From 6749829c423e58591d91b33d54ee45d1089df73a Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 29 Jun 2026 13:30:34 +0200 Subject: [PATCH 1/3] Smith: more informative legend entries --- .../measurementData_Smith_BMCSystBiol2013.tsv | 26 +++++----- ...ionSpecification_Smith_BMCSystBiol2013.tsv | 48 +++++++++---------- 2 files changed, 37 insertions(+), 37 deletions(-) diff --git a/Benchmark-Models/Smith_BMCSystBiol2013/measurementData_Smith_BMCSystBiol2013.tsv b/Benchmark-Models/Smith_BMCSystBiol2013/measurementData_Smith_BMCSystBiol2013.tsv index c577a9dc..c4b6abb9 100644 --- a/Benchmark-Models/Smith_BMCSystBiol2013/measurementData_Smith_BMCSystBiol2013.tsv +++ b/Benchmark-Models/Smith_BMCSystBiol2013/measurementData_Smith_BMCSystBiol2013.tsv @@ -3,19 +3,19 @@ time observableId measurement simulationConditionId datasetId 240.0 Glucose_uptake__240__3B 220.0 figure3B__0_0__0_0 Basal (time = 240) 120.0 Glucose_uptake__120__3B 270.0 figure3B__60_0__0_0 H2O2 (time = 120) 240.0 Glucose_uptake__240__3B 350.0 figure3B__60_0__0_0 H2O2 (time = 240) -0.0 IRSYp__2C 0.0 figure2C__0_0__500000 fig2A -1.0 IRSYp__2C 220.0 figure2C__0_0__500000 fig2A -1.25 IRSYp__2C 200.0 figure2C__0_0__500000 fig2A -1.4 IRSYp__2C 165.0 figure2C__0_0__500000 fig2A -2.2 IRSYp__2C 145.0 figure2C__0_0__500000 fig2A -3.3 IRSYp__2C 125.0 figure2C__0_0__500000 fig2A -5.25 IRSYp__2C 112.0 figure2C__0_0__500000 fig2A -7.2 IRSYp__2C 95.0 figure2C__0_0__500000 fig2A -10.0 IRSYp__2C 120.0 figure2C__0_0__500000 fig2A -15.0 IRSYp__2C 90.0 figure2C__0_0__500000 fig2A -0.0 PTP_activ__2D 0.16 figure2D__0_0__500000 fig2A -1.0 PTP_activ__2D 0.1 figure2D__0_0__500000 fig2A -5.0 PTP_activ__2D 0.05 figure2D__0_0__500000 fig2A +0.0 IRSYp__2C 0.0 figure2C__0_0__500000 fig2C +1.0 IRSYp__2C 220.0 figure2C__0_0__500000 fig2C +1.25 IRSYp__2C 200.0 figure2C__0_0__500000 fig2C +1.4 IRSYp__2C 165.0 figure2C__0_0__500000 fig2c +2.2 IRSYp__2C 145.0 figure2C__0_0__500000 fig2C +3.3 IRSYp__2C 125.0 figure2C__0_0__500000 fig2C +5.25 IRSYp__2C 112.0 figure2C__0_0__500000 fig2C +7.2 IRSYp__2C 95.0 figure2C__0_0__500000 fig2C +10.0 IRSYp__2C 120.0 figure2C__0_0__500000 fig2C +15.0 IRSYp__2C 90.0 figure2C__0_0__500000 fig2C +0.0 PTP_activ__2D 0.16 figure2D__0_0__500000 fig2D +1.0 PTP_activ__2D 0.1 figure2D__0_0__500000 fig2D +5.0 PTP_activ__2D 0.05 figure2D__0_0__500000 fig2D 960.0 FOXO4__3C 1.0 figure3C__0_0__0_0 0.0 960.0 MnSOD_fold_induction__3C 5.0 figure3C__0_0__0_0 0.0 960.0 FOXO4__3C 1.0 figure3C__5_0__0_0 5.0 diff --git a/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv b/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv index 4216ed73..af24ffb9 100644 --- a/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv +++ b/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv @@ -1,24 +1,24 @@ -plotId plotName plotTypeSimulation plotTypeData datasetId xValues xScale xLabel yValues yLabel -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H2O2 (uM) FOXO4__3C fold-induction -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H2O2 (uM) MnSOD_fold_induction__3C fold-induction -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H2O2 (uM) FOXO4__3C fold-induction -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H2O2 (uM) MnSOD_fold_induction__3C fold-induction -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H2O2 (uM) FOXO4__3C fold-induction -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H2O2 (uM) MnSOD_fold_induction__3C fold-induction -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H2O2 (uM) FOXO4__3C fold-induction -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H2O2 (uM) MnSOD_fold_induction__3C fold-induction -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H2O2 (uM) FOXO4__3C fold-induction -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H2O2 (uM) MnSOD_fold_induction__3C fold-induction -figure3B Figure 3B BarPlot MeanAndSD Basal (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake -figure3B Figure 3B BarPlot MeanAndSD Basal (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake -figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake -figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake -figure3B Figure 3B BarPlot MeanAndSD Ins (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake -figure3B Figure 3B BarPlot MeanAndSD Ins (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake -figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake -figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake -figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) Cell_Bound_Ins__2B Active Enzyme [a.u.] -figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) Glucose_uptake__2B Active Enzyme [a.u.] -figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) PI3K_activity__2B Active Enzyme [a.u.] -figure2C Figure 2C LinePlot MeanAndSD fig2A time lin time [min] IRSYp__2C Active Enzyme [a.u.] -figure2D Figure 2D LinePlot MeanAndSD fig2A time lin time [min] PTP_activ__2D Active Enzyme [a.u.] +plotId plotName plotTypeSimulation plotTypeData datasetId xValues xScale xLabel yValues yLabel legendEntry +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 0.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 0.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 10.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 10.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 20.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 20.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 5.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 5.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 50.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 50.0 +figure3B Figure 3B BarPlot MeanAndSD Basal (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Basal (time = 120) +figure3B Figure 3B BarPlot MeanAndSD Basal (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Basal (time = 240) +figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake H₂O₂ (time = 120) +figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake H₂O₂ (time = 240) +figure3B Figure 3B BarPlot MeanAndSD Ins (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Ins (time = 120) +figure3B Figure 3B BarPlot MeanAndSD Ins (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Ins (time = 240) +figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Ins+H₂O₂ (time = 120) +figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Ins+H₂O₂ (time = 240) +figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) Cell_Bound_Ins__2B Active Enzyme [a.u.] Cell_Bound_Ins__2B +figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) Glucose_uptake__2B Active Enzyme [a.u.] Glucose_uptake__2B +figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) PI3K_activity__2B Active Enzyme [a.u.] PI3K_activity__2B +figure2C Figure 2C LinePlot MeanAndSD fig2C time lin time [min] IRSYp__2C Active Enzyme [a.u.] IRS-Yp +figure2D Figure 2D LinePlot MeanAndSD fig2D time lin time [min] PTP_activ__2D Active Enzyme [a.u.] PTP1B From d61232855e842acf0e1e613fc9e3d5a981961001 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 29 Jun 2026 14:12:09 +0200 Subject: [PATCH 2/3] Fix Ins unit -- amount-based, not concentration based --- .../visualizationSpecification_Smith_BMCSystBiol2013.tsv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv b/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv index af24ffb9..052676ee 100644 --- a/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv +++ b/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv @@ -17,8 +17,8 @@ figure3B Figure 3B BarPlot MeanAndSD Ins (time = 120) extracellular_ROS lin cond figure3B Figure 3B BarPlot MeanAndSD Ins (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Ins (time = 240) figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Ins+H₂O₂ (time = 120) figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Ins+H₂O₂ (time = 240) -figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) Cell_Bound_Ins__2B Active Enzyme [a.u.] Cell_Bound_Ins__2B -figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) Glucose_uptake__2B Active Enzyme [a.u.] Glucose_uptake__2B -figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (M) PI3K_activity__2B Active Enzyme [a.u.] PI3K_activity__2B +figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (number of molecules) Cell_Bound_Ins__2B Active Enzyme [a.u.] Cell_Bound_Ins__2B +figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (number of molecules) Glucose_uptake__2B Active Enzyme [a.u.] Glucose_uptake__2B +figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (number of molecules) PI3K_activity__2B Active Enzyme [a.u.] PI3K_activity__2B figure2C Figure 2C LinePlot MeanAndSD fig2C time lin time [min] IRSYp__2C Active Enzyme [a.u.] IRS-Yp figure2D Figure 2D LinePlot MeanAndSD fig2D time lin time [min] PTP_activ__2D Active Enzyme [a.u.] PTP1B From a2fecd167aaf38a8d5e6cb5d6e008514b8a298e7 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 29 Jun 2026 15:55:26 +0200 Subject: [PATCH 3/3] tex --- ...ionSpecification_Smith_BMCSystBiol2013.tsv | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv b/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv index 052676ee..29eeb8ae 100644 --- a/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv +++ b/Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv @@ -1,22 +1,22 @@ plotId plotName plotTypeSimulation plotTypeData datasetId xValues xScale xLabel yValues yLabel legendEntry -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 0.0 -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 0.0 -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 10.0 -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 10.0 -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 20.0 -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 20.0 -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 5.0 -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 5.0 -FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H₂O₂ (uM) FOXO4__3C fold-induction 50.0 -MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H₂O₂ (uM) MnSOD_fold_induction__3C fold-induction 50.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H$_2$O$_2$ (uM) FOXO4__3C fold-induction 0.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 0.0 extracellular_ROS lin H$_2$O$_2$ (uM) MnSOD_fold_induction__3C fold-induction 0.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H$_2$O$_2$ (uM) FOXO4__3C fold-induction 10.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 10.0 extracellular_ROS lin H$_2$O$_2$ (uM) MnSOD_fold_induction__3C fold-induction 10.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H$_2$O$_2$ (uM) FOXO4__3C fold-induction 20.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 20.0 extracellular_ROS lin H$_2$O$_2$ (uM) MnSOD_fold_induction__3C fold-induction 20.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H$_2$O$_2$ (uM) FOXO4__3C fold-induction 5.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 5.0 extracellular_ROS lin H$_2$O$_2$ (uM) MnSOD_fold_induction__3C fold-induction 5.0 +FOXO4__3C FOXO4 Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H$_2$O$_2$ (uM) FOXO4__3C fold-induction 50.0 +MnSOD_fold_induction__3C MnSOD_fold_induction Figure 3C BarPlot MeanAndSD 50.0 extracellular_ROS lin H$_2$O$_2$ (uM) MnSOD_fold_induction__3C fold-induction 50.0 figure3B Figure 3B BarPlot MeanAndSD Basal (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Basal (time = 120) figure3B Figure 3B BarPlot MeanAndSD Basal (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Basal (time = 240) -figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake H₂O₂ (time = 120) -figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake H₂O₂ (time = 240) +figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake H$_2$O$_2$ (time = 120) +figure3B Figure 3B BarPlot MeanAndSD H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake H$_2$O$_2$ (time = 240) figure3B Figure 3B BarPlot MeanAndSD Ins (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Ins (time = 120) figure3B Figure 3B BarPlot MeanAndSD Ins (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Ins (time = 240) -figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Ins+H₂O₂ (time = 120) -figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Ins+H₂O₂ (time = 240) +figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 120) extracellular_ROS lin condition Glucose_uptake__120__3B glucose uptake Ins+H$_2$O$_2$ (time = 120) +figure3B Figure 3B BarPlot MeanAndSD Ins+H2O2 (time = 240) extracellular_ROS lin condition Glucose_uptake__240__3B glucose uptake Ins+H$_2$O$_2$ (time = 240) figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (number of molecules) Cell_Bound_Ins__2B Active Enzyme [a.u.] Cell_Bound_Ins__2B figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (number of molecules) Glucose_uptake__2B Active Enzyme [a.u.] Glucose_uptake__2B figure2B Figure 2B LinePlot MeanAndSD base Ins log10 insulin (number of molecules) PI3K_activity__2B Active Enzyme [a.u.] PI3K_activity__2B