From 542ca38d244de5bf9ec231aa97e7313759e27009 Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Thu, 27 Jun 2024 12:19:52 +0200 Subject: [PATCH 1/4] Fix visualization specification for Zhao. --- ...sualizationSpecification_Zhao_QuantBiol2020.tsv | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv b/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv index 3655c20..42f078a 100644 --- a/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv +++ b/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv @@ -1,8 +1,8 @@ plotId plotName plotTypeSimulation plotTypeData datasetId xValues xOffset xLabel yValues yOffset yLabel legendEntry xScale yScale -plot1 China_Stage_I LinePlot model1_data_observable_confirmed_infected_China_Stage_I time -30 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot2 China_Stage_II LinePlot model1_data_observable_confirmed_infected_China_Stage_II time 0 Time [d] from 2020-1-30 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot3 Wuhan_Stage_I LinePlot model1_data_observable_confirmed_infected_Wuhan_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot4 Wuhan_Stage_II LinePlot model1_data_observable_confirmed_infected_Wuhan_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot5 Wuhan_Stage_III LinePlot model1_data_observable_confirmed_infected_Wuhan_Stage_III time 0 Time [d] from 2020-2-13 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot6 Hubei_Stage_I LinePlot model1_data_observable_confirmed_infected_Hubei_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot7 Hubei_Stage_II LinePlot model1_data_observable_confirmed_infected_Hubei_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot1 China_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_China_Stage_I time -30 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot2 China_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_China_Stage_II time 0 Time [d] from 2020-1-30 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot3 Wuhan_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot4 Wuhan_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot5 Wuhan_Stage_III LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_III time 0 Time [d] from 2020-2-13 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot6 Hubei_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_Hubei_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot7 Hubei_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_Hubei_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin From 8f39b744b187be86f3532b25d7e3491ffe26f9ad Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Thu, 27 Jun 2024 14:14:51 +0200 Subject: [PATCH 2/4] Fix. --- ...sualizationSpecification_Zhao_QuantBiol2020.tsv | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv b/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv index 42f078a..50e7e92 100644 --- a/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv +++ b/Benchmark-Models/Zhao_QuantBiol2020/visualizationSpecification_Zhao_QuantBiol2020.tsv @@ -1,8 +1,8 @@ plotId plotName plotTypeSimulation plotTypeData datasetId xValues xOffset xLabel yValues yOffset yLabel legendEntry xScale yScale -plot1 China_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_China_Stage_I time -30 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot2 China_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_China_Stage_II time 0 Time [d] from 2020-1-30 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot3 Wuhan_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot4 Wuhan_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot5 Wuhan_Stage_III LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_III time 0 Time [d] from 2020-2-13 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot6 Hubei_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_Hubei_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin -plot7 Hubei_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_Hubei_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot1 China_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_China_Stage_I time -30 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot2 China_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_China_Stage_II time 0 Time [d] from 2020-1-30 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot3 Wuhan_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot4 Wuhan_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot5 Wuhan_Stage_III LinePlot MeanAndSD model1_data_observable_confirmed_infected_Wuhan_Stage_III time 0 Time [d] from 2020-2-13 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot6 Hubei_Stage_I LinePlot MeanAndSD model1_data_observable_confirmed_infected_Hubei_Stage_I time -15 Time [d] from 2020-1-20 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin +plot7 Hubei_Stage_II LinePlot MeanAndSD model1_data_observable_confirmed_infected_Hubei_Stage_II time 0 Time [d] from 2020-1-28 observable_confirmed_infected 0 Cumulative confirmed infected number Confirmed_Infected lin lin From 10ee29ca9f941326f6c359acd2aa3c5b2ffdfb30 Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Fri, 21 Nov 2025 17:11:55 +0100 Subject: [PATCH 3/4] Backward compatible changes to avoid nan in plot title (Brannmark). Perhaps relevant only for older petab versions, might be relevant for Lucarelli as well. --- .../visualizationSpecification_Brannmark_JBC2010.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv b/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv index 534401d..44c01af 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 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 +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 fd79168188d860cb4f6ea0e7aaa3d1d8ff5bb659 Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Fri, 21 Nov 2025 19:07:32 +0100 Subject: [PATCH 4/4] Fix. --- .../visualizationSpecification_Brannmark_JBC2010.tsv | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv b/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv index fa0a6dc..627a08c 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 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 +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