Skip to content

Smith: more informative legend entries #311

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dweindl merged 3 commits into from
Jul 1, 2026
Merged

Smith: more informative legend entries #311

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6749829
Smith: more informative legend entries
dweindl Jun 29, 2026
d612328
Fix Ins unit -- amount-based, not concentration based
dweindl Jun 29, 2026
a2fecd1
tex
dweindl Jun 29, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 13 additions & 13 deletions Benchmark-Models/Smith_BMCSystBiol2013/measurementData_Smith_BMCSystBiol2013.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
48 changes: 24 additions & 24 deletions Benchmark-Models/Smith_BMCSystBiol2013/visualizationSpecification_Smith_BMCSystBiol2013.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 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 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+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
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