624 1 +s_pErk_rel_20140505_gel1 s_{pErk_rel,20140505,gel1} log10 1E-04 1E02 9.945014474175611 1 +s_pErk_rel_20140505_gel2 s_{pErk_rel,20140505,gel2} log10 1E-04 1E02 2.93201266036779 1 +sigma_pMek_rel \sigma_{pMek_rel} log10 1E-10 1E02 0.005555731242143642 1 +sigma_pErk_rel \sigma_{pErk_rel} log10 1E-10 1E02 0.042968298321873856 1 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/simulatedData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/simulatedData_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..389b3e4 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/reformulated/simulatedData_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,73 @@ +observableId simulationConditionId simulation time observableParameters noiseParameters datasetId +pErk_rel model1_data1 0.03562601663400499 0.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.07699231174258513 0.25 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.14402998418113844 1.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.03574741674348277 5.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.035609796661362776 7.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.035628205279640356 8.5 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.03562574483699764 10.0 s_pErk_rel_20140430_gel1 s_pErk_rel_20140430_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8809709849473971 0.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 1.9038893235260133 0.25 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 3.561617295852907 1.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8839730038123768 5.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8805698925260571 7.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8810251064429573 8.5 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pErk_rel model1_data1 0.8809642638682561 10.0 s_pErk_rel_20140505_gel1 s_pErk_rel_20140505_gel1;sigma_pErk_rel control +pMek_rel model1_data1 0.053304487267850226 0.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2890457361885378 0.25 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2664185694635477 1.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05326846796565126 5.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05330751822204037 7.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05330430271665209 8.5 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.05330448502782727 10.0 s_pMek_rel_20140430_gel1 s_pMek_rel_20140430_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.26947804098443656 0.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.4612555665641016 0.25 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 1.3468651113771104 1.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2692959472904211 5.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.26949336381445216 7.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.26947710799552915 8.5 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pMek_rel model1_data1 0.2694780296601179 10.0 s_pMek_rel_20140505_gel1 s_pMek_rel_20140505_gel1;sigma_pMek_rel control +pErk_rel model1_data2 0.022820619330195413 0.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.037750653794211476 1.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011577563362067483 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011576634634047235 7.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011576970135300398 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.011576893591693477 10.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.2597299468985005 0.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.42965421593009245 1.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.1317685499124472 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.13175797971380834 7.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.13176179817821582 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pErk_rel model1_data2 0.131760927006988 10.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel Sorafenib +pMek_rel model1_data2 0.23699003356071716 0.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.357828707080205 1.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11440162749435745 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11477459986885565 7.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11472507878847057 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.11473163273667024 10.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.5849255281066625 0.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.8831727744660174 1.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.28235968986963594 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.28328023939589553 7.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.2831580142387383 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pMek_rel model1_data2 0.28317419032662805 10.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel Sorafenib +pErk_rel model1_data3 0.006736047578857687 1.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0037868589718997466 5.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0037913343479712073 7.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.003790745494772537 8.5 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0037908227143303723 10.0 s_pErk_rel_20140430_gel2 s_pErk_rel_20140430_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.07666546006696386 1.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.043099648850555936 5.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.043150584768314015 7.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.0431438828112896 8.5 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pErk_rel model1_data3 0.04314476167576588 10.0 s_pErk_rel_20140505_gel2 s_pErk_rel_20140505_gel2;sigma_pErk_rel UO126 +pMek_rel model1_data3 2.078148965157676 1.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.375499754701807 5.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.377579664273273 7.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.3772966402008164 8.5 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 1.3773351165383614 10.0 s_pMek_rel_20140430_gel2 s_pMek_rel_20140430_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 5.129170888183106 1.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.394931459104624 5.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.4000649754226933 7.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.39936643125794 8.5 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 +pMek_rel model1_data3 3.3994613963993845 10.0 s_pMek_rel_20140505_gel2 s_pMek_rel_20140505_gel2;sigma_pMek_rel UO126 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv index 77a5836..134774d 100644 --- a/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/simulatedData_Fiedler_BMCSystBiol2016.tsv @@ -1,73 +1,73 @@ -observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters -pErk model1_data1 0.03361643271144515 0.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.08384600871194502 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.14529413431664095 1.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.03373888438216745 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.03361660721448361 7.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.033614606544540175 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.03361682359235068 10.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk -pErk model1_data1 0.8126060252664574 0.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 2.0267995851526917 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 3.5121778088422517 1.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.8155660349226578 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.8126102435076284 7.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.812561881551303 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pErk model1_data1 0.8126154739840452 10.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk -pMek model1_data1 0.04863500550105047 0.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.28579620668392197 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.28761271518189074 1.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.04892443748331804 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.04861268829425418 7.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.048635535764149945 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.04863522217188459 10.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek -pMek model1_data1 0.24552376547695293 0.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.4427830345891586 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 1.45195330200966 1.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.24698490297254252 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.24541110167459282 7.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.2455264424005296 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pMek model1_data1 0.2455248592948422 10.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek -pErk model1_data2 0.022771734786134104 0.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.03631870697453655 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.011295410041568654 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.011240689927851936 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.01124690853273153 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.011246374775472459 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data2 0.2600384889733869 0.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.41473615303461114 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.12898628001468046 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.1283614116934487 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.12843242414074793 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data2 0.12842632897793177 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pMek model1_data2 0.25288130419190086 0.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.38089387885488346 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11921586344671047 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11881098439949271 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11887339130720243 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.11886560414931766 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data2 0.6256030660476078 0.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.9422933783572799 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29492812816711056 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29392649788001884 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29408088633087925 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data2 0.29406162168075384 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pErk model1_data3 0.00678828316965931 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.0041676476822826445 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.00416424385399046 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.004164954335288319 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.004164841688668539 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk -pErk model1_data3 0.07751780506580175 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.04759184208197086 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.04755297256350257 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.04756108580058681 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pErk model1_data3 0.047559799449016726 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk -pMek model1_data3 2.0430841389034655 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.377916119880504 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.378050495730159 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.3781283022947328 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 1.3781066885745035 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek -pMek model1_data3 5.05438591269406 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.408826730423337 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.4091591628418403 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.40935164850428 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek -pMek model1_data3 3.4092981783211544 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek +observableId simulationConditionId simulation time observableParameters noiseParameters datasetId +pErk model1_data1 0.03361643271144515 0.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.08384600871194502 0.25 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.14529413431664095 1.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.03373888438216745 5.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.03361660721448361 7.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.033614606544540175 8.5 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.03361682359235068 10.0 s_pErk_20140430_gel1 s_pErk_20140430_gel1;sigma_pErk control +pErk model1_data1 0.8126060252664574 0.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 2.0267995851526917 0.25 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 3.5121778088422517 1.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.8155660349226578 5.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.8126102435076284 7.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.812561881551303 8.5 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pErk model1_data1 0.8126154739840452 10.0 s_pErk_20140505_gel1 s_pErk_20140505_gel1;sigma_pErk control +pMek model1_data1 0.04863500550105047 0.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.28579620668392197 0.25 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.28761271518189074 1.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.04892443748331804 5.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.04861268829425418 7.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.048635535764149945 8.5 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.04863522217188459 10.0 s_pMek_20140430_gel1 s_pMek_20140430_gel1;sigma_pMek control +pMek model1_data1 0.24552376547695293 0.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 1.4427830345891586 0.25 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 1.45195330200966 1.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.24698490297254252 5.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.24541110167459282 7.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.2455264424005296 8.5 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pMek model1_data1 0.2455248592948422 10.0 s_pMek_20140505_gel1 s_pMek_20140505_gel1;sigma_pMek control +pErk model1_data2 0.022771734786134104 0.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.03631870697453655 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.011295410041568654 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.011240689927851936 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.01124690853273153 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.011246374775472459 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.2600384889733869 0.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.41473615303461114 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.12898628001468046 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.1283614116934487 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.12843242414074793 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pErk model1_data2 0.12842632897793177 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk Sorafenib +pMek model1_data2 0.25288130419190086 0.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.38089387885488346 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11921586344671047 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11881098439949271 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11887339130720243 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.11886560414931766 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.6256030660476078 0.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.9422933783572799 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29492812816711056 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29392649788001884 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29408088633087925 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pMek model1_data2 0.29406162168075384 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek Sorafenib +pErk model1_data3 0.00678828316965931 1.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.0041676476822826445 5.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.00416424385399046 7.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.004164954335288319 8.5 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.004164841688668539 10.0 s_pErk_20140430_gel2 s_pErk_20140430_gel2;sigma_pErk UO126 +pErk model1_data3 0.07751780506580175 1.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.04759184208197086 5.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.04755297256350257 7.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.04756108580058681 8.5 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pErk model1_data3 0.047559799449016726 10.0 s_pErk_20140505_gel2 s_pErk_20140505_gel2;sigma_pErk UO126 +pMek model1_data3 2.0430841389034655 1.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.377916119880504 5.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.378050495730159 7.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.3781283022947328 8.5 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 1.3781066885745035 10.0 s_pMek_20140430_gel2 s_pMek_20140430_gel2;sigma_pMek UO126 +pMek model1_data3 5.05438591269406 1.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.408826730423337 5.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.4091591628418403 7.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.40935164850428 8.5 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 +pMek model1_data3 3.4092981783211544 10.0 s_pMek_20140505_gel2 s_pMek_20140505_gel2;sigma_pMek UO126 diff --git a/Benchmark-Models/Fiedler_BMCSystBiol2016/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv b/Benchmark-Models/Fiedler_BMCSystBiol2016/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv new file mode 100644 index 0000000..6ac3521 --- /dev/null +++ b/Benchmark-Models/Fiedler_BMCSystBiol2016/visualizationSpecification_Fiedler_BMCSystBiol2016.tsv @@ -0,0 +1,7 @@ +plotId plotName plotTypeSimulation plotTypeData xLabel yValues yLabel datasetId +pMek_control pMek - control LinePlot replicate time [h] pMek pMek control +pMek_Sorafenib pMek - 5 muM Sorafenib LinePlot replicate time [h] pMek pMek Sorafenib +pMek_UO126 pMek - 30 muM UO126 LinePlot replicate time [h] pMek pMek UO126 +pErk_control pErk - control LinePlot replicate time [h] pErk pErk control +pErk_Sorafenib pErk - 5 muM Sorafenib LinePlot replicate time [h] pErk pErk Sorafenib +pErk_UO126 pErk - 30 muM UO126 LinePlot replicate time [h] pErk pErk UO126