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Merge pull request #191 from m-philipps/model_Raia_CancerResearch2011
Add model Raia_CancerResearch2011
2 parents 08a0430 + 0775f54 commit ac228b5

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‎Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml‎

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format_version: 1
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parameter_file: parameters_Raia_CancerResearch2011.tsv
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problems:
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- condition_files:
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- experimentalCondition_Raia_CancerResearch2011.tsv
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measurement_files:
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- measurementData_Raia_CancerResearch2011.tsv
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observable_files:
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- observables_Raia_CancerResearch2011.tsv
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sbml_files:
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- model_Raia_CancerResearch2011.xml
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visualization_files:
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- visualizationSpecification_Raia_CancerResearch2011.tsv

‎Benchmark-Models/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv‎

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conditionId conditionName il13_level
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model1_data1 Il13 level = 0 0
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model1_data2 il13 level = 20 20
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model1_data3 il13 level = 4 4
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model1_data4 il13 level = 80 80

‎Benchmark-Models/Raia_CancerResearch2011/measurementData_Raia_CancerResearch2011.tsv‎

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‎Benchmark-Models/Raia_CancerResearch2011/model_Raia_CancerResearch2011.xml‎

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‎Benchmark-Models/Raia_CancerResearch2011/observables_Raia_CancerResearch2011.tsv‎

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observableId observableName observableFormula noiseFormula observableTransformation noiseDistribution
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observable_CD274mRNA CD274mRNA * observableParameter1_observable_CD274mRNA noiseParameter1_observable_CD274mRNA + noiseParameter2_observable_CD274mRNA * observable_CD274mRNA lin normal
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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
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observable_RecSurf IL13_Rec + Rec + p_IL13_Rec noiseParameter1_observable_RecSurf + noiseParameter2_observable_RecSurf * observable_RecSurf lin normal
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observable_SOCS3 SOCS3 noiseParameter1_observable_SOCS3 + noiseParameter2_observable_SOCS3 * observable_SOCS3 lin normal
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observable_SOCS3mRNA SOCS3mRNA * observableParameter1_observable_SOCS3mRNA noiseParameter1_observable_SOCS3mRNA + noiseParameter2_observable_SOCS3mRNA * observable_SOCS3mRNA lin normal
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observable_pIL4Ra observableParameter1_observable_pIL4Ra * (p_IL13_Rec + p_IL13_Rec_i) noiseParameter1_observable_pIL4Ra + noiseParameter2_observable_pIL4Ra * observable_pIL4Ra lin normal
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observable_pJAK2 pJAK2 * observableParameter1_observable_pJAK2 noiseParameter1_observable_pJAK2 + noiseParameter2_observable_pJAK2 * observable_pJAK2 lin normal
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observable_pSTAT5 pSTAT5 noiseParameter1_observable_pSTAT5 + noiseParameter2_observable_pSTAT5 * observable_pSTAT5 lin normal

‎Benchmark-Models/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv‎

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parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate
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CD274mRNA_production CD274mRNA_{production} log10 1E-05 1000 0.021208853684209 1
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DecoyR_binding DecoyR_{binding} log10 1E-05 1000 0.003851039137402 1
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JAK2_p_inhibition JAK2_{p,inhibition} log10 1E-05 1000 0.078140000505809 1
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JAK2_phosphorylation JAK2_{phosphorylation} log10 1E-05 1000 1.01721171826747 1
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Kon_IL13Rec Kon_{IL13Rec} log10 1E-05 1000 0.002278141087201 1
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Rec_intern Rec_{intern} log10 1E-05 1000 0.344129281159739 1
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Rec_phosphorylation Rec_{phosphorylation} log10 1E-05 1000 999.999816483984 1
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Rec_recycle Rec_{recycle} log10 1E-05 1000 0.00209774906794 1
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SOCS3_accumulation SOCS3_{accumulation} log10 1E-05 1000 451.777901711184 1
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SOCS3_degradation SOCS3_{degradation} log10 1E-05 1000 0.043380223348167 1
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SOCS3_translation SOCS3_{translation} log10 1E-05 1000 15.7186888386006 1
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SOCS3mRNA_production SOCS3mRNA_{production} log10 1E-05 1000 0.14337151776186 1
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STAT5_phosphorylation STAT5_{phosphorylation} log10 1E-05 1000 0.01948207479306 1
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init_Rec_i init_{Rec,i} log10 1E-05 1000 235.058493601113 1
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pJAK2_dephosphorylation pJAK2_{dephosphorylation} log10 1E-05 1000 0.000175894009439 1
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pRec_degradation pRec_{degradation} log10 1E-05 1000 0.209573978543856 1
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pRec_intern pRec_{intern} log10 1E-05 1000 0.585271535297764 1
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pSTAT5_dephosphorylation pSTAT5_{dephosphorylation} log10 1E-05 1000 0.000274832319318 1
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scaling_CD274mRNA scaling_{CD274mRNA} log10 1E-05 1000 0.00815283660871 1
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scaling_IL13_cell scaling_{IL13,cell} log10 1E-05 1000 5.50098613841361 1
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scaling_SOCS3mRNA scaling_{SOCS3mRNA} log10 1E-05 1000 0.581287913862507 1
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scaling_pIL4Ra scaling_{pIL4Ra} log10 1E-05 1000 2.9757729322919 1
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scaling_pJAK2 scaling_{pJAK2} log10 1E-05 1000 0.857246885626022 1
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sd_SOCS3mRNA_abs sd_SOCS3mRNA_abs log10 1E-05 1000 9.2 1
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sd_RecSurf_abs sd_RecSurf_abs log10 1E-05 1000 1.00E-05 1
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sd_pSTAT5_rel sd_pSTAT5_rel log10 1E-05 1000 0.18 1
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sd_IL13_cell_rel sd_IL13_cell_rel log10 1E-05 1000 0.065 1
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sd_RecSurf_rel sd_RecSurf_rel log10 1E-05 1000 0.078 1
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sd_pJAK2_abs sd_pJAK2_abs log10 1E-05 1000 0.32 1
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sd_pIL4Ra_abs sd_pIL4Ra_abs log10 1E-05 1000 0.62 1
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sd_CD274mRNA_rel sd_CD274mRNA_rel log10 1E-05 1000 0.61 1
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sd_SOCS3mRNA_rel sd_SOCS3mRNA_rel log10 1E-05 1000 0.52 1
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sd_pIL4Ra_rel sd_pIL4Ra_rel log10 1E-05 1000 1.10E-05 1
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sd_IL13_cell_abs sd_IL13_cell_abs log10 1E-05 1000 0.28 1
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sd_SOCS3_rel sd_SOCS3_rel log10 1E-05 1000 0.18 1
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sd_CD274mRNA_abs sd_CD274mRNA_abs log10 1E-05 1000 0.024 1
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sd_pSTAT5_abs sd_pSTAT5_abs log10 1E-05 1000 1.4 1
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sd_SOCS3_abs sd_SOCS3_abs log10 1E-05 1000 15 1
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sd_pJAK2_rel sd_pJAK2_rel log10 1E-05 1000 1.00E-05 1

‎Benchmark-Models/Raia_CancerResearch2011/simulatedData_Raia_CancerResearch2011.tsv‎

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observableId preequilibrationCondition simulationCondition simulation time observableParameters noiseParameters
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RecSurf model1_data1 1.3 0
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RecSurf model1_data1 1.427926242 10
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RecSurf model1_data1 1.4319383562 20
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RecSurf model1_data1 1.432064218 30
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RecSurf model1_data1 1.4320683867 60
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RecSurf model1_data1 1.4320684562 90
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RecSurf model1_data1 1.4320684584 120
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IL13_cell model1_data1 0 0
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IL13_cell model1_data1 0 15
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IL13_cell model1_data1 0 30
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IL13_cell model1_data1 0 60
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IL13_cell model1_data1 0 90
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IL13_cell model1_data1 0 120
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SOCS3mRNA model1_data1 0 0
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SOCS3mRNA model1_data1 0 20
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SOCS3mRNA model1_data1 0 30
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SOCS3mRNA model1_data1 0 40
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SOCS3mRNA model1_data1 0 60
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SOCS3mRNA model1_data1 0 80
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SOCS3mRNA model1_data1 0 90
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SOCS3mRNA model1_data1 0 100
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SOCS3mRNA model1_data1 0 120
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CD274mRNA model1_data1 0 30
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CD274mRNA model1_data1 0 60
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CD274mRNA model1_data1 0 90
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CD274mRNA model1_data1 0 120
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SOCS3 model1_data1 0 0
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SOCS3 model1_data1 0 20
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SOCS3 model1_data1 0 40
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SOCS3 model1_data1 0 60
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SOCS3 model1_data1 0 90
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SOCS3 model1_data1 0 120
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IL13_cell model1_data2 3.7024348123 5
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IL13_cell model1_data2 5.1026012059 10
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IL13_cell model1_data2 5.6061765227 15
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IL13_cell model1_data2 5.7871881096 20
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IL13_cell model1_data2 5.8672215586 30
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IL13_cell model1_data2 5.8625775062 40
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IL13_cell model1_data2 5.8456085207 50
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IL13_cell model1_data2 5.8268553725 60
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IL13_cell model1_data2 5.788996529 80
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IL13_cell model1_data2 5.7514395189 100
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IL13_cell model1_data2 5.7142386514 120
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pIL4Ra model1_data2 0 0
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pIL4Ra model1_data2 1.226370545 4
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pIL4Ra model1_data2 1.4137574553 5
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pIL4Ra model1_data2 1.6865488089 7
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pIL4Ra model1_data2 1.9251305934 10
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pIL4Ra model1_data2 2.0946684877 15
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pIL4Ra model1_data2 2.1495822965 20
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pIL4Ra model1_data2 2.1673789234 30
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pIL4Ra model1_data2 2.160402643 40
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pIL4Ra model1_data2 2.1555141743 45
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pIL4Ra model1_data2 2.140140007 60
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pJAK2 model1_data2 0 0
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pJAK2 model1_data2 0.9775092322 4
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pJAK2 model1_data2 1.2102338931 5
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pJAK2 model1_data2 1.5564372517 7
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pJAK2 model1_data2 1.8547029057 10
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pJAK2 model1_data2 2.0411811523 15
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pJAK2 model1_data2 2.0678225772 20
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pJAK2 model1_data2 2.036161077 25
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pJAK2 model1_data2 1.9807970906 30
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pJAK2 model1_data2 1.8462457668 40
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pJAK2 model1_data2 1.7766686151 45
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pJAK2 model1_data2 1.7084751945 50
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pJAK2 model1_data2 1.57993676 60
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pJAK2 model1_data2 1.3627465451 80
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pJAK2 model1_data2 1.1975863655 100
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pJAK2 model1_data2 1.0750810942 120
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SOCS3mRNA model1_data2 0 0
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SOCS3mRNA model1_data2 54.7642430565 20
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SOCS3mRNA model1_data2 122.3095653067 30
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SOCS3mRNA model1_data2 200.2799185297 40
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SOCS3mRNA model1_data2 364.8542894841 60
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SOCS3mRNA model1_data2 527.0847080334 80
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SOCS3mRNA model1_data2 605.5634673119 90
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SOCS3mRNA model1_data2 682.051466418 100
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SOCS3mRNA model1_data2 829.1181009635 120
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CD274mRNA model1_data2 0.253765268 30
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CD274mRNA model1_data2 0.75699187 60
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CD274mRNA model1_data2 1.2564101197 90
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CD274mRNA model1_data2 1.7202364883 120
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SOCS3 model1_data2 0 0
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SOCS3 model1_data2 14.3117853821 20
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SOCS3 model1_data2 75.5899554372 40
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SOCS3 model1_data2 142.0469159486 60
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SOCS3 model1_data2 192.9222195204 80
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SOCS3 model1_data2 212.2654948088 90
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SOCS3 model1_data2 228.2361275238 100
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SOCS3 model1_data2 252.3148540949 120
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pSTAT5 model1_data2 0 0
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pSTAT5 model1_data2 9.8369693678 5
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pSTAT5 model1_data2 33.0656452021 10
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pSTAT5 model1_data2 54.527209543 15
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pSTAT5 model1_data2 70.5470742104 20
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pSTAT5 model1_data2 81.6623451946 25
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pSTAT5 model1_data2 89.0829820535 30
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pSTAT5 model1_data2 93.8642092334 35
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pSTAT5 model1_data2 96.7932901915 40
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pSTAT5 model1_data2 98.4294175031 45
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pSTAT5 model1_data2 99.1632089984 50
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pSTAT5 model1_data2 98.9293869832 60
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pSTAT5 model1_data2 97.4282678713 70
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pSTAT5 model1_data2 95.3294708838 80
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pSTAT5 model1_data2 92.9819600134 90
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pSTAT5 model1_data2 90.5750752559 100
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pSTAT5 model1_data2 85.9613665968 120
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RecSurf model1_data3 1.3 0
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RecSurf model1_data3 1.3964620975 10
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RecSurf model1_data3 1.3963221638 20
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RecSurf model1_data3 1.3947086697 30
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RecSurf model1_data3 1.3897823176 60
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RecSurf model1_data3 1.3848761993 90
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RecSurf model1_data3 1.3799892107 120
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IL13_cell model1_data3 0.8943932753 5
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IL13_cell model1_data3 1.4008696495 10
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IL13_cell model1_data3 1.7047650106 15
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IL13_cell model1_data3 1.9146632507 20
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IL13_cell model1_data3 2.2033843979 30
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IL13_cell model1_data3 2.397562842 40
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IL13_cell model1_data3 2.5330812121 50
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IL13_cell model1_data3 2.6282078445 60
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IL13_cell model1_data3 2.7417122581 80
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IL13_cell model1_data3 2.7970503617 100
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IL13_cell model1_data3 2.8234478969 120
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pIL4Ra model1_data3 0 0
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pIL4Ra model1_data3 0.2744955332 4
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pIL4Ra model1_data3 0.3216578772 5
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pIL4Ra model1_data3 0.3933567687 7
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pIL4Ra model1_data3 0.4597043427 10
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pIL4Ra model1_data3 0.5098622422 15
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pIL4Ra model1_data3 0.5209355598 17.5
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pIL4Ra model1_data3 0.5274474002 20
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pIL4Ra model1_data3 0.5312455475 22.5
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pIL4Ra model1_data3 0.5334322396 25
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pIL4Ra model1_data3 0.5353274577 30
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pIL4Ra model1_data3 0.5357859807 35
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pIL4Ra model1_data3 0.5357406973 40
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pIL4Ra model1_data3 0.5355190019 45
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pIL4Ra model1_data3 0.5352357244 50
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pIL4Ra model1_data3 0.5346192231 60
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pJAK2 model1_data3 0 0
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pJAK2 model1_data3 0.1344067902 2.5
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pJAK2 model1_data3 0.2642849089 4
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pJAK2 model1_data3 0.3526639874 5
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pJAK2 model1_data3 0.521188721 7
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pJAK2 model1_data3 0.5607467453 7.5
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pJAK2 model1_data3 0.7405410267 10
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pJAK2 model1_data3 0.8896091434 12.5
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pJAK2 model1_data3 1.0088202039 15
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pJAK2 model1_data3 1.1002654097 17.5
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pJAK2 model1_data3 1.1670068 20
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pJAK2 model1_data3 1.241456966 25
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pJAK2 model1_data3 1.2614818608 30
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pJAK2 model1_data3 1.2493256128 35
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pJAK2 model1_data3 1.2189568692 40
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pJAK2 model1_data3 1.1786213845 45
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pJAK2 model1_data3 1.1331778076 50
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pJAK2 model1_data3 1.0374903391 60
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pJAK2 model1_data3 0.8999485342 75
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pJAK2 model1_data3 0.7799605406 90
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pJAK2 model1_data3 0.6795218428 105
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pJAK2 model1_data3 0.5971065427 120
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pSTAT5 model1_data3 0 0
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pSTAT5 model1_data3 2.634483631 5
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pSTAT5 model1_data3 11.7531433701 10
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pSTAT5 model1_data3 24.2748997534 15
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pSTAT5 model1_data3 37.1275881585 20
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pSTAT5 model1_data3 48.5191839147 25
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pSTAT5 model1_data3 57.7724617566 30
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pSTAT5 model1_data3 64.8726802287 35
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pSTAT5 model1_data3 70.0862329678 40
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pSTAT5 model1_data3 73.7501381984 45
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pSTAT5 model1_data3 76.1821120513 50
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pSTAT5 model1_data3 78.3751652344 60
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pSTAT5 model1_data3 78.2340324455 70
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pSTAT5 model1_data3 76.7224653597 80
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pSTAT5 model1_data3 71.6980840069 100
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pSTAT5 model1_data3 65.7771184221 120
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RecSurf model1_data4 1.3 0
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RecSurf model1_data4 1.1049968747 10
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RecSurf model1_data4 1.0898045247 20
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RecSurf model1_data4 1.0774192011 30
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RecSurf model1_data4 1.041131316 60
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RecSurf model1_data4 1.0060657941 90
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RecSurf model1_data4 0.9721785729 120
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IL13_cell model1_data4 8.8441547846 5
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IL13_cell model1_data4 10.572248259 10
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IL13_cell model1_data4 11.0789193277 15
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IL13_cell model1_data4 11.218392462 20
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IL13_cell model1_data4 11.2025120759 30
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IL13_cell model1_data4 11.1076204284 40
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IL13_cell model1_data4 11.0040750003 50
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IL13_cell model1_data4 10.9005095881 60
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IL13_cell model1_data4 10.6965838267 80
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IL13_cell model1_data4 10.497236095 100
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IL13_cell model1_data4 10.3023831625 120
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SOCS3 model1_data4 0 0
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SOCS3 model1_data4 20.248449512 20
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SOCS3 model1_data4 87.1663276835 40
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SOCS3 model1_data4 153.238083014 60
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SOCS3 model1_data4 202.2629088523 80
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SOCS3 model1_data4 235.9720185864 100
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SOCS3 model1_data4 258.9746918774 120

‎Benchmark-Models/Raia_CancerResearch2011/visualizationSpecification_Raia_CancerResearch2011.tsv‎

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plotId plotName plotTypeSimulation plotTypeData datasetId xValues xLabel yValues yLabel legendEntry
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plot1 RecSurf LinePlot MeanAndSD model1_data1_RecSurf time Time [s] observable_RecSurf Phosphorylation (AU) IL13 = 0
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plot1 RecSurf LinePlot MeanAndSD model1_data3_RecSurf time Time [s] observable_RecSurf Phosphorylation (AU) IL13 = 4
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plot1 RecSurf LinePlot MeanAndSD model1_data4_RecSurf time Time [s] observable_RecSurf Phosphorylation (AU) IL13 = 80
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plot2 IL13_cell LinePlot MeanAndSD model1_data1_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 0
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plot2 IL13_cell LinePlot MeanAndSD model1_data2_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 20
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plot2 IL13_cell LinePlot MeanAndSD model1_data3_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 4
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plot2 IL13_cell LinePlot MeanAndSD model1_data4_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 80
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plot3 SOCS3mRNA LinePlot MeanAndSD model1_data1_SOCS3mRNA time Time [s] observable_SOCS3mRNA Phosphorylation (AU) IL13 = 0
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plot3 SOCS3mRNA LinePlot MeanAndSD model1_data2_SOCS3mRNA time Time [s] observable_SOCS3mRNA Phosphorylation (AU) IL13 = 20
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plot4 CD274mRNA LinePlot MeanAndSD model1_data1_CD274mRNA time Time [s] observable_CD274mRNA Phosphorylation (AU) IL13 = 0
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plot4 CD274mRNA LinePlot MeanAndSD model1_data2_CD274mRNA time Time [s] observable_CD274mRNA Phosphorylation (AU) IL13 = 20
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plot5 SOCS3 LinePlot MeanAndSD model1_data1_SOCS3 time Time [s] observable_SOCS3 Phosphorylation (AU) IL13 = 0
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plot5 SOCS3 LinePlot MeanAndSD model1_data2_SOCS3 time Time [s] observable_SOCS3 Phosphorylation (AU) IL13 = 20
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plot5 SOCS3 LinePlot MeanAndSD model1_data4_SOCS3 time Time [s] observable_SOCS3 Phosphorylation (AU) IL13 = 80
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plot6 IL13_cell LinePlot MeanAndSD model1_data2_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 20
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plot6 IL13_cell LinePlot MeanAndSD model1_data3_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 4
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plot6 IL13_cell LinePlot MeanAndSD model1_data4_IL13_cell time Time [s] observable_IL13_cell Phosphorylation (AU) IL13 = 80
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plot7 pIL4Ra LinePlot MeanAndSD model1_data2_pIL4Ra time Time [s] observable_pIL4Ra Phosphorylation (AU) IL13 = 20
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plot7 pIL4Ra LinePlot MeanAndSD model1_data3_pIL4Ra time Time [s] observable_pIL4Ra Phosphorylation (AU) IL13 = 4
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plot8 pJAK2 LinePlot MeanAndSD model1_data2_pJAK2 time Time [s] observable_pJAK2 Phosphorylation (AU) IL13 = 20
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plot8 pJAK2 LinePlot MeanAndSD model1_data3_pJAK2 time Time [s] observable_pJAK2 Phosphorylation (AU) IL13 = 4
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plot9 pSTAT5 LinePlot MeanAndSD model1_data2_pSTAT5 time Time [s] observable_pSTAT5 Phosphorylation (AU) IL13 = 20
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plot9 pSTAT5 LinePlot MeanAndSD model1_data3_pSTAT5 time Time [s] observable_pSTAT5 Phosphorylation (AU) IL13 = 4

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