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Visualization fixes for some benchmark models. #289

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Merged
m-philipps merged 9 commits into from
Nov 20, 2025
Merged

Visualization fixes for some benchmark models. #289

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542ca38
Fix visualization specification for Zhao.
stephanmg Jun 27, 2024
8f39b74
Fix.
stephanmg Jun 27, 2024
ce27c30
Merge branch 'Benchmarking-Initiative:master' into master
stephanmg Jul 8, 2025
364e200
Merge remote-tracking branch 'upstream/master'
stephanmg Nov 19, 2025
673817f
Adding unit for x-axis label for Giordano.
stephanmg Nov 20, 2025
7e2522f
Adding unit for x-axis label for Okuonghae
stephanmg Nov 20, 2025
36aea3b
Correct cation superscripts for Sneyd.
stephanmg Nov 20, 2025
1029433
Adding unit for x-axis label for Zheng
stephanmg Nov 20, 2025
2d746ac
Consistent capitalization for Brannmark.
stephanmg Nov 20, 2025
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6 changes: 3 additions & 3 deletions Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv
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Original file line number Diff line number Diff line change
@@ -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
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
plot4 MeanAndSD LinePlot Time [min] lin IRS1 phosphorylation lin IRS1_P time 0 0 TwoSteps
16 changes: 8 additions & 8 deletions Benchmark-Models/Giordano_Nature2020/visualizationSpecification_Giordano_Nature2020.tsv
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
plotId plotName plotTypeSimulation xValues yValues yLabel legendEntry xScale yScale datasetId
TotalDiagnosedCases Data vs Sim TotalDiagnosedCases Data vs Sim LinePlot time observable_TotalCases TotalCases TotalCases lin lin test
Deaths Data vs Sim Deaths Data vs Sim LinePlot time observable_Deaths Deaths Deaths lin lin test
Recovered Data vs Sim Recovered Data vs Sim LinePlot time observable_Recovered Recovered Recovered lin lin test
CurrentDiagnosedCases Data vs Sim CurrentDiagnosedCases Data vs Sim LinePlot time observable_CurrentCases CurrentCases CurrentCases lin lin test
Diagnosed Data vs Sim Diagnosed Data vs Sim LinePlot time observable_DiagHome Diagnosed Diagnosed lin lin test
Recognized Data vs Sim Recognized Data vs Sim LinePlot time observable_Hospit Recognized Recognized lin lin test
Threatened Data vs Sim Threatened Data vs Sim LinePlot time observable_ICU Threatened Threatened lin lin test
plotId plotName plotTypeSimulation xValues yValues yLabel legendEntry xScale yScale datasetId xLabel
TotalDiagnosedCases Data vs Sim TotalDiagnosedCases Data vs Sim LinePlot time observable_TotalCases TotalCases TotalCases lin lin test Time [days]
Deaths Data vs Sim Deaths Data vs Sim LinePlot time observable_Deaths Deaths Deaths lin lin test Time [days]
Recovered Data vs Sim Recovered Data vs Sim LinePlot time observable_Recovered Recovered Recovered lin lin test Time[days]
CurrentDiagnosedCases Data vs Sim CurrentDiagnosedCases Data vs Sim LinePlot time observable_CurrentCases CurrentCases CurrentCases lin lin test Time [days]
Diagnosed Data vs Sim Diagnosed Data vs Sim LinePlot time observable_DiagHome Diagnosed Diagnosed lin lin test Time [days]
Recognized Data vs Sim Recognized Data vs Sim LinePlot time observable_Hospit Recognized Recognized lin lin test Time [days]
Threatened Data vs Sim Threatened Data vs Sim LinePlot time observable_ICU Threatened Threatened lin lin test Time [days]
6 changes: 3 additions & 3 deletions ...osSolitonsFractals2020/visualizationSpecification_Okuonghae_ChaosSolitonsFractals2020.tsv
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
plotId plotTypeSimulation xValues yValues yLabel datasetId legendEntry
ActiveCases Sim vs Data LinePlot time observable_ActiveCases Number of Active Cases id1 Activecases
Cumulative Sim vs Data LinePlot time observable_Cumulative Number of Cumulative Cases id1 CumCases
plotId plotTypeSimulation xValues yValues yLabel datasetId legendEntry xLabel
ActiveCases Sim vs Data LinePlot time observable_ActiveCases Number of Active Cases id1 Activecases Time [days]
Cumulative Sim vs Data LinePlot time observable_Cumulative Number of Cumulative Cases id1 CumCases Time [days]
18 changes: 9 additions & 9 deletions Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale datasetId legendEntry yValues xValues xOffset yOffset
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__1_open_probability 10 μM IP_3, 0.1 μM Ca^{2+} - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP_3, 0.2 μM Ca^{2+} - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP_3, 1 μM Ca^{2+} - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP_3, 3 μM Ca^{2+} - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP_3, 10 μM Ca^{2+} - open_probability open_probability time 0 0
plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0
plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0
plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__1_open_probability 10 μM IP_3, 0.1 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP_3, 0.2 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP_3, 1 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP_3, 3 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP_3, 10 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0
plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0
30 changes: 15 additions & 15 deletions Benchmark-Models/Zheng_PNAS2012/visualizationSpecification_Zheng_PNAS2012.tsv
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
plotId plotTypeData plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset
plot1 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me0K36me0 observable_K27me0K36me0 time 0 0
plot2 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me0K36me1 observable_K27me0K36me1 time 0 0
plot3 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me1K36me0 observable_K27me1K36me0 time 0 0
plot4 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me0K36me2 observable_K27me0K36me2 time 0 0
plot5 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me1K36me1 observable_K27me1K36me1 time 0 0
plot6 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me2K36me0 observable_K27me2K36me0 time 0 0
plot7 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me0K36me3 observable_K27me0K36me3 time 0 0
plot8 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me1K36me2 observable_K27me1K36me2 time 0 0
plot9 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me2K36me1 observable_K27me2K36me1 time 0 0
plot10 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me3K36me0 observable_K27me3K36me0 time 0 0
plot11 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me1K36me3 observable_K27me1K36me3 time 0 0
plot12 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me2K36me2 observable_K27me2K36me2 time 0 0
plot13 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me3K36me1 observable_K27me3K36me1 time 0 0
plot14 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me2K36me3 observable_K27me2K36me3 time 0 0
plot15 MeanAndSD LinePlot time lin values lin simCondition - observable_K27me3K36me2 observable_K27me3K36me2 time 0 0
plot1 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me0K36me0 observable_K27me0K36me0 time 0 0
plot2 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me0K36me1 observable_K27me0K36me1 time 0 0
plot3 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me1K36me0 observable_K27me1K36me0 time 0 0
plot4 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me0K36me2 observable_K27me0K36me2 time 0 0
plot5 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me1K36me1 observable_K27me1K36me1 time 0 0
plot6 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me2K36me0 observable_K27me2K36me0 time 0 0
plot7 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me0K36me3 observable_K27me0K36me3 time 0 0
plot8 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me1K36me2 observable_K27me1K36me2 time 0 0
plot9 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me2K36me1 observable_K27me2K36me1 time 0 0
plot10 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me3K36me0 observable_K27me3K36me0 time 0 0
plot11 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me1K36me3 observable_K27me1K36me3 time 0 0
plot12 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me2K36me2 observable_K27me2K36me2 time 0 0
plot13 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me3K36me1 observable_K27me3K36me1 time 0 0
plot14 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me2K36me3 observable_K27me2K36me3 time 0 0
plot15 MeanAndSD LinePlot Time [s] lin values lin simCondition - observable_K27me3K36me2 observable_K27me3K36me2 time 0 0