add visualization files Brannmark, Borghans, Crauste, Elowitz, Perelson, Weber, Zheng (#179)

plakrisenko · web-flow · commit caa052a26d71 · 2023-02-14T09:52:33.000+01:00
diff --git a/Benchmark-Models/Borghans_BiophysChem1997/Borghans_BiophysChem1997.yaml b/Benchmark-Models/Borghans_BiophysChem1997/Borghans_BiophysChem1997.yaml
@@ -9,3 +9,5 @@ problems:
   - observables_Borghans_BiophysChem1997.tsv
   sbml_files:
   - model_Borghans_BiophysChem1997.xml
+  visualization_files:
+  - visualizationSpecification_Borghans_BiophysChem1997.tsv
diff --git a/Benchmark-Models/Borghans_BiophysChem1997/visualizationSpecification_Borghans_BiophysChem1997.tsv b/Benchmark-Models/Borghans_BiophysChem1997/visualizationSpecification_Borghans_BiophysChem1997.tsv
@@ -0,0 +1,2 @@
+plotId	plotTypeData	plotName	plotTypeSimulation	xLabel	xScale	yLabel	yScale	legendEntry	yValues	xValues	xOffset	yOffset
+plot1	MeanAndSD		LinePlot	time	lin	values	lin	model1_data1 - Ca	Ca	time	0	0.0
diff --git a/Benchmark-Models/Brannmark_JBC2010/Brannmark_JBC2010.yaml b/Benchmark-Models/Brannmark_JBC2010/Brannmark_JBC2010.yaml
@@ -9,3 +9,5 @@ problems:
   - observables_Brannmark_JBC2010.tsv
   sbml_files:
   - model_Brannmark_JBC2010.xml
+  visualization_files:
+  - visualizationSpecification_Brannmark_JBC2010.tsv
diff --git a/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv b/Benchmark-Models/Brannmark_JBC2010/visualizationSpecification_Brannmark_JBC2010.tsv
@@ -0,0 +1,5 @@
+plotId	plotTypeData	plotName	plotTypeSimulation	xLabel	xScale	yLabel	yScale	yValues	xValues	xOffset	yOffset
+plot1	MeanAndSD		ScatterPlot	simulation	lin	measurements	lin	IRS1_P_DosR	time	0	0
+plot4	MeanAndSD		LinePlot	time	lin	values	lin	IRS1_P_DosR	time	1	1
+plot2	MeanAndSD		LinePlot	time	lin	values	lin	IR1_P	time	0	0
+plot3	MeanAndSD		LinePlot	time	lin	values	lin	IRS1_P	time	0	0
diff --git a/Benchmark-Models/Crauste_CellSystems2017/Crauste_CellSystems2017.yaml b/Benchmark-Models/Crauste_CellSystems2017/Crauste_CellSystems2017.yaml
@@ -9,3 +9,5 @@ problems:
   - observables_Crauste_CellSystems2017.tsv
   sbml_files:
   - model_Crauste_CellSystems2017.xml
+  visualization_files:
+  - visualizationSpecification_Crauste_CellSystems2017.tsv
diff --git a/Benchmark-Models/Crauste_CellSystems2017/visualizationSpecification_Crauste_CellSystems2017.tsv b/Benchmark-Models/Crauste_CellSystems2017/visualizationSpecification_Crauste_CellSystems2017.tsv
@@ -0,0 +1,5 @@
+plotId	plotTypeData	plotName	plotTypeSimulation	xLabel	xScale	yLabel	yScale	legendEntry	yValues	xValues	xOffset	yOffset
+plot1	MeanAndSD		LinePlot	time	lin	values	lin	condition1 - observable_Naive	observable_Naive	time	0	0
+plot2	MeanAndSD		LinePlot	time	lin	values	lin	condition1 - observable_EarlyEffector	observable_EarlyEffector	time	0	0
+plot3	MeanAndSD		LinePlot	time	lin	values	lin	condition1 - observable_LateEffector	observable_LateEffector	time	0	0
+plot4	MeanAndSD		LinePlot	time	lin	values	lin	condition1 - observable_Memory	observable_Memory	time	0	0
diff --git a/Benchmark-Models/Elowitz_Nature2000/Elowitz_Nature2000.yaml b/Benchmark-Models/Elowitz_Nature2000/Elowitz_Nature2000.yaml
@@ -9,3 +9,5 @@ problems:
   - observables_Elowitz_Nature2000.tsv
   sbml_files:
   - model_Elowitz_Nature2000.xml
+  visualization_files:
+  - visualizationSpecification_Elowitz_Nature2000.tsv
diff --git a/Benchmark-Models/Elowitz_Nature2000/visualizationSpecification_Elowitz_Nature2000.tsv b/Benchmark-Models/Elowitz_Nature2000/visualizationSpecification_Elowitz_Nature2000.tsv
@@ -0,0 +1,2 @@
+plotId	plotTypeData	plotTypeSimulation	xLabel	xScale	yLabel	yScale	legendEntry	yValues	xValues	xOffset	yOffset
+plot1	MeanAndSD	LinePlot	time	lin	values	lin	model1_data1 - fluorescence	fluorescence	time	0	0
diff --git a/Benchmark-Models/Perelson_Science1996/Perelson_Science1996.yaml b/Benchmark-Models/Perelson_Science1996/Perelson_Science1996.yaml
@@ -9,3 +9,5 @@ problems:
   - observables_Perelson_Science1996.tsv
   sbml_files:
   - model_Perelson_Science1996.xml
+  visualization_files:
+  - visualizationSpecification_Perelson_Science1996.tsv
diff --git a/Benchmark-Models/Perelson_Science1996/visualizationSpecification_Perelson_Science1996.tsv b/Benchmark-Models/Perelson_Science1996/visualizationSpecification_Perelson_Science1996.tsv
@@ -0,0 +1,2 @@
+plotId	plotTypeData	plotTypeSimulation	xLabel	xScale	yLabel	yScale	legendEntry	yValues	xValues	xOffset	yOffset
+plot1	MeanAndSD	LinePlot	time	lin	values	lin	HIV-mRNA copies - task0_model0_perelson1_V	task0_model0_perelson1_V	time	0	0
diff --git a/Benchmark-Models/Weber_BMC2015/Weber_BMC2015.yaml b/Benchmark-Models/Weber_BMC2015/Weber_BMC2015.yaml
@@ -9,3 +9,5 @@ problems:
   - observables_Weber_BMC2015.tsv
   sbml_files:
   - model_Weber_BMC2015.xml
+  visualization_files:
+  - visualizationSpecification_Weber_BMC2015.tsv
diff --git a/Benchmark-Models/Weber_BMC2015/visualizationSpecification_Weber_BMC2015.tsv b/Benchmark-Models/Weber_BMC2015/visualizationSpecification_Weber_BMC2015.tsv
@@ -0,0 +1,9 @@
+plotId	plotTypeData	plotTypeSimulation	xLabel	xScale	yLabel	yScale	yValues	xValues	xOffset	yOffset
+plot1	MeanAndSD	LinePlot	time	lin	values	lin	yPKDpN0	time	0	0
+plot2	MeanAndSD	LinePlot	time	lin	values	lin	yPKDpN24	time	0	0
+plot3	MeanAndSD	LinePlot	time	lin	values	lin	yPKDpN25	time	0	0
+plot4	MeanAndSD	LinePlot	time	lin	values	lin	yPI4K3BpRN24	time	0	0
+plot5	MeanAndSD	LinePlot	time	lin	values	lin	yPI4K3Bt	time	0	0
+plot6	MeanAndSD	LinePlot	time	lin	values	lin	yCERTt	time	0	0
+plot7	MeanAndSD	LinePlot	time	lin	values	lin	yCERTpRN24	time	0	0
+plot8	MeanAndSD	LinePlot	time	lin	values	lin	yPKDt	time	0	0
diff --git a/Benchmark-Models/Zheng_PNAS2012/Zheng_PNAS2012.yaml b/Benchmark-Models/Zheng_PNAS2012/Zheng_PNAS2012.yaml
@@ -9,3 +9,5 @@ problems:
   - observables_Zheng_PNAS2012.tsv
   sbml_files:
   - model_Zheng_PNAS2012.xml
+  visualization_files:
+  - visualizationSpecification_Zheng_PNAS2012.tsv
diff --git a/Benchmark-Models/Zheng_PNAS2012/visualizationSpecification_Zheng_PNAS2012.tsv b/Benchmark-Models/Zheng_PNAS2012/visualizationSpecification_Zheng_PNAS2012.tsv
@@ -0,0 +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

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset`
	`2`	`+plot1 MeanAndSD LinePlot time lin values lin model1_data1 - Ca Ca time 0 0.0`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+plotId plotTypeData plotTypeSimulation xLabel xScale yLabel yScale legendEntry yValues xValues xOffset yOffset`
	`2`	`+plot1 MeanAndSD LinePlot time lin values lin model1_data1 - fluorescence fluorescence time 0 0`