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Benchmark-Models/Raia_CancerResearch2011/Raia_CancerResearch2011.yaml
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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 |
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Benchmark-Models/Raia_CancerResearch2011/experimentalCondition_Raia_CancerResearch2011.tsv
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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 |
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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 | ||
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 |
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Benchmark-Models/Raia_CancerResearch2011/parameters_Raia_CancerResearch2011.tsv
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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 |
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Benchmark-Models/Raia_CancerResearch2011/simulatedData_Raia_CancerResearch2011.tsv
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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 model1_data2 1.7766686151 45 | ||
pJAK2 model1_data2 1.7084751945 50 | ||
pJAK2 model1_data2 1.57993676 60 | ||
pJAK2 model1_data2 1.3627465451 80 | ||
pJAK2 model1_data2 1.1975863655 100 | ||
pJAK2 model1_data2 1.0750810942 120 | ||
SOCS3mRNA model1_data2 0 0 | ||
SOCS3mRNA model1_data2 54.7642430565 20 | ||
SOCS3mRNA model1_data2 122.3095653067 30 | ||
SOCS3mRNA model1_data2 200.2799185297 40 | ||
SOCS3mRNA model1_data2 364.8542894841 60 | ||
SOCS3mRNA model1_data2 527.0847080334 80 | ||
SOCS3mRNA model1_data2 605.5634673119 90 | ||
SOCS3mRNA model1_data2 682.051466418 100 | ||
SOCS3mRNA model1_data2 829.1181009635 120 | ||
CD274mRNA model1_data2 0.253765268 30 | ||
CD274mRNA model1_data2 0.75699187 60 | ||
CD274mRNA model1_data2 1.2564101197 90 | ||
CD274mRNA model1_data2 1.7202364883 120 | ||
SOCS3 model1_data2 0 0 | ||
SOCS3 model1_data2 14.3117853821 20 | ||
SOCS3 model1_data2 75.5899554372 40 | ||
SOCS3 model1_data2 142.0469159486 60 | ||
SOCS3 model1_data2 192.9222195204 80 | ||
SOCS3 model1_data2 212.2654948088 90 | ||
SOCS3 model1_data2 228.2361275238 100 | ||
SOCS3 model1_data2 252.3148540949 120 | ||
pSTAT5 model1_data2 0 0 | ||
pSTAT5 model1_data2 9.8369693678 5 | ||
pSTAT5 model1_data2 33.0656452021 10 | ||
pSTAT5 model1_data2 54.527209543 15 | ||
pSTAT5 model1_data2 70.5470742104 20 | ||
pSTAT5 model1_data2 81.6623451946 25 | ||
pSTAT5 model1_data2 89.0829820535 30 | ||
pSTAT5 model1_data2 93.8642092334 35 | ||
pSTAT5 model1_data2 96.7932901915 40 | ||
pSTAT5 model1_data2 98.4294175031 45 | ||
pSTAT5 model1_data2 99.1632089984 50 | ||
pSTAT5 model1_data2 98.9293869832 60 | ||
pSTAT5 model1_data2 97.4282678713 70 | ||
pSTAT5 model1_data2 95.3294708838 80 | ||
pSTAT5 model1_data2 92.9819600134 90 | ||
pSTAT5 model1_data2 90.5750752559 100 | ||
pSTAT5 model1_data2 85.9613665968 120 | ||
RecSurf model1_data3 1.3 0 | ||
RecSurf model1_data3 1.3964620975 10 | ||
RecSurf model1_data3 1.3963221638 20 | ||
RecSurf model1_data3 1.3947086697 30 | ||
RecSurf model1_data3 1.3897823176 60 | ||
RecSurf model1_data3 1.3848761993 90 | ||
RecSurf model1_data3 1.3799892107 120 | ||
IL13_cell model1_data3 0.8943932753 5 | ||
IL13_cell model1_data3 1.4008696495 10 | ||
IL13_cell model1_data3 1.7047650106 15 | ||
IL13_cell model1_data3 1.9146632507 20 | ||
IL13_cell model1_data3 2.2033843979 30 | ||
IL13_cell model1_data3 2.397562842 40 | ||
IL13_cell model1_data3 2.5330812121 50 | ||
IL13_cell model1_data3 2.6282078445 60 | ||
IL13_cell model1_data3 2.7417122581 80 | ||
IL13_cell model1_data3 2.7970503617 100 | ||
IL13_cell model1_data3 2.8234478969 120 | ||
pIL4Ra model1_data3 0 0 | ||
pIL4Ra model1_data3 0.2744955332 4 | ||
pIL4Ra model1_data3 0.3216578772 5 | ||
pIL4Ra model1_data3 0.3933567687 7 | ||
pIL4Ra model1_data3 0.4597043427 10 | ||
pIL4Ra model1_data3 0.5098622422 15 | ||
pIL4Ra model1_data3 0.5209355598 17.5 | ||
pIL4Ra model1_data3 0.5274474002 20 | ||
pIL4Ra model1_data3 0.5312455475 22.5 | ||
pIL4Ra model1_data3 0.5334322396 25 | ||
pIL4Ra model1_data3 0.5353274577 30 | ||
pIL4Ra model1_data3 0.5357859807 35 | ||
pIL4Ra model1_data3 0.5357406973 40 | ||
pIL4Ra model1_data3 0.5355190019 45 | ||
pIL4Ra model1_data3 0.5352357244 50 | ||
pIL4Ra model1_data3 0.5346192231 60 | ||
pJAK2 model1_data3 0 0 | ||
pJAK2 model1_data3 0.1344067902 2.5 | ||
pJAK2 model1_data3 0.2642849089 4 | ||
pJAK2 model1_data3 0.3526639874 5 | ||
pJAK2 model1_data3 0.521188721 7 | ||
pJAK2 model1_data3 0.5607467453 7.5 | ||
pJAK2 model1_data3 0.7405410267 10 | ||
pJAK2 model1_data3 0.8896091434 12.5 | ||
pJAK2 model1_data3 1.0088202039 15 | ||
pJAK2 model1_data3 1.1002654097 17.5 | ||
pJAK2 model1_data3 1.1670068 20 | ||
pJAK2 model1_data3 1.241456966 25 | ||
pJAK2 model1_data3 1.2614818608 30 | ||
pJAK2 model1_data3 1.2493256128 35 | ||
pJAK2 model1_data3 1.2189568692 40 | ||
pJAK2 model1_data3 1.1786213845 45 | ||
pJAK2 model1_data3 1.1331778076 50 | ||
pJAK2 model1_data3 1.0374903391 60 | ||
pJAK2 model1_data3 0.8999485342 75 | ||
pJAK2 model1_data3 0.7799605406 90 | ||
pJAK2 model1_data3 0.6795218428 105 | ||
pJAK2 model1_data3 0.5971065427 120 | ||
pSTAT5 model1_data3 0 0 | ||
pSTAT5 model1_data3 2.634483631 5 | ||
pSTAT5 model1_data3 11.7531433701 10 | ||
pSTAT5 model1_data3 24.2748997534 15 | ||
pSTAT5 model1_data3 37.1275881585 20 | ||
pSTAT5 model1_data3 48.5191839147 25 | ||
pSTAT5 model1_data3 57.7724617566 30 | ||
pSTAT5 model1_data3 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 |
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...ark-Models/Raia_CancerResearch2011/visualizationSpecification_Raia_CancerResearch2011.tsv
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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 |
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