diff --git a/Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml b/Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml new file mode 100644 index 0000000..4ac6086 --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml @@ -0,0 +1,13 @@ +format_version: 1 +parameter_file: parameters_Raia_CancerResearch2011.tsv +problems: +- condition_files: + - experimentalCondition_Raia_CancerResearch2011.tsv + measurement_files: + - measurementData_Raia_CancerResearch2011.tsv + observable_files: + - observables_Raia_CancerResearch2011.tsv + sbml_files: + - model_Raia_CancerResearch2011.xml + visualization_files: + - visualizationSpecification_Raia_CancerResearch2011.tsv diff --git a/Benchmark-Models/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv b/Benchmark-Models/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..4bce4aa --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv @@ -0,0 +1,5 @@ +conditionId conditionName il13_level +model1_data1 Il13 level = 0 0 +model1_data2 il13 level = 20 20 +model1_data3 il13 level = 4 4 +model1_data4 il13 level = 80 80 diff --git a/Benchmark-Models/Raia_CancerResearch2011/measurementData_Raia_CancerResearch2011.tsv b/Benchmark-Models/Raia_CancerResearch2011/measurementData_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..e5dd513 --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/measurementData_Raia_CancerResearch2011.tsv @@ -0,0 +1,206 @@ +observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters observableTransformation noiseDistribution datasetId +observable_RecSurf model1_data1 1.289752779 0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +observable_RecSurf model1_data1 1.57854438 10 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +observable_RecSurf model1_data1 1.515091272 20 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +observable_RecSurf model1_data1 1.50496416 30 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +observable_RecSurf model1_data1 1.617802874 60 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +observable_RecSurf model1_data1 1.572371701 90 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +observable_RecSurf model1_data1 1.430619477 120 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data1_RecSurf +observable_IL13_cell model1_data1 0.615740257 0 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +observable_IL13_cell model1_data1 0.295868505 15 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +observable_IL13_cell model1_data1 0.322285203 30 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +observable_IL13_cell model1_data1 0.169527777 60 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +observable_IL13_cell model1_data1 0.257966287 90 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +observable_IL13_cell model1_data1 0.231549589 120 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data1_IL13_cell +observable_SOCS3mRNA model1_data1 1.562357019 0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 0.992868163 20 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 14.83449477 30 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 11.675177 40 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 11.62681448 60 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 5.710282463 80 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 1.24343046 90 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 0.659244766 100 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_SOCS3mRNA model1_data1 14.54733886 120 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data1_SOCS3mRNA +observable_CD274mRNA model1_data1 0.01 30 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +observable_CD274mRNA model1_data1 0.042114502 60 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +observable_CD274mRNA model1_data1 0.01 90 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +observable_CD274mRNA model1_data1 0.009833619 120 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data1_CD274mRNA +observable_SOCS3 model1_data1 8.334077674 0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +observable_SOCS3 model1_data1 6.442655791 20 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +observable_SOCS3 model1_data1 7.624794468 40 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +observable_SOCS3 model1_data1 8.688719277 60 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +observable_SOCS3 model1_data1 13.29906012 90 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +observable_SOCS3 model1_data1 16.43172761 120 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data1_SOCS3 +observable_IL13_cell model1_data2 3.974680793 5 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 4.129735323 10 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 5.016417523 15 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 4.932573221 20 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 6.024846242 30 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 6.352183583 40 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 5.878980129 50 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 5.07614223 60 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 6.210911678 80 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 5.946744701 100 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_IL13_cell model1_data2 5.094519064 120 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data2_IL13_cell +observable_pIL4Ra model1_data2 0.185418978 0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 0.442239546 4 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 1.63082953 5 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 1.926293409 7 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 1.40013759 10 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 2.223954642 15 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 2.258737723 20 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 1.541743723 30 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 1.659951486 40 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 2.283486889 45 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pIL4Ra model1_data2 1.364989369 60 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data2_pIL4Ra +observable_pJAK2 model1_data2 0.221391383 0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 0.689572875 4 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.278252103 5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.688749897 7 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.388817503 10 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 2.02085372 15 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 2.10261027 20 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.642938963 25 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 2.055630098 30 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.764426702 40 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.81682256 45 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.099656357 50 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.480674485 60 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.584028801 80 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 0.922925871 100 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_pJAK2 model1_data2 1.204385534 120 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data2_pJAK2 +observable_SOCS3mRNA model1_data2 1.399863921 0 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 15.59376831 20 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 29.66110989 30 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 250.7513584 40 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 208.0216845 60 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 719.6189149 80 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 1154.942401 90 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 504.6313426 100 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_SOCS3mRNA model1_data2 1017.019576 120 scaling_SOCS3mRNA sd_SOCS3mRNA_abs;sd_SOCS3mRNA_rel lin normal model1_data2_SOCS3mRNA +observable_CD274mRNA model1_data2 0.01 30 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +observable_CD274mRNA model1_data2 0.67477531 60 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +observable_CD274mRNA model1_data2 2.304976603 90 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +observable_CD274mRNA model1_data2 1.774992771 120 scaling_CD274mRNA sd_CD274mRNA_abs;sd_CD274mRNA_rel lin normal model1_data2_CD274mRNA +observable_SOCS3 model1_data2 35.10201482 0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_SOCS3 model1_data2 23.88158667 20 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_SOCS3 model1_data2 79.71985958 40 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_SOCS3 model1_data2 148.678 60 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_SOCS3 model1_data2 259.1129009 80 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_SOCS3 model1_data2 271.9076533 90 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_SOCS3 model1_data2 255.3756956 100 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_SOCS3 model1_data2 204.4612162 120 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data2_SOCS3 +observable_pSTAT5 model1_data2 1.716733095 0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 9.772025181 5 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 32.81159437 10 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 50.80322648 15 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 68.99256124 20 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 107.9066904 25 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 111.5714137 30 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 106.7423055 35 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 104.28 40 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 125.2740088 45 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 115.7026455 50 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 128.2373073 60 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 123.2374928 70 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 89.65411083 80 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 65.83056831 90 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 108.2978696 100 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_pSTAT5 model1_data2 80.75011175 120 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data2_pSTAT5 +observable_RecSurf model1_data3 1.40469351 0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +observable_RecSurf model1_data3 1.36298049 10 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +observable_RecSurf model1_data3 1.333586237 20 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +observable_RecSurf model1_data3 1.210536056 30 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +observable_RecSurf model1_data3 1.256908767 60 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +observable_RecSurf model1_data3 1.255595571 90 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +observable_RecSurf model1_data3 1.230653226 120 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data3_RecSurf +observable_IL13_cell model1_data3 1.185996361 5 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 1.458203202 10 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 1.797026064 15 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 1.783243439 20 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 2.295497663 30 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 2.470077578 40 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 2.514871109 50 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 2.656143014 60 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 2.955915105 80 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 3.199408144 100 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_IL13_cell model1_data3 2.6205379 120 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data3_IL13_cell +observable_pIL4Ra model1_data3 0.338107913 0 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.084337349 4 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 0.539111503 5 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 0.299787385 7 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 0.845156744 10 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.175990856 15 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.35788895 17.5 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.442254159 20 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.123066049 22.5 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.551873086 25 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.147885063 30 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 0.995444907 35 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.242317637 40 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.28102483 45 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.194533888 50 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pIL4Ra model1_data3 1.133331567 60 scaling_pIL4Ra sd_pIL4Ra_abs;sd_pIL4Ra_rel lin normal model1_data3_pIL4Ra +observable_pJAK2 model1_data3 0.187105104 0 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.533560311 2.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.645132088 4 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.639432248 5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.245165007 7 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.152528245 7.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.834682988 10 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.45841689 12.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.288880253 15 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.275386838 17.5 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.432895442 20 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.842800855 25 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.36716485 30 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.753162054 35 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.434440914 40 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.036951691 45 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.150316562 50 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.37390999 60 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.216679546 75 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 1.490035697 90 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.365588806 105 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pJAK2 model1_data3 0.66753154 120 scaling_pJAK2 sd_pJAK2_abs;sd_pJAK2_rel lin normal model1_data3_pJAK2 +observable_pSTAT5 model1_data3 1.598406966 0 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 2.012148639 5 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 7.644693901 10 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 30.339995 15 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 34.49644889 20 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 54.73958911 25 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 48.86794422 30 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 57.76829847 35 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 68.400004 40 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 57.5319745 45 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 84.08635186 50 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 80.47435164 60 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 66.61604471 70 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 57.65815916 80 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 52.79857246 100 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_pSTAT5 model1_data3 56.17671662 120 sd_pSTAT5_abs;sd_pSTAT5_rel lin normal model1_data3_pSTAT5 +observable_RecSurf model1_data4 1.321308168 0 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +observable_RecSurf model1_data4 1.179069779 10 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +observable_RecSurf model1_data4 1.042164123 20 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +observable_RecSurf model1_data4 1.056526564 30 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +observable_RecSurf model1_data4 1.056091246 60 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +observable_RecSurf model1_data4 1.078735295 90 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +observable_RecSurf model1_data4 0.929233191 120 sd_RecSurf_abs;sd_RecSurf_rel lin normal model1_data4_RecSurf +observable_IL13_cell model1_data4 9.781760071 5 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 9.951745778 10 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 10.67418503 15 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 11.24846107 20 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 12.74732152 30 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 12.39816169 40 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 10.96936291 50 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 8.286345273 60 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 11.34493944 80 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 11.19792478 100 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_IL13_cell model1_data4 10.55243851 120 scaling_IL13_cell sd_IL13_cell_abs;sd_IL13_cell_rel lin normal model1_data4_IL13_cell +observable_SOCS3 model1_data4 6.04829306 0 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +observable_SOCS3 model1_data4 6.231540693 20 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +observable_SOCS3 model1_data4 87.45060405 40 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +observable_SOCS3 model1_data4 103.2714398 60 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +observable_SOCS3 model1_data4 221.7408479 80 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +observable_SOCS3 model1_data4 262.8501062 100 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 +observable_SOCS3 model1_data4 140.7680663 120 sd_SOCS3_abs;sd_SOCS3_rel lin normal model1_data4_SOCS3 diff --git a/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml b/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml new file mode 100644 index 0000000..c9381f7 --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml @@ -0,0 +1,441 @@ + + + + + + 
PEtab implementation of the model from Raia et al. (2011), Cancer Res February 1 2011 (71) (3) 693-704
+ + + + + + + + + + Raia + Valentina + + + + + + 2019-11-29T09:41:48Z + + + 2019-11-29T09:41:48Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + init_Rec_i + + + + + + + + + + + + + + + + cyt + 2.265 + il13_level + Kon_IL13Rec + Rec + + + + + + + + + + + + + + + + cyt + Rec + Rec_intern + + + + + + + + + + + + + + + + cyt + Rec_i + Rec_recycle + + + + + + + + + + + + + + + + + + + cyt + IL13_Rec + Rec_phosphorylation + pJAK2 + + + + + + + + + + + + + + + + + + + + cyt + + + + + IL13_Rec + JAK2 + JAK2_phosphorylation + + + + + + JAK2_p_inhibition + SOCS3 + + 1 + + + + + + + + + + + + + + + + + + + + + + cyt + + + + + JAK2 + JAK2_phosphorylation + p_IL13_Rec + + + + + + JAK2_p_inhibition + SOCS3 + + 1 + + + + + + + + + + + + + + + + + + cyt + pRec_intern + p_IL13_Rec + + + + + + + + + + + + + cyt + pRec_degradation + p_IL13_Rec_i + + + + + + + + + + + + + + + + cyt + 91 + pJAK2 + pJAK2_dephosphorylation + + + + + + + + + + + + + + + + + + + cyt + STAT5 + STAT5_phosphorylation + pJAK2 + + + + + + + + + + + + + + + + cyt + 91 + pSTAT5 + pSTAT5_dephosphorylation + + + + + + + + + + + + + + + + cyt + 2.265 + il13_level + DecoyR + DecoyR_binding + + + + + + + + + + + + + + + + nuc + SOCS3mRNA_production + pSTAT5 + + + + + + + + + + + + + + + + cyt + + + + + SOCS3mRNA + SOCS3_translation + + + + SOCS3mRNA + SOCS3_accumulation + + + + + + + + + + + + + + + cyt + SOCS3 + SOCS3_degradation + + + + + + + + + + + + + + + + nuc + CD274mRNA_production + pSTAT5 + + + + + + + diff --git a/Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv b/Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..4bf1ba0 --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv @@ -0,0 +1,9 @@ +observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution +observable_CD274mRNA CD274mRNA * observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA + noiseParameter2_observable_CD274mRNA * observable_CD274mRNA lin normal +observable_IL13_cell observableParameter1_observable_IL13_cell * (IL13_Rec + IL13_DecoyR + p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_IL13_cell + noiseParameter2_observable_IL13_cell * observable_IL13_cell lin normal +observable_RecSurf IL13_Rec + Rec + p_IL13_Rec noiseParameter1_observable_RecSurf + noiseParameter2_observable_RecSurf * observable_RecSurf lin normal +observable_SOCS3 SOCS3 noiseParameter1_observable_SOCS3 + noiseParameter2_observable_SOCS3 * observable_SOCS3 lin normal +observable_SOCS3mRNA SOCS3mRNA * observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA + noiseParameter2_observable_SOCS3mRNA * observable_SOCS3mRNA lin normal +observable_pIL4Ra observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_pIL4Ra + noiseParameter2_observable_pIL4Ra * observable_pIL4Ra lin normal +observable_pJAK2 pJAK2 * observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2 + noiseParameter2_observable_pJAK2 * observable_pJAK2 lin normal +observable_pSTAT5 pSTAT5 noiseParameter1_observable_pSTAT5 + noiseParameter2_observable_pSTAT5 * observable_pSTAT5 lin normal diff --git a/Benchmark-Models/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv b/Benchmark-Models/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..0526a8a --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv @@ -0,0 +1,40 @@ +parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate +CD274mRNA_production CD274mRNA_{production} log10 1E-05 1000 0.021208853684209 1 +DecoyR_binding DecoyR_{binding} log10 1E-05 1000 0.003851039137402 1 +JAK2_p_inhibition JAK2_{p,inhibition} log10 1E-05 1000 0.078140000505809 1 +JAK2_phosphorylation JAK2_{phosphorylation} log10 1E-05 1000 1.01721171826747 1 +Kon_IL13Rec Kon_{IL13Rec} log10 1E-05 1000 0.002278141087201 1 +Rec_intern Rec_{intern} log10 1E-05 1000 0.344129281159739 1 +Rec_phosphorylation Rec_{phosphorylation} log10 1E-05 1000 999.999816483984 1 +Rec_recycle Rec_{recycle} log10 1E-05 1000 0.00209774906794 1 +SOCS3_accumulation SOCS3_{accumulation} log10 1E-05 1000 451.777901711184 1 +SOCS3_degradation SOCS3_{degradation} log10 1E-05 1000 0.043380223348167 1 +SOCS3_translation SOCS3_{translation} log10 1E-05 1000 15.7186888386006 1 +SOCS3mRNA_production SOCS3mRNA_{production} log10 1E-05 1000 0.14337151776186 1 +STAT5_phosphorylation STAT5_{phosphorylation} log10 1E-05 1000 0.01948207479306 1 +init_Rec_i init_{Rec,i} log10 1E-05 1000 235.058493601113 1 +pJAK2_dephosphorylation pJAK2_{dephosphorylation} log10 1E-05 1000 0.000175894009439 1 +pRec_degradation pRec_{degradation} log10 1E-05 1000 0.209573978543856 1 +pRec_intern pRec_{intern} log10 1E-05 1000 0.585271535297764 1 +pSTAT5_dephosphorylation pSTAT5_{dephosphorylation} log10 1E-05 1000 0.000274832319318 1 +scaling_CD274mRNA scaling_{CD274mRNA} log10 1E-05 1000 0.00815283660871 1 +scaling_IL13_cell scaling_{IL13,cell} log10 1E-05 1000 5.50098613841361 1 +scaling_SOCS3mRNA scaling_{SOCS3mRNA} log10 1E-05 1000 0.581287913862507 1 +scaling_pIL4Ra scaling_{pIL4Ra} log10 1E-05 1000 2.9757729322919 1 +scaling_pJAK2 scaling_{pJAK2} log10 1E-05 1000 0.857246885626022 1 +sd_SOCS3mRNA_abs sd_SOCS3mRNA_abs log10 1E-05 1000 9.2 1 +sd_RecSurf_abs sd_RecSurf_abs log10 1E-05 1000 1.00E-05 1 +sd_pSTAT5_rel sd_pSTAT5_rel log10 1E-05 1000 0.18 1 +sd_IL13_cell_rel sd_IL13_cell_rel log10 1E-05 1000 0.065 1 +sd_RecSurf_rel sd_RecSurf_rel log10 1E-05 1000 0.078 1 +sd_pJAK2_abs sd_pJAK2_abs log10 1E-05 1000 0.32 1 +sd_pIL4Ra_abs sd_pIL4Ra_abs log10 1E-05 1000 0.62 1 +sd_CD274mRNA_rel sd_CD274mRNA_rel log10 1E-05 1000 0.61 1 +sd_SOCS3mRNA_rel sd_SOCS3mRNA_rel log10 1E-05 1000 0.52 1 +sd_pIL4Ra_rel sd_pIL4Ra_rel log10 1E-05 1000 1.10E-05 1 +sd_IL13_cell_abs sd_IL13_cell_abs log10 1E-05 1000 0.28 1 +sd_SOCS3_rel sd_SOCS3_rel log10 1E-05 1000 0.18 1 +sd_CD274mRNA_abs sd_CD274mRNA_abs log10 1E-05 1000 0.024 1 +sd_pSTAT5_abs sd_pSTAT5_abs log10 1E-05 1000 1.4 1 +sd_SOCS3_abs sd_SOCS3_abs log10 1E-05 1000 15 1 +sd_pJAK2_rel sd_pJAK2_rel log10 1E-05 1000 1.00E-05 1 diff --git a/Benchmark-Models/Raia_CancerResearch2011/simulatedData_Raia_CancerResearch2011.tsv b/Benchmark-Models/Raia_CancerResearch2011/simulatedData_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..d1c9579 --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/simulatedData_Raia_CancerResearch2011.tsv @@ -0,0 +1,206 @@ +observableId preequilibrationCondition simulationCondition simulation time observableParameters noiseParameters +RecSurf model1_data1 1.3 0 +RecSurf model1_data1 1.427926242 10 +RecSurf model1_data1 1.4319383562 20 +RecSurf model1_data1 1.432064218 30 +RecSurf model1_data1 1.4320683867 60 +RecSurf model1_data1 1.4320684562 90 +RecSurf model1_data1 1.4320684584 120 +IL13_cell model1_data1 0 0 +IL13_cell model1_data1 0 15 +IL13_cell model1_data1 0 30 +IL13_cell model1_data1 0 60 +IL13_cell model1_data1 0 90 +IL13_cell model1_data1 0 120 +SOCS3mRNA model1_data1 0 0 +SOCS3mRNA model1_data1 0 20 +SOCS3mRNA model1_data1 0 30 +SOCS3mRNA model1_data1 0 40 +SOCS3mRNA model1_data1 0 60 +SOCS3mRNA model1_data1 0 80 +SOCS3mRNA model1_data1 0 90 +SOCS3mRNA model1_data1 0 100 +SOCS3mRNA model1_data1 0 120 +CD274mRNA model1_data1 0 30 +CD274mRNA model1_data1 0 60 +CD274mRNA model1_data1 0 90 +CD274mRNA model1_data1 0 120 +SOCS3 model1_data1 0 0 +SOCS3 model1_data1 0 20 +SOCS3 model1_data1 0 40 +SOCS3 model1_data1 0 60 +SOCS3 model1_data1 0 90 +SOCS3 model1_data1 0 120 +IL13_cell model1_data2 3.7024348123 5 +IL13_cell model1_data2 5.1026012059 10 +IL13_cell model1_data2 5.6061765227 15 +IL13_cell model1_data2 5.7871881096 20 +IL13_cell model1_data2 5.8672215586 30 +IL13_cell model1_data2 5.8625775062 40 +IL13_cell model1_data2 5.8456085207 50 +IL13_cell model1_data2 5.8268553725 60 +IL13_cell model1_data2 5.788996529 80 +IL13_cell model1_data2 5.7514395189 100 +IL13_cell model1_data2 5.7142386514 120 +pIL4Ra model1_data2 0 0 +pIL4Ra model1_data2 1.226370545 4 +pIL4Ra model1_data2 1.4137574553 5 +pIL4Ra model1_data2 1.6865488089 7 +pIL4Ra model1_data2 1.9251305934 10 +pIL4Ra model1_data2 2.0946684877 15 +pIL4Ra model1_data2 2.1495822965 20 +pIL4Ra model1_data2 2.1673789234 30 +pIL4Ra model1_data2 2.160402643 40 +pIL4Ra model1_data2 2.1555141743 45 +pIL4Ra model1_data2 2.140140007 60 +pJAK2 model1_data2 0 0 +pJAK2 model1_data2 0.9775092322 4 +pJAK2 model1_data2 1.2102338931 5 +pJAK2 model1_data2 1.5564372517 7 +pJAK2 model1_data2 1.8547029057 10 +pJAK2 model1_data2 2.0411811523 15 +pJAK2 model1_data2 2.0678225772 20 +pJAK2 model1_data2 2.036161077 25 +pJAK2 model1_data2 1.9807970906 30 +pJAK2 model1_data2 1.8462457668 40 +pJAK2 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64.8726802287 35 +pSTAT5 model1_data3 70.0862329678 40 +pSTAT5 model1_data3 73.7501381984 45 +pSTAT5 model1_data3 76.1821120513 50 +pSTAT5 model1_data3 78.3751652344 60 +pSTAT5 model1_data3 78.2340324455 70 +pSTAT5 model1_data3 76.7224653597 80 +pSTAT5 model1_data3 71.6980840069 100 +pSTAT5 model1_data3 65.7771184221 120 +RecSurf model1_data4 1.3 0 +RecSurf model1_data4 1.1049968747 10 +RecSurf model1_data4 1.0898045247 20 +RecSurf model1_data4 1.0774192011 30 +RecSurf model1_data4 1.041131316 60 +RecSurf model1_data4 1.0060657941 90 +RecSurf model1_data4 0.9721785729 120 +IL13_cell model1_data4 8.8441547846 5 +IL13_cell model1_data4 10.572248259 10 +IL13_cell model1_data4 11.0789193277 15 +IL13_cell model1_data4 11.218392462 20 +IL13_cell model1_data4 11.2025120759 30 +IL13_cell model1_data4 11.1076204284 40 +IL13_cell model1_data4 11.0040750003 50 +IL13_cell model1_data4 10.9005095881 60 +IL13_cell model1_data4 10.6965838267 80 +IL13_cell model1_data4 10.497236095 100 +IL13_cell model1_data4 10.3023831625 120 +SOCS3 model1_data4 0 0 +SOCS3 model1_data4 20.248449512 20 +SOCS3 model1_data4 87.1663276835 40 +SOCS3 model1_data4 153.238083014 60 +SOCS3 model1_data4 202.2629088523 80 +SOCS3 model1_data4 235.9720185864 100 +SOCS3 model1_data4 258.9746918774 120 diff --git a/Benchmark-Models/Raia_CancerResearch2011/visualizationSpecification_Raia_CancerResearch2011.tsv b/Benchmark-Models/Raia_CancerResearch2011/visualizationSpecification_Raia_CancerResearch2011.tsv new file mode 100644 index 0000000..203ef82 --- /dev/null +++ b/Benchmark-Models/Raia_CancerResearch2011/visualizationSpecification_Raia_CancerResearch2011.tsv @@ -0,0 +1,24 @@ +plotId plotName plotTypeSimulation plotTypeData datasetId xValues xLabel yValues yLabel legendEntry +plot1 RecSurf LinePlot MeanAndSD model1_data1_RecSurf time Time [s] observable_RecSurf Phosphorylation (AU) IL13 = 0 +plot1 RecSurf LinePlot MeanAndSD model1_data3_RecSurf time Time [s] observable_RecSurf Phosphorylation (AU) IL13 = 4 +plot1 RecSurf LinePlot MeanAndSD model1_data4_RecSurf time Time [s] observable_RecSurf Phosphorylation (AU) IL13 = 80 +plot2 IL13_cell LinePlot MeanAndSD model1_data1_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 0 +plot2 IL13_cell LinePlot MeanAndSD model1_data2_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 20 +plot2 IL13_cell LinePlot MeanAndSD model1_data3_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 4 +plot2 IL13_cell LinePlot MeanAndSD model1_data4_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 80 +plot3 SOCS3mRNA LinePlot MeanAndSD model1_data1_SOCS3mRNA time Time [s] observable_SOCS3mRNA Phosphorylation (AU) IL13 = 0 +plot3 SOCS3mRNA LinePlot MeanAndSD model1_data2_SOCS3mRNA time Time [s] observable_SOCS3mRNA Phosphorylation (AU) IL13 = 20 +plot4 CD274mRNA LinePlot MeanAndSD model1_data1_CD274mRNA time Time [s] observable_CD274mRNA Phosphorylation (AU) IL13 = 0 +plot4 CD274mRNA LinePlot MeanAndSD model1_data2_CD274mRNA time Time [s] observable_CD274mRNA Phosphorylation (AU) IL13 = 20 +plot5 SOCS3 LinePlot MeanAndSD model1_data1_SOCS3 time Time [s] observable_SOCS3 Phosphorylation (AU) IL13 = 0 +plot5 SOCS3 LinePlot MeanAndSD model1_data2_SOCS3 time Time [s] observable_SOCS3 Phosphorylation (AU) IL13 = 20 +plot5 SOCS3 LinePlot MeanAndSD model1_data4_SOCS3 time Time [s] observable_SOCS3 Phosphorylation (AU) IL13 = 80 +plot6 IL13_cell LinePlot MeanAndSD model1_data2_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 20 +plot6 IL13_cell LinePlot MeanAndSD model1_data3_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 4 +plot6 IL13_cell LinePlot MeanAndSD model1_data4_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 80 +plot7 pIL4Ra LinePlot MeanAndSD model1_data2_pIL4Ra time Time [s] observable_pIL4Ra Phosphorylation (AU) IL13 = 20 +plot7 pIL4Ra LinePlot MeanAndSD model1_data3_pIL4Ra time Time [s] observable_pIL4Ra Phosphorylation (AU) IL13 = 4 +plot8 pJAK2 LinePlot MeanAndSD model1_data2_pJAK2 time Time [s] observable_pJAK2 Phosphorylation (AU) IL13 = 20 +plot8 pJAK2 LinePlot MeanAndSD model1_data3_pJAK2 time Time [s] observable_pJAK2 Phosphorylation (AU) IL13 = 4 +plot9 pSTAT5 LinePlot MeanAndSD model1_data2_pSTAT5 time Time [s] observable_pSTAT5 Phosphorylation (AU) IL13 = 20 +plot9 pSTAT5 LinePlot MeanAndSD model1_data3_pSTAT5 time Time [s] observable_pSTAT5 Phosphorylation (AU) IL13 = 4 diff --git a/README.md b/README.md index 4923d85..4b12012 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,7 @@ Contributions to the collection are very welcome. For this, please create a new | [Oliveira_NatCommun2021](Benchmark-Models/Oliveira_NatCommun2021/) | 1 | 12 | 0 | 0 | 0 | 120 | 2 | normal | 9 | [\[1\]](http://identifiers.org/doi/10.1038/s41467-020-19798-3) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Oliveira_NatCommun2021/Oliveira_NatCommun2021_model.xml) | | [Perelson_Science1996](Benchmark-Models/Perelson_Science1996/) | 1 | 3 | 0 | 0 | 0 | 16 | 1 | log10-normal | 4 | [\[1\]](http://identifiers.org/doi/10.1126/science.271.5255.1582) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Perelson_Science1996/model_Perelson_Science1996.xml) | | [Rahman_MBS2016](Benchmark-Models/Rahman_MBS2016/) | 1 | 9 | 0 | 0 | 0 | 23 | 1 | normal | 7 | [\[1\]](http://identifiers.org/doi/10.1016/j.mbs.2016.07.009) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml) | +| [Raia_CancerResearch2011](Benchmark-Models/Raia_CancerResearch2011/) | 4 | 39 | 0 | 0 | 0 | 205 | 8 | normal | 14 | [\[1\]](https://doi.org/10.1158/0008-5472.CAN-10-2987) "MedB-1 model" | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml) | | [Raimundez_PCB2020](Benchmark-Models/Raimundez_PCB2020/) | 170 | 136 | 0 | 4 | 0 | 627 | 79 | normal | 22 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pcbi.1007147) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Raimundez_PCB2020/model_Raimundez_PCB2020.xml) | | [SalazarCavazos_MBoC2020](Benchmark-Models/SalazarCavazos_MBoC2020/) | 4 | 6 | 0 | 0 | 0 | 18 | 3 | normal | 75 | [\[1\]](http://identifiers.org/doi/10.1091/mbc.E19-09-0548) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/SalazarCavazos_MBoC2020/model_SalazarCavazos_MBoC2020.xml) | | [Schwen_PONE2014](Benchmark-Models/Schwen_PONE2014/) | 19 | 30 | 0 | 0 | 0 | 286 | 4 | log10-normal | 11 | [\[1\]](http://identifiers.org/doi/10.1371/journal.pone.0133653) | [\[1\]](https://sbml4humans.de/model_url?url=https://raw.githubusercontent.com/Benchmarking-Initiative/Benchmark-Models-PEtab/master/Benchmark-Models/Schwen_PONE2014/model_Schwen_PONE2014.xml) |