From 6eb1e3096c5885322a57ac43e2ff6881f8250792 Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Wed, 29 Oct 2025 17:42:19 +0100 Subject: [PATCH 01/11] merge two plots --- Benchmark-Models/Bertozzi_PNAS2020/visualizations.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Benchmark-Models/Bertozzi_PNAS2020/visualizations.tsv b/Benchmark-Models/Bertozzi_PNAS2020/visualizations.tsv index e0e07fe2..ee2b8d5b 100644 --- a/Benchmark-Models/Bertozzi_PNAS2020/visualizations.tsv +++ b/Benchmark-Models/Bertozzi_PNAS2020/visualizations.tsv @@ -1,3 +1,3 @@ plotId plotName plotTypeSimulation datasetId xValues xOffset xLabel yValues yOffset yLabel legendEntry xScale yScale -conf_CA Confirmed case data from California LinePlot data_CA time 0 Time [d] after 2020-03-20 y_I_CA 0 Confirmed cases Confirmed cases lin log10 -conf_NY Confirmed case data from New York LinePlot data_NY time 0 Time [d] after 2020-03-20 y_I_NY 0 Confirmed cases Confirmed cases lin log10 +plot1 Confirmed case data LinePlot data_CA time 0 Time [d] after 2020-03-20 y_I_CA 0 Confirmed cases California lin log10 +plot1 Confirmed case data LinePlot data_NY time 0 Time [d] after 2020-03-20 y_I_NY 0 Confirmed cases New York lin log10 From 1523fd7db18928487d70d2fa97ffee30e02c7d6c Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Wed, 29 Oct 2025 17:43:45 +0100 Subject: [PATCH 02/11] elowitz, update axes labels --- .../visualizationSpecification_Elowitz_Nature2000.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Benchmark-Models/Elowitz_Nature2000/visualizationSpecification_Elowitz_Nature2000.tsv b/Benchmark-Models/Elowitz_Nature2000/visualizationSpecification_Elowitz_Nature2000.tsv index ab763a87..a035c833 100644 --- a/Benchmark-Models/Elowitz_Nature2000/visualizationSpecification_Elowitz_Nature2000.tsv +++ b/Benchmark-Models/Elowitz_Nature2000/visualizationSpecification_Elowitz_Nature2000.tsv @@ -1,2 +1,2 @@ plotId plotTypeData plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset -plot1 MeanAndSD LinePlot time lin values lin model1_data1 - fluorescence fluorescence time 0 0 +plot1 MeanAndSD LinePlot time [min] lin fluorescence [a. u.] lin model1_data1 - fluorescence fluorescence time 0 0 From b04bdc8680e2c6d78d0754b6240e0ab23861e6aa Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Wed, 29 Oct 2025 19:11:17 +0100 Subject: [PATCH 03/11] change scale, Laske model --- .../visualizationSpecification_Laske_PLOSComputBiol2019.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Benchmark-Models/Laske_PLOSComputBiol2019/visualizationSpecification_Laske_PLOSComputBiol2019.tsv b/Benchmark-Models/Laske_PLOSComputBiol2019/visualizationSpecification_Laske_PLOSComputBiol2019.tsv index 5cd27c2c..1a2742f1 100644 --- a/Benchmark-Models/Laske_PLOSComputBiol2019/visualizationSpecification_Laske_PLOSComputBiol2019.tsv +++ b/Benchmark-Models/Laske_PLOSComputBiol2019/visualizationSpecification_Laske_PLOSComputBiol2019.tsv @@ -2,5 +2,5 @@ plotId plotName plotTypeData datasetId xValues xLabel yValues yOffset yLabel leg plot1 mRNA_abundance MeanAndSD dataset_RM5 time Time [h] RM5 1 Abundance of mRNA mRNA lin log10 plot2 cRNA_abundance MeanAndSD dataset_RC time Time [h] RCSegTot 0 Abundance of cRNA molecules/cell cRNA lin log10 plot3 vRNA_abundance MeanAndSD dataset_RV time Time [h] RVSegTot 0 Abundance of vRNA molecules/cell vRNA lin log10 -plot4 Released_virions MeanAndSD dataset_Vrel time Time [h] Vrel 1 Released virions/cell VRel lin log10 +plot4 Released_virions MeanAndSD dataset_Vrel time Time [h] Vrel 1 Released virions/cell VRel lin lin plot5 frac_FI_nucleus MeanAndSD dataset_FracNucInt time Time [h] FracNucInt_1 0 Fraction of nuclear FI [%] nuclear FI lin lin From 3445a1e5e76cd7478788f300723a618d4ad8de7e Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Wed, 29 Oct 2025 19:28:40 +0100 Subject: [PATCH 04/11] fix zheng reference --- Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml b/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml index a7202291..c32f1b90 100644 --- a/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml +++ b/Benchmark-Models/Zheng_PNAS2012/model_Zheng_PNAS2012.xml @@ -27,7 +27,7 @@ - + From e48e96e5f0d76ad2a775f07f248947eada5cd87c Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Wed, 29 Oct 2025 20:48:27 +0100 Subject: [PATCH 05/11] brannmark, add datasetId and fix visualization spec --- .../measurementData_Brannmark_JBC2010.tsv | 88 +++++++++---------- .../simulatedData_Brannmark_JBC2010.tsv | 88 +++++++++---------- ...izationSpecification_Brannmark_JBC2010.tsv | 10 +-- 3 files changed, 93 insertions(+), 93 deletions(-) diff --git a/Benchmark-Models/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv b/Benchmark-Models/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv index c51cbac1..f42277da 100644 --- a/Benchmark-Models/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv +++ b/Benchmark-Models/Brannmark_JBC2010/measurementData_Brannmark_JBC2010.tsv @@ -1,44 +1,44 @@ -observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters experimentId independentVariableId -IRS1_P_DosR Dose_0 Dose_0 18.385 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_001 29.115 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_01 26.365 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_1 28.292 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_3 42.308 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_10 105.029 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_100 94.971 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IR1_P Dose_0 Dose_100 0 0 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 100 0.9 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 82.667 1.15 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 77.333 1.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 60 2.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 50.667 3.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 56.667 5.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 45.667 7 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 52.333 10 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 41.333 15 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 42.667 20 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 35.333 30 k_IRP_1Step sigmaY1TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 0 0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 227.667 0.9 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 205 1.15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 169.667 1.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 145.5 2.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 121.667 3.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 110.333 5.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 95 7 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 110 10 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 86.667 15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 73 20 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 100 30 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 TwoSteps 14.417 0 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 26.724 0.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 42.035 0.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 58.258 0.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 58.752 1.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 52.465 1.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 56.405 4 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 67.901 4.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 66.297 4.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 69.522 4.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 74.644 5.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 70.367 5.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time +observableId preequilibrationConditionId simulationConditionId measurement time observableParameters noiseParameters experimentId independentVariableId datasetId +IRS1_P_DosR Dose_0 Dose_0 18.385 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_001 29.115 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_01 26.365 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_1 28.292 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_3 42.308 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_10 105.029 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_100 94.971 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IR1_P Dose_0 Dose_100 0 0 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 100 0.9 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 82.667 1.15 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 77.333 1.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 60 2.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 50.667 3.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 56.667 5.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 45.667 7 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 52.333 10 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 41.333 15 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 42.667 20 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 35.333 30 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 0 0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 227.667 0.9 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 205 1.15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 169.667 1.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 145.5 2.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 121.667 3.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 110.333 5.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 95 7 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 110 10 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 86.667 15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 73 20 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 100 30 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 TwoSteps 14.417 0 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 26.724 0.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 42.035 0.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 58.258 0.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 58.752 1.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 52.465 1.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 56.405 4 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 67.901 4.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 66.297 4.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 69.522 4.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 74.644 5.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 70.367 5.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps diff --git a/Benchmark-Models/Brannmark_JBC2010/simulatedData_Brannmark_JBC2010.tsv b/Benchmark-Models/Brannmark_JBC2010/simulatedData_Brannmark_JBC2010.tsv index 027fec02..86eccf79 100644 --- a/Benchmark-Models/Brannmark_JBC2010/simulatedData_Brannmark_JBC2010.tsv +++ b/Benchmark-Models/Brannmark_JBC2010/simulatedData_Brannmark_JBC2010.tsv @@ -1,44 +1,44 @@ -observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters experimentId independentVariableId -IRS1_P_DosR Dose_0 Dose_0 5.04030994035096 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_001 11.3541437232139 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_01 30.7569560314701 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_1 48.0671566365257 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_3 68.8054777834928 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_10 83.567481341805 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IRS1_P_DosR Dose_0 Dose_100 85.0149890438906 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 -IR1_P Dose_0 Dose_100 2.22763226881289 0 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 99.3331254449145 0.9 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 83.1108237692557 1.15 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 76.9137049972788 1.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 59.6539158908547 2.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 55.0961009395699 3.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 52.0284374778894 5.3 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 50.2150261365795 7 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 47.2797089543243 10 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 43.4189654446421 15 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 40.6603409656943 20 k_IRP_1Step sigmaY1TimR one_step_time_response time -IR1_P Dose_0 Dose_100 37.3490089527785 30 k_IRP_1Step sigmaY1TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 5.99870254944543 0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 220.689083467924 0.9 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 198.298517693265 1.15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 186.555740507902 1.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 137.837672156427 2.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 119.482691052972 3.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 109.357485387644 5.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 106.058083099213 7 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 101.180212633368 10 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 94.476981200747 15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 89.5032574659874 20 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 Dose_100 83.3227983363282 30 k_IRSiP_1Step sigmaY2TimR one_step_time_response time -IRS1_P Dose_0 TwoSteps 3.58855311350541 0 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 23.5338571138169 0.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 43.6504194612097 0.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 55.3099963766159 0.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 59.4210435260655 1.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 60.1662824814612 1.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 53.9990033886593 4 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 58.8159608997996 4.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 64.9114355656794 4.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 70.7034173503167 4.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 74.223872149066 5.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time -IRS1_P Dose_0 TwoSteps 75.7194078733588 5.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time +observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters experimentId independentVariableId datasetId +IRS1_P_DosR Dose_0 Dose_0 5.04030994035096 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_001 11.3541437232139 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_01 30.7569560314701 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_1 48.0671566365257 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_3 68.8054777834928 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_10 83.567481341805 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IRS1_P_DosR Dose_0 Dose_100 85.0149890438906 10 k_IRSiP_DosR sigmaYDosR dose_response insulin_dose_1 DosR +IR1_P Dose_0 Dose_100 2.22763226881289 0 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 99.3331254449145 0.9 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 83.1108237692557 1.15 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 76.9137049972788 1.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 59.6539158908547 2.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 55.0961009395699 3.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 52.0284374778894 5.3 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 50.2150261365795 7 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 47.2797089543243 10 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 43.4189654446421 15 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 40.6603409656943 20 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IR1_P Dose_0 Dose_100 37.3490089527785 30 k_IRP_1Step sigmaY1TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 5.99870254944543 0 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 220.689083467924 0.9 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 198.298517693265 1.15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 186.555740507902 1.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 137.837672156427 2.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 119.482691052972 3.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 109.357485387644 5.3 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 106.058083099213 7 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 101.180212633368 10 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 94.476981200747 15 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 89.5032574659874 20 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 Dose_100 83.3227983363282 30 k_IRSiP_1Step sigmaY2TimR one_step_time_response time Dose_100 +IRS1_P Dose_0 TwoSteps 3.58855311350541 0 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 23.5338571138169 0.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 43.6504194612097 0.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 55.3099963766159 0.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 59.4210435260655 1.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 60.1662824814612 1.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 53.9990033886593 4 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 58.8159608997996 4.34 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 64.9114355656794 4.6 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 70.7034173503167 4.9 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 74.223872149066 5.2 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps +IRS1_P Dose_0 TwoSteps 75.7194078733588 5.5 k_IRSiP_2Step sigmaY2Step two_step_time_response time TwoSteps diff --git a/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv b/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv index 15d75df4..534401d5 100644 --- a/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv +++ b/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv @@ -1,5 +1,5 @@ -plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale yValues xValues xOffset yOffset -plot1 MeanAndSD ScatterPlot simulation lin measurements lin IRS1_P_DosR time 0 0 -plot4 MeanAndSD LinePlot time lin values lin IRS1_P_DosR time 1 1 -plot2 MeanAndSD LinePlot time lin values lin IR1_P time 0 0 -plot3 MeanAndSD LinePlot time lin values lin IRS1_P time 0 0 +plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale yValues xValues xOffset yOffset datasetId +plot1 MeanAndSD LinePlot time [min] lin IR phosphorylation lin IR1_P time 0 0 Dose_100 +plot2 MeanAndSD LinePlot time [min] lin IRS1 phosphorylation lin IRS1_P time 0 0 Dose_100 +plot3 MeanAndSD LinePlot Insulin [nM] log10 IRS1 phosphorylation lin IRS1_P_DosR insulin_dose_1 0 0 DosR +plot4 MeanAndSD LinePlot time [min] lin IRS1 phosphorylation lin IRS1_P time 0 0 TwoSteps From edb9894b6e88702063fbc0205c90083304c33203 Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Thu, 6 Nov 2025 19:25:49 +0100 Subject: [PATCH 06/11] fix Borghans axes labels --- .../visualizationSpecification_Borghans_BiophysChem1997.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Benchmark-Models/Borghans_BiophysChem1997/visualizationSpecification_Borghans_BiophysChem1997.tsv b/Benchmark-Models/Borghans_BiophysChem1997/visualizationSpecification_Borghans_BiophysChem1997.tsv index ec4ec1f1..9e59dc22 100644 --- a/Benchmark-Models/Borghans_BiophysChem1997/visualizationSpecification_Borghans_BiophysChem1997.tsv +++ b/Benchmark-Models/Borghans_BiophysChem1997/visualizationSpecification_Borghans_BiophysChem1997.tsv @@ -1,2 +1,2 @@ plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset -plot1 MeanAndSD LinePlot time lin values lin model1_data1 - Ca Ca time 0 0.0 +plot1 MeanAndSD LinePlot time [min] lin Ca$^{2+}$ in cytosol [$\mu$M] lin model1_data1 - Ca Ca time 0 0 From fcce00c58762487ec3da280dc9edaa0c214bc15e Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Thu, 6 Nov 2025 19:46:46 +0100 Subject: [PATCH 07/11] fix Bruno axes labels --- ...izationSpecification_Bruno_JExpBot2016.tsv | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv b/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv index 795bfa2d..21163ddf 100644 --- a/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv +++ b/Benchmark-Models/Bruno_JExpBot2016/visualizationSpecification_Bruno_JExpBot2016.tsv @@ -1,19 +1,19 @@ plotId plotName plotTypeSimulation plotTypeData datasetId xValues xOffset xLabel yValues yOffset yLabel legendEntry xScale yScale -plot1 model1_data1 LinePlot MeanAndSD model1_data1_ob10 time 0 Time [min] ob10 0 measurement ob10 lin lin -plot2 model1_data2 LinePlot MeanAndSD model1_data2_obcar time 0 Time [min] obcar 0 measurement obcar lin lin -plot2 model1_data2 LinePlot MeanAndSD model1_data2_ob10 time 0 Time [min] ob10 0 measurement ob10 lin lin -plot3 model1_data3 LinePlot MeanAndSD model1_data3_obcar time 0 Time [min] obcar 0 measurement obcar lin log10 -plot3 model1_data3 LinePlot MeanAndSD model1_data3_ob10 time 0 Time [min] ob10 0 measurement ob10 lin log10 -plot5 model1_data5 LinePlot MeanAndSD model1_data5_oohb10 time 0 Time [min] oohb10 0 measurement oohb10 lin lin -plot6 model1_data6 LinePlot MeanAndSD model1_data6_oohb10 time 0 Time [min] oohb10 0 measurement oohb10 lin log10 -plot6 model1_data6 LinePlot MeanAndSD model1_data6_ozea time 0 Time [min] ozea 0 measurement ozea lin log10 -plot7 ob10 LinePlot MeanAndSD model1_data1_ob10 time 0 Time [min] ob10 0 ob10 model1_data1 lin lin -plot7 ob10 LinePlot MeanAndSD model1_data2_ob10 time 0 Time [min] ob10 0 ob10 model1_data2 lin lin -plot7 ob10 LinePlot MeanAndSD model1_data3_ob10 time 0 Time [min] ob10 0 ob10 model1_data3 lin lin -plot7 ob10 LinePlot MeanAndSD model1_data4_ob10 time 0 Time [min] ob10 0 ob10 model1_data4 lin lin -plot8 obcar LinePlot MeanAndSD model1_data2_obcar time 0 Time [min] obcar 0 obcar model1_data2 lin lin -plot8 obcar LinePlot MeanAndSD model1_data3_obcar time 0 Time [min] obcar 0 obcar model1_data3 lin lin -plot9 oobh10 LinePlot MeanAndSD model1_data4_oohb10 time 0 Time [min] oohb10 0 oohb10 model1_data4 lin lin -plot9 oobh10 LinePlot MeanAndSD model1_data5_oohb10 time 0 Time [min] oohb10 0 oohb10 model1_data5 lin lin -plot9 oobh10 LinePlot MeanAndSD model1_data6_oohb10 time 0 Time [min] oohb10 0 oohb10 model1_data6 lin log10 -plot10 ozea LinePlot MeanAndSD model1_data6_ozea time 0 Time [min] ozea 0 ozea model1_data6 lin log10 +plot1 model1_data1 LinePlot MeanAndSD model1_data1_ob10 time 0 Time [min] ob10 0 concentration [nmol] $\beta$-apo-10-carotenal lin lin +plot2 model1_data2 LinePlot MeanAndSD model1_data2_obcar time 0 Time [min] obcar 0 concentration [nmol] $\beta$-carotene lin lin +plot2 model1_data2 LinePlot MeanAndSD model1_data2_ob10 time 0 Time [min] ob10 0 concentration [nmol] $\beta$-apo-10-carotenal lin lin +plot3 model1_data3 LinePlot MeanAndSD model1_data3_obcar time 0 Time [min] obcar 0 concentration [nmol] $\beta$-carotene lin log10 +plot3 model1_data3 LinePlot MeanAndSD model1_data3_ob10 time 0 Time [min] ob10 0 concentration [nmol] $\beta$-apo-10-carotenal lin log10 +plot5 model1_data5 LinePlot MeanAndSD model1_data5_oohb10 time 0 Time [min] oohb10 0 concentration [nmol] 3-OH-$\beta$-apo-10-carotenal lin lin +plot6 model1_data6 LinePlot MeanAndSD model1_data6_oohb10 time 0 Time [min] oohb10 0 concentration [nmol] 3-OH-$\beta$-apo-10-carotenal lin log10 +plot6 model1_data6 LinePlot MeanAndSD model1_data6_ozea time 0 Time [min] ozea 0 concentration [nmol] zeaxanthin lin log10 +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data1_ob10 time 0 Time [min] ob10 0 concentration [nmol] model1_data1 lin lin +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data2_ob10 time 0 Time [min] ob10 0 concentration [nmol] model1_data2 lin lin +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data3_ob10 time 0 Time [min] ob10 0 concentration [nmol] model1_data3 lin lin +plot7 $\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data4_ob10 time 0 Time [min] ob10 0 concentration [nmol] model1_data4 lin lin +plot8 $\beta$-carotene LinePlot MeanAndSD model1_data2_obcar time 0 Time [min] obcar 0 concentration [nmol] model1_data2 lin lin +plot8 $\beta$-carotene LinePlot MeanAndSD model1_data3_obcar time 0 Time [min] obcar 0 concentration [nmol] model1_data3 lin lin +plot9 3-OH-$\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data4_oohb10 time 0 Time [min] oohb10 0 concentration [nmol] model1_data4 lin lin +plot9 3-OH-$\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data5_oohb10 time 0 Time [min] oohb10 0 concentration [nmol] model1_data5 lin lin +plot9 3-OH-$\beta$-apo-10-carotenal LinePlot MeanAndSD model1_data6_oohb10 time 0 Time [min] oohb10 0 concentration [nmol] model1_data6 lin log10 +plot10 zeaxanthin LinePlot MeanAndSD model1_data6_ozea time 0 Time [min] ozea 0 concentration [nmol] model1_data6 lin log10 From 86097cb77fb4b8ae4bb07a8296fc71cda00ad6e6 Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Thu, 6 Nov 2025 20:36:04 +0100 Subject: [PATCH 08/11] fix Crauste axes labels --- ...visualizationSpecification_Crauste_CellSystems2017.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Benchmark-Models/Crauste_CellSystems2017/visualizationSpecification_Crauste_CellSystems2017.tsv b/Benchmark-Models/Crauste_CellSystems2017/visualizationSpecification_Crauste_CellSystems2017.tsv index ffe73f5e..b7a3a8fa 100644 --- a/Benchmark-Models/Crauste_CellSystems2017/visualizationSpecification_Crauste_CellSystems2017.tsv +++ b/Benchmark-Models/Crauste_CellSystems2017/visualizationSpecification_Crauste_CellSystems2017.tsv @@ -1,5 +1,5 @@ plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset -plot1 MeanAndSD LinePlot time lin values lin condition1 - observable_Naive observable_Naive time 0 0 -plot2 MeanAndSD LinePlot time lin values lin condition1 - observable_EarlyEffector observable_EarlyEffector time 0 0 -plot3 MeanAndSD LinePlot time lin values lin condition1 - observable_LateEffector observable_LateEffector time 0 0 -plot4 MeanAndSD LinePlot time lin values lin condition1 - observable_Memory observable_Memory time 0 0 +plot1 MeanAndSD LinePlot time [days] lin CD8 T cell counts log10 condition1 - observable_Naive observable_Naive time 0 0 +plot2 MeanAndSD LinePlot time [days] lin CD8 T cell counts log10 condition1 - observable_EarlyEffector observable_EarlyEffector time 0 0 +plot3 MeanAndSD LinePlot time [days] lin CD8 T cell counts log10 condition1 - observable_LateEffector observable_LateEffector time 0 0 +plot4 MeanAndSD LinePlot time [days] lin CD8 T cell counts log10 condition1 - observable_Memory observable_Memory time 0 0 From d5e93964b6270b6d72e53215e19787b089797ed5 Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Thu, 6 Nov 2025 20:44:28 +0100 Subject: [PATCH 09/11] Salazar, add visualization spec to the yaml file --- .../SalazarCavazos_MBoC2020/SalazarCavazos_MBoC2020.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Benchmark-Models/SalazarCavazos_MBoC2020/SalazarCavazos_MBoC2020.yaml b/Benchmark-Models/SalazarCavazos_MBoC2020/SalazarCavazos_MBoC2020.yaml index 62359511..5a67a62a 100644 --- a/Benchmark-Models/SalazarCavazos_MBoC2020/SalazarCavazos_MBoC2020.yaml +++ b/Benchmark-Models/SalazarCavazos_MBoC2020/SalazarCavazos_MBoC2020.yaml @@ -9,3 +9,5 @@ problems: - observables_SalazarCavazos_MBoC2020.tsv sbml_files: - model_SalazarCavazos_MBoC2020.xml + visualization_files: + - visualizationSpecification_SalazarCavazos_MBoC2020.tsv From ce1fc4100fcf8e806d2ef6cd0290f4fc3aefc82c Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Thu, 6 Nov 2025 21:36:19 +0100 Subject: [PATCH 10/11] fix Weber axes labels --- .../simulatedData_Weber_BMC2015.tsv | 272 +++++++++--------- ...sualizationSpecification_Weber_BMC2015.tsv | 16 +- 2 files changed, 144 insertions(+), 144 deletions(-) diff --git a/Benchmark-Models/Weber_BMC2015/simulatedData_Weber_BMC2015.tsv b/Benchmark-Models/Weber_BMC2015/simulatedData_Weber_BMC2015.tsv index fee80011..05afc6d8 100644 --- a/Benchmark-Models/Weber_BMC2015/simulatedData_Weber_BMC2015.tsv +++ b/Benchmark-Models/Weber_BMC2015/simulatedData_Weber_BMC2015.tsv @@ -1,136 +1,136 @@ -observableId preequilibrationConditionId simulationConditionId simulation time observableParameters noiseParameters observableTransformation -yPI4K3Bt model1_data2 80032724.6249776 24 -yPI4K3Bt model1_data2 80032724.6249776 24 -yPI4K3Bt model1_data2 80032724.6249776 24 -yCERTt model1_data2 74192014.9947344 0 -yCERTt model1_data2 74192014.9947344 0 -yCERTt model1_data2 74192014.9947344 0 -yPKDpN0 model1_data2 0.888880630910278 0 -yPKDpN0 model1_data2 1.341413518981 3 -yPKDpN0 model1_data2 1.42148291988296 6 -yPKDpN0 model1_data2 0.888880630910278 0 -yPKDpN0 model1_data2 1.341413518981 3 -yPKDpN0 model1_data2 1.42148291988296 6 -yPKDpN0 model1_data2 0.888880630910278 0 -yPKDpN0 model1_data2 1.341413518981 3 -yPKDpN0 model1_data2 1.42148291988296 6 -yPKDpN24 model1_data2 1.0001914554897 24 -yPKDpN24 model1_data2 8.97029203560068 27 -yPKDpN24 model1_data2 7.20791269123149 30 -yPKDpN24 model1_data2 1.0001914554897 24 -yPKDpN24 model1_data2 8.97029203560068 27 -yPKDpN24 model1_data2 7.20791269123149 30 -yPKDpN24 model1_data2 1.0001914554897 24 -yPKDpN24 model1_data2 8.97029203560068 27 -yPKDpN24 model1_data2 7.20791269123149 30 -yPKDpN25 model1_data2 0.070440612817842 24 -yPKDpN25 model1_data2 0.808170672260932 24.08 -yPKDpN25 model1_data2 1.03952881016581 24.17 -yPKDpN25 model1_data2 1.15815771361015 24.25 -yPKDpN25 model1_data2 1.21309198533554 24.5 -yPKDpN25 model1_data2 1.02144596799516 25 -yPKDpN25 model1_data2 0.070440612817842 24 -yPKDpN25 model1_data2 0.808170672260932 24.08 -yPKDpN25 model1_data2 1.03952881016581 24.17 -yPKDpN25 model1_data2 1.15815771361015 24.25 -yPKDpN25 model1_data2 1.21309198533554 24.5 -yPKDpN25 model1_data2 1.02144596799516 25 -yPKDpN25 model1_data2 0.070440612817842 24 -yPKDpN25 model1_data2 0.808170672260932 24.08 -yPKDpN25 model1_data2 1.03952881016581 24.17 -yPKDpN25 model1_data2 1.15815771361015 24.25 -yPKDpN25 model1_data2 1.21309198533554 24.5 -yPKDpN25 model1_data2 1.02144596799516 25 -yPKDpN25 model1_data2 0.808170672260932 24.08 -yPKDpN25 model1_data2 1.03952881016581 24.17 -yPKDpN25 model1_data2 1.15815771361015 24.25 -yPKDpN25 model1_data2 1.21309198533554 24.5 -yPKDpN25 model1_data2 1.02144596799516 25 -yPI4K3BpRN24 model1_data2 1.08021879123485 24 -yPI4K3BpRN24 model1_data2 1.93873306920031 24.08 -yPI4K3BpRN24 model1_data2 2.29601035446913 24.17 -yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 -yPI4K3BpRN24 model1_data2 2.42628245063557 24.5 -yPI4K3BpRN24 model1_data2 2.41317156090719 25 -yPI4K3BpRN24 model1_data2 2.30969773234004 27 -yPI4K3BpRN24 model1_data2 2.23667583844731 30 -yPI4K3BpRN24 model1_data2 1.08021879123485 24 -yPI4K3BpRN24 model1_data2 1.93873306920031 24.08 -yPI4K3BpRN24 model1_data2 2.29601035446913 24.17 -yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 -yPI4K3BpRN24 model1_data2 2.42628245063557 24.5 -yPI4K3BpRN24 model1_data2 2.41317156090719 25 -yPI4K3BpRN24 model1_data2 2.30969773234004 27 -yPI4K3BpRN24 model1_data2 2.23667583844731 30 -yPI4K3BpRN24 model1_data2 1.08021879123485 24 -yPI4K3BpRN24 model1_data2 2.29601035446913 24.17 -yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 -yPI4K3BpRN24 model1_data2 2.42628245063557 24.5 -yPI4K3BpRN24 model1_data2 2.41317156090719 25 -yPI4K3BpRN24 model1_data2 2.30969773234004 27 -yPI4K3BpRN24 model1_data2 2.23667583844731 30 -yPI4K3BpRN24 model1_data2 1.08021879123485 24 -yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 -yPI4K3BpRN24 model1_data2 2.41317156090719 25 -yPI4K3BpRN24 model1_data2 1.08021879123485 24 -yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 -yPI4K3BpRN24 model1_data2 2.41317156090719 25 -yPKDt model1_data3 466658.660176716 0 -yPKDt model1_data3 466658.660176716 0 -yPKDt model1_data3 466658.660176716 0 -yPI4K3Bt model1_data3 1909595.04348728 0 -yPI4K3Bt model1_data3 1909595.04348728 0 -yPI4K3Bt model1_data3 1909595.04348728 0 -yCERTt model1_data3 450494197.9386 24 -yCERTt model1_data3 450494197.9386 24 -yCERTt model1_data3 450494197.9386 24 -yPKDpN0 model1_data3 0.888880630910278 0 -yPKDpN0 model1_data3 1.42074344951867 3 -yPKDpN0 model1_data3 1.91020373097105 6 -yPKDpN0 model1_data3 3.84925799873664 24 -yPKDpN0 model1_data3 3.37033898457824 24.25 -yPKDpN0 model1_data3 3.29502919416858 24.5 -yPKDpN0 model1_data3 3.22121571284561 25 -yPKDpN0 model1_data3 3.16404551331482 26 -yPKDpN0 model1_data3 3.17592397605905 27 -yPKDpN0 model1_data3 0.888880630910278 0 -yPKDpN0 model1_data3 1.42074344951867 3 -yPKDpN0 model1_data3 1.91020373097105 6 -yPKDpN0 model1_data3 3.84925799873664 24 -yPKDpN0 model1_data3 3.37033898457824 24.25 -yPKDpN0 model1_data3 3.29502919416858 24.5 -yPKDpN0 model1_data3 3.22121571284561 25 -yPKDpN0 model1_data3 3.16404551331482 26 -yPKDpN0 model1_data3 3.17592397605905 27 -yPKDpN0 model1_data3 0.888880630910278 0 -yPKDpN0 model1_data3 1.42074344951867 3 -yPKDpN0 model1_data3 1.91020373097105 6 -yPKDpN0 model1_data3 3.84925799873664 24 -yPKDpN0 model1_data3 3.37033898457824 24.25 -yPKDpN0 model1_data3 3.29502919416858 24.5 -yPKDpN0 model1_data3 3.22121571284561 25 -yPKDpN0 model1_data3 3.16404551331482 26 -yPKDpN0 model1_data3 3.17592397605905 27 -yPKDpN0 model1_data3 0.888880630910278 0 -yPKDpN0 model1_data3 1.42074344951867 3 -yPKDpN0 model1_data3 1.91020373097105 6 -yCERTpRN24 model1_data3 1.00732873833082 24 -yCERTpRN24 model1_data3 0.897553386233455 24.25 -yCERTpRN24 model1_data3 0.874765591088416 24.5 -yCERTpRN24 model1_data3 0.858989185429608 25 -yCERTpRN24 model1_data3 0.848482208428127 26 -yCERTpRN24 model1_data3 0.852942572711505 27 -yCERTpRN24 model1_data3 1.00732873833082 24 -yCERTpRN24 model1_data3 0.897553386233455 24.25 -yCERTpRN24 model1_data3 0.874765591088416 24.5 -yCERTpRN24 model1_data3 0.858989185429608 25 -yCERTpRN24 model1_data3 0.848482208428127 26 -yCERTpRN24 model1_data3 0.852942572711505 27 -yCERTpRN24 model1_data3 1.00732873833082 24 -yCERTpRN24 model1_data3 0.897553386233455 24.25 -yCERTpRN24 model1_data3 0.874765591088416 24.5 -yCERTpRN24 model1_data3 0.858989185429608 25 -yCERTpRN24 model1_data3 0.848482208428127 26 -yCERTpRN24 model1_data3 0.852942572711505 27 -yCERTpRN24 model1_data3 1.00732873833082 24 -yCERTpRN24 model1_data3 0.874765591088416 24.5 +observableId preequilibrationConditionId simulationConditionId simulation time +yPI4K3Bt model1_data2 80032724.6249776 24 +yPI4K3Bt model1_data2 80032724.6249776 24 +yPI4K3Bt model1_data2 80032724.6249776 24 +yCERTt model1_data2 74192014.9947344 0 +yCERTt model1_data2 74192014.9947344 0 +yCERTt model1_data2 74192014.9947344 0 +yPKDpN0 model1_data2 0.888880630910278 0 +yPKDpN0 model1_data2 1.341413518981 3 +yPKDpN0 model1_data2 1.42148291988296 6 +yPKDpN0 model1_data2 0.888880630910278 0 +yPKDpN0 model1_data2 1.341413518981 3 +yPKDpN0 model1_data2 1.42148291988296 6 +yPKDpN0 model1_data2 0.888880630910278 0 +yPKDpN0 model1_data2 1.341413518981 3 +yPKDpN0 model1_data2 1.42148291988296 6 +yPKDpN24 model1_data2 1.0001914554897 24 +yPKDpN24 model1_data2 8.97029203560068 27 +yPKDpN24 model1_data2 7.20791269123149 30 +yPKDpN24 model1_data2 1.0001914554897 24 +yPKDpN24 model1_data2 8.97029203560068 27 +yPKDpN24 model1_data2 7.20791269123149 30 +yPKDpN24 model1_data2 1.0001914554897 24 +yPKDpN24 model1_data2 8.97029203560068 27 +yPKDpN24 model1_data2 7.20791269123149 30 +yPKDpN25 model1_data2 0.070440612817842 24 +yPKDpN25 model1_data2 0.808170672260932 24.08 +yPKDpN25 model1_data2 1.03952881016581 24.17 +yPKDpN25 model1_data2 1.15815771361015 24.25 +yPKDpN25 model1_data2 1.21309198533554 24.5 +yPKDpN25 model1_data2 1.02144596799516 25 +yPKDpN25 model1_data2 0.070440612817842 24 +yPKDpN25 model1_data2 0.808170672260932 24.08 +yPKDpN25 model1_data2 1.03952881016581 24.17 +yPKDpN25 model1_data2 1.15815771361015 24.25 +yPKDpN25 model1_data2 1.21309198533554 24.5 +yPKDpN25 model1_data2 1.02144596799516 25 +yPKDpN25 model1_data2 0.070440612817842 24 +yPKDpN25 model1_data2 0.808170672260932 24.08 +yPKDpN25 model1_data2 1.03952881016581 24.17 +yPKDpN25 model1_data2 1.15815771361015 24.25 +yPKDpN25 model1_data2 1.21309198533554 24.5 +yPKDpN25 model1_data2 1.02144596799516 25 +yPKDpN25 model1_data2 0.808170672260932 24.08 +yPKDpN25 model1_data2 1.03952881016581 24.17 +yPKDpN25 model1_data2 1.15815771361015 24.25 +yPKDpN25 model1_data2 1.21309198533554 24.5 +yPKDpN25 model1_data2 1.02144596799516 25 +yPI4K3BpRN24 model1_data2 1.08021879123485 24 +yPI4K3BpRN24 model1_data2 1.93873306920031 24.08 +yPI4K3BpRN24 model1_data2 2.29601035446913 24.17 +yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 +yPI4K3BpRN24 model1_data2 2.42628245063557 24.5 +yPI4K3BpRN24 model1_data2 2.41317156090719 25 +yPI4K3BpRN24 model1_data2 2.30969773234004 27 +yPI4K3BpRN24 model1_data2 2.23667583844731 30 +yPI4K3BpRN24 model1_data2 1.08021879123485 24 +yPI4K3BpRN24 model1_data2 1.93873306920031 24.08 +yPI4K3BpRN24 model1_data2 2.29601035446913 24.17 +yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 +yPI4K3BpRN24 model1_data2 2.42628245063557 24.5 +yPI4K3BpRN24 model1_data2 2.41317156090719 25 +yPI4K3BpRN24 model1_data2 2.30969773234004 27 +yPI4K3BpRN24 model1_data2 2.23667583844731 30 +yPI4K3BpRN24 model1_data2 1.08021879123485 24 +yPI4K3BpRN24 model1_data2 2.29601035446913 24.17 +yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 +yPI4K3BpRN24 model1_data2 2.42628245063557 24.5 +yPI4K3BpRN24 model1_data2 2.41317156090719 25 +yPI4K3BpRN24 model1_data2 2.30969773234004 27 +yPI4K3BpRN24 model1_data2 2.23667583844731 30 +yPI4K3BpRN24 model1_data2 1.08021879123485 24 +yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 +yPI4K3BpRN24 model1_data2 2.41317156090719 25 +yPI4K3BpRN24 model1_data2 1.08021879123485 24 +yPI4K3BpRN24 model1_data2 2.37827314571914 24.25 +yPI4K3BpRN24 model1_data2 2.41317156090719 25 +yPKDt model1_data3 466658.660176716 0 +yPKDt model1_data3 466658.660176716 0 +yPKDt model1_data3 466658.660176716 0 +yPI4K3Bt model1_data3 1909595.04348728 0 +yPI4K3Bt model1_data3 1909595.04348728 0 +yPI4K3Bt model1_data3 1909595.04348728 0 +yCERTt model1_data3 450494197.9386 24 +yCERTt model1_data3 450494197.9386 24 +yCERTt model1_data3 450494197.9386 24 +yPKDpN0 model1_data3 0.888880630910278 0 +yPKDpN0 model1_data3 1.42074344951867 3 +yPKDpN0 model1_data3 1.91020373097105 6 +yPKDpN0 model1_data3 3.84925799873664 24 +yPKDpN0 model1_data3 3.37033898457824 24.25 +yPKDpN0 model1_data3 3.29502919416858 24.5 +yPKDpN0 model1_data3 3.22121571284561 25 +yPKDpN0 model1_data3 3.16404551331482 26 +yPKDpN0 model1_data3 3.17592397605905 27 +yPKDpN0 model1_data3 0.888880630910278 0 +yPKDpN0 model1_data3 1.42074344951867 3 +yPKDpN0 model1_data3 1.91020373097105 6 +yPKDpN0 model1_data3 3.84925799873664 24 +yPKDpN0 model1_data3 3.37033898457824 24.25 +yPKDpN0 model1_data3 3.29502919416858 24.5 +yPKDpN0 model1_data3 3.22121571284561 25 +yPKDpN0 model1_data3 3.16404551331482 26 +yPKDpN0 model1_data3 3.17592397605905 27 +yPKDpN0 model1_data3 0.888880630910278 0 +yPKDpN0 model1_data3 1.42074344951867 3 +yPKDpN0 model1_data3 1.91020373097105 6 +yPKDpN0 model1_data3 3.84925799873664 24 +yPKDpN0 model1_data3 3.37033898457824 24.25 +yPKDpN0 model1_data3 3.29502919416858 24.5 +yPKDpN0 model1_data3 3.22121571284561 25 +yPKDpN0 model1_data3 3.16404551331482 26 +yPKDpN0 model1_data3 3.17592397605905 27 +yPKDpN0 model1_data3 0.888880630910278 0 +yPKDpN0 model1_data3 1.42074344951867 3 +yPKDpN0 model1_data3 1.91020373097105 6 +yCERTpRN24 model1_data3 1.00732873833082 24 +yCERTpRN24 model1_data3 0.897553386233455 24.25 +yCERTpRN24 model1_data3 0.874765591088416 24.5 +yCERTpRN24 model1_data3 0.858989185429608 25 +yCERTpRN24 model1_data3 0.848482208428127 26 +yCERTpRN24 model1_data3 0.852942572711505 27 +yCERTpRN24 model1_data3 1.00732873833082 24 +yCERTpRN24 model1_data3 0.897553386233455 24.25 +yCERTpRN24 model1_data3 0.874765591088416 24.5 +yCERTpRN24 model1_data3 0.858989185429608 25 +yCERTpRN24 model1_data3 0.848482208428127 26 +yCERTpRN24 model1_data3 0.852942572711505 27 +yCERTpRN24 model1_data3 1.00732873833082 24 +yCERTpRN24 model1_data3 0.897553386233455 24.25 +yCERTpRN24 model1_data3 0.874765591088416 24.5 +yCERTpRN24 model1_data3 0.858989185429608 25 +yCERTpRN24 model1_data3 0.848482208428127 26 +yCERTpRN24 model1_data3 0.852942572711505 27 +yCERTpRN24 model1_data3 1.00732873833082 24 +yCERTpRN24 model1_data3 0.874765591088416 24.5 diff --git a/Benchmark-Models/Weber_BMC2015/visualizationSpecification_Weber_BMC2015.tsv b/Benchmark-Models/Weber_BMC2015/visualizationSpecification_Weber_BMC2015.tsv index 7991c716..880cf52b 100644 --- a/Benchmark-Models/Weber_BMC2015/visualizationSpecification_Weber_BMC2015.tsv +++ b/Benchmark-Models/Weber_BMC2015/visualizationSpecification_Weber_BMC2015.tsv @@ -1,9 +1,9 @@ plotId plotTypeData plotTypeSimulation xLabel xScale yLabel yScale yValues xValues xOffset yOffset -plot1 MeanAndSD LinePlot time lin values lin yPKDpN0 time 0 0 -plot2 MeanAndSD LinePlot time lin values lin yPKDpN24 time 0 0 -plot3 MeanAndSD LinePlot time lin values lin yPKDpN25 time 0 0 -plot4 MeanAndSD LinePlot time lin values lin yPI4K3BpRN24 time 0 0 -plot5 MeanAndSD LinePlot time lin values lin yPI4K3Bt time 0 0 -plot6 MeanAndSD LinePlot time lin values lin yCERTt time 0 0 -plot7 MeanAndSD LinePlot time lin values lin yCERTpRN24 time 0 0 -plot8 MeanAndSD LinePlot time lin values lin yPKDt time 0 0 +plot1 MeanAndSD LinePlot time [h] lin relative signal lin yPKDpN0 time 0 0 +plot2 MeanAndSD LinePlot time [h] lin relative signal lin yPKDpN24 time 0 0 +plot3 MeanAndSD LinePlot time [h] lin relative signal lin yPKDpN25 time 0 0 +plot4 MeanAndSD LinePlot time [h] lin relative signal lin yPI4K3BpRN24 time 0 0 +plot5 MeanAndSD LinePlot time [h] lin molecules / cell lin yPI4K3Bt time 0 0 +plot6 MeanAndSD LinePlot time [h] lin molecules / cell lin yCERTt time 0 0 +plot7 MeanAndSD LinePlot time [h] lin relative signal lin yCERTpRN24 time 0 0 +plot8 MeanAndSD LinePlot time [h] lin molecules / cell lin yPKDt time 0 0 From 2fca448ca368e114fd087620e0f1e45ccab4cc8d Mon Sep 17 00:00:00 2001 From: Polina Lakrisenko Date: Thu, 6 Nov 2025 21:41:37 +0100 Subject: [PATCH 11/11] fix Perelson axes labels --- .../visualizationSpecification_Perelson_Science1996.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Benchmark-Models/Perelson_Science1996/visualizationSpecification_Perelson_Science1996.tsv b/Benchmark-Models/Perelson_Science1996/visualizationSpecification_Perelson_Science1996.tsv index 5c4b0476..262254a7 100644 --- a/Benchmark-Models/Perelson_Science1996/visualizationSpecification_Perelson_Science1996.tsv +++ b/Benchmark-Models/Perelson_Science1996/visualizationSpecification_Perelson_Science1996.tsv @@ -1,2 +1,2 @@ plotId plotTypeData plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset -plot1 MeanAndSD LinePlot time lin values lin HIV-mRNA copies - task0_model0_perelson1_V task0_model0_perelson1_V time 0 0 +plot1 MeanAndSD LinePlot time [days] lin RNA copies/ml lin HIV-mRNA copies - task0_model0_perelson1_V task0_model0_perelson1_V time 0 0