From d334ac8f978d1f8df804d0ee6d6a0fbf5f03d72d Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 29 Jun 2026 12:50:24 +0200 Subject: [PATCH 1/2] Sneyd: prettify visualization * Fix italics * Fix subscripts * Remove observable name from legend which is redundant with the y-label --- ...sualizationSpecification_Sneyd_PNAS2002.tsv | 18 +++++++++--------- ...onSpecification_Sneyd_PNAS2002_subplots.tsv | 18 +++++++++--------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv index 0ccea48..058fb8f 100644 --- a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv +++ b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv @@ -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 IP₃, 0.1 μM Ca²⁺ open_probability time 0 0 +plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP₃, 0.2 μM Ca²⁺ open_probability time 0 0 +plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 +plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP₃, 1 μM Ca²⁺ open_probability time 0 0 +plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP₃, 3 μM Ca²⁺ open_probability time 0 0 +plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP₃, 10 μM Ca²⁺ open_probability time 0 0 +plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 +plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 +plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 diff --git a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv index f251558..2487367 100644 --- a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv +++ b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv @@ -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 -plot2 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 -plot3 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 -plot4 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 -plot5 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 -plot6 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 -plot7 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 -plot8 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 -plot9 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 IP₃, 0.1 μM Ca²⁺ open_probability time 0 0 +plot2 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP₃, 0.2 μM Ca²⁺ open_probability time 0 0 +plot3 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 +plot4 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP₃, 1 μM Ca²⁺ open_probability time 0 0 +plot5 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP₃, 3 μM Ca²⁺ open_probability time 0 0 +plot6 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP₃, 10 μM Ca²⁺ open_probability time 0 0 +plot7 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 +plot8 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 +plot9 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 From 159b167b944bcfb0ff5b890311938cbbb9b48db7 Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Mon, 29 Jun 2026 15:50:42 +0200 Subject: [PATCH 2/2] tex --- ...sualizationSpecification_Sneyd_PNAS2002.tsv | 18 +++++++++--------- ...onSpecification_Sneyd_PNAS2002_subplots.tsv | 18 +++++++++--------- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv index 058fb8f..4c0ace6 100644 --- a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv +++ b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv @@ -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 IP₃, 0.1 μM Ca²⁺ open_probability time 0 0 -plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP₃, 0.2 μM Ca²⁺ open_probability time 0 0 -plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 -plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP₃, 1 μM Ca²⁺ open_probability time 0 0 -plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP₃, 3 μM Ca²⁺ open_probability time 0 0 -plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP₃, 10 μM Ca²⁺ open_probability time 0 0 -plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 -plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 -plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ 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 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 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 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 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 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 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 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 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 time 0 0 diff --git a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv index 2487367..342d3e2 100644 --- a/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv +++ b/Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv @@ -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 IP₃, 0.1 μM Ca²⁺ open_probability time 0 0 -plot2 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP₃, 0.2 μM Ca²⁺ open_probability time 0 0 -plot3 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 -plot4 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP₃, 1 μM Ca²⁺ open_probability time 0 0 -plot5 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP₃, 3 μM Ca²⁺ open_probability time 0 0 -plot6 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP₃, 10 μM Ca²⁺ open_probability time 0 0 -plot7 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 -plot8 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP₃, 0.4 μM Ca²⁺ open_probability time 0 0 -plot9 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP₃, 0.4 μM Ca²⁺ 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 time 0 0 +plot2 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 time 0 0 +plot3 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 time 0 0 +plot4 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP$_3$, 1 μM Ca$^{2{+}}$ open_probability time 0 0 +plot5 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP$_3$, 3 μM Ca$^{2{+}}$ open_probability time 0 0 +plot6 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP$_3$, 10 μM Ca$^{2{+}}$ open_probability time 0 0 +plot7 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 time 0 0 +plot8 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 time 0 0 +plot9 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 time 0 0