From 542ca38d244de5bf9ec231aa97e7313759e27009 Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Thu, 27 Jun 2024 12:19:52 +0200 Subject: [PATCH 1/3] 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 2/3] 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 66336fcbe3e96ab395c7077bb0dc6e021e3fe2d9 Mon Sep 17 00:00:00 2001 From: Stephan Grein Date: Thu, 20 Nov 2025 17:30:50 +0100 Subject: [PATCH 3/3] Assigning names for CD8 T cell subpopulations in Crauste. --- ...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 b7a3a8f..d44b068 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 [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 +plot1 MeanAndSD LinePlot time [days] lin CD8 naive T cell counts log10 condition1 - observable_Naive observable_Naive time 0 0 +plot2 MeanAndSD LinePlot time [days] lin CD8 early effector T cell counts log10 condition1 - observable_EarlyEffector observable_EarlyEffector time 0 0 +plot3 MeanAndSD LinePlot time [days] lin CD8 late effector T cell counts log10 condition1 - observable_LateEffector observable_LateEffector time 0 0 +plot4 MeanAndSD LinePlot time [days] lin CD8 memory T cell counts log10 condition1 - observable_Memory observable_Memory time 0 0