rename files, add visualization spec

Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.yaml → Benchmark-Models/Liu_IFACPapersOnLine2025/Liu_IFAC-PapersOnLine2025.yaml

@@ -4,10 +4,10 @@ problems:
   - condition_files:
     - conditions.tsv
     measurement_files:
-    - measurements_scaled.tsv
+    - measurements.tsv
     observable_files:
     - observables.tsv
     sbml_files:
-    - age_of_infection_model.xml
+    - model.xml
     visualization_files:
-    - visualizations.tsv
+    - visualization.tsv

Benchmark-Models/Liu_IFACPapersOnLine2025/measurements.tsv

@@ -0,0 +1,101 @@
+observableId	simulationConditionId	measurement	time	datasetId
+tumor_num	vvDD	451.73401707247393	0	virus
+tumor_num	vvDD	477.41006706423315	0	virus
+tumor_num	vvDD	509.5051295539299	0	virus
+tumor_num	vvDD	554.4382170395085	0	virus
+tumor_num	vvDD	852.9222981937005	0	virus
+tumor_num	vvDD	1016.607116891161	0	virus
+tumor_num	vvDD	1058.3306981277697	0	virus
+tumor_num	vvDD	1084.006748119529	0	virus
+tumor_num	vvDD	1241.2725543190497	0	virus
+tumor_num	vvDD	1263.7390980618388	0	virus
+tumor_num	vvDD	679.6089607493324	1	virus
+tumor_num	vvDD	817.6177294550338	1	virus
+tumor_num	vvDD	535.1811795456891	1	virus
+tumor_num	vvDD	824.0367419529714	1	virus
+tumor_num	vvDD	1055.1211918788	1	virus
+tumor_num	vvDD	926.740941920006	1	virus
+tumor_num	vvDD	1571.8516979629405	1	virus
+tumor_num	vvDD	1331.1387292902025	1	virus
+tumor_num	vvDD	1481.9855229917855	1	virus
+tumor_num	vvDD	968.4645231566146	1	virus
+tumor_num	vvDD	406.80092958689744	2	virus
+tumor_num	vvDD	483.82907956217286	2	virus
+tumor_num	vvDD	294.4682108729532	2	virus
+tumor_num	vvDD	885.0173606833995	2	virus
+tumor_num	vvDD	291.25870462398325	2	virus
+tumor_num	vvDD	814.4082232060639	2	virus
+tumor_num	vvDD	958.836004409705	2	virus
+tumor_num	vvDD	1119.3113168581956	2	virus
+tumor_num	vvDD	1132.1493418540751	2	virus
+tumor_num	vvDD	1000.5595856463136	2	virus
+tumor_num	vvDD	355.4488296033791	3	virus
+tumor_num	vvDD	349.0298171054393	3	virus
+tumor_num	vvDD	220.64956714664766	3	virus
+tumor_num	vvDD	194.97351715488847	3	virus
+tumor_num	vvDD	252.74462963634662	3	virus
+tumor_num	vvDD	422.84846083174693	3	virus
+tumor_num	vvDD	772.6846419694551	3	virus
+tumor_num	vvDD	464.5720420683534	3	virus
+tumor_num	vvDD	785.5226669653348	3	virus
+tumor_num	vvDD	339.40129835853173	3	virus
+tumor_num	vvDD	50.545735951247316	4	virus
+tumor_num	vvDD	101.89783593476568	4	virus
+tumor_num	vvDD	76.2217859430065	4	virus
+tumor_num	vvDD	53.75524220021722	4	virus
+tumor_num	vvDD	191.76401090591855	4	virus
+tumor_num	vvDD	262.3731483832563	4	virus
+tumor_num	vvDD	589.7427857781752	4	virus
+tumor_num	vvDD	345.8203108564694	4	virus
+tumor_num	vvDD	631.4663670147839	4	virus
+tumor_num	vvDD	374.7058670971985	4	virus
+tumor_num	ctrl	349.1039275702164	0	control
+tumor_num	ctrl	370.50979635893606	0	control
+tumor_num	ctrl	407.93829872021803	0	control
+tumor_num	ctrl	552.3499369974998	0	control
+tumor_num	ctrl	632.5786249293225	0	control
+tumor_num	ctrl	657.550182543784	0	control
+tumor_num	ctrl	945.4762838668787	0	control
+tumor_num	ctrl	985.5848518293386	0	control
+tumor_num	ctrl	1244.9967188123485	0	control
+tumor_num	ctrl	1343.9454339282627	0	control
+tumor_num	ctrl	508.3483427091911	1	control
+tumor_num	ctrl	323.8108084590962	1	control
+tumor_num	ctrl	516.3654354989194	1	control
+tumor_num	ctrl	917.5146511614834	1	control
+tumor_num	ctrl	965.6460879171242	1	control
+tumor_num	ctrl	830.874501593137	1	control
+tumor_num	ctrl	1345.400986797869	1	control
+tumor_num	ctrl	1404.2411339513233	1	control
+tumor_num	ctrl	1086.00067182176	1	control
+tumor_num	ctrl	1372.138106771691	1	control
+tumor_num	ctrl	648.8611786571674	2	control
+tumor_num	ctrl	343.986388512792	2	control
+tumor_num	ctrl	480.36360598998806	2	control
+tumor_num	ctrl	1250.5821141492872	2	control
+tumor_num	ctrl	1140.9304646390121	2	control
+tumor_num	ctrl	771.4696645965797	2	control
+tumor_num	ctrl	1400.3481076254745	2	control
+tumor_num	ctrl	1357.553698058382	2	control
+tumor_num	ctrl	1400.3423316220221	2	control
+tumor_num	ctrl	1592.8854066549445	2	control
+tumor_num	ctrl	612.8651251516885	3	control
+tumor_num	ctrl	441.73369491093814	3	control
+tumor_num	ctrl	449.7392356937657	3	control
+tumor_num	ctrl	1091.5802911552485	3	control
+tumor_num	ctrl	1265.4091150075299	3	control
+tumor_num	ctrl	959.3493729329441	3	control
+tumor_num	ctrl	1669.2210682609186	3	control
+tumor_num	ctrl	1441.9064524540886	3	control
+tumor_num	ctrl	1262.7232734028994	3	control
+tumor_num	ctrl	1749.461308199642	3	control
+tumor_num	ctrl	705.2811803647304	4	control
+tumor_num	ctrl	416.469455817074	4	control
+tumor_num	ctrl	496.70391975234486	4	control
+tumor_num	ctrl	1499.550966893223	4	control
+tumor_num	ctrl	1357.8136182136711	4	control
+tumor_num	ctrl	1026.0423760760882	4	control
+tumor_num	ctrl	1531.6539940728533	4	control
+tumor_num	ctrl	1700.1226867227788	4	control
+tumor_num	ctrl	1470.1280053147707	4	control
+tumor_num	ctrl	1876.6258001727879	4	control

Benchmark-Models/Liu_IFACPapersOnLine2025/age_of_infection_model.xml → Benchmark-Models/Liu_IFACPapersOnLine2025/model.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model metaid="age_of_infection_model" id="age_of_infection_model">
+  <model metaid="Liu_IFACPapersOnLine2025" id="Liu_IFACPapersOnLine2025">
     <listOfParameters>
       <parameter id="U" constant="false"/>
       <parameter id="rho" value="0.01" constant="true"/>

Benchmark-Models/Liu_IFACPapersOnLine2025/visualization.tsv

@@ -0,0 +1,3 @@
+plotId	plotTypeData	plotTypeSimulation	xValues	xLabel	yValues	yLabel	datasetId	legendEntry
+plot1	MeanAndSD	ScatterPlot	time	Time [Days]	tumor_num	Tumor [#]	control	Control
+plot1	MeanAndSD	ScatterPlot	time	Time [Days]	tumor_num	Tumor [#]	virus	OncVirus