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add the petab files for Liu_IFACPapersOnLine2025
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‎Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
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<model metaid="baseline_model" id="baseline_model">
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<listOfParameters>
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<parameter id="U" constant="false"/>
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<parameter id="rho" value="0.01" constant="true"/>
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<parameter id="I" value="0" constant="false"/>
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<parameter id="kappa" value="0.01" constant="true"/>
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<parameter id="psi" value="0.01" constant="true"/>
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<parameter id="V" constant="false"/>
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<parameter id="alpha" value="0.01" constant="true"/>
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<parameter id="beta" value="0.01" constant="true"/>
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<parameter id="delta" value="0.01" constant="true"/>
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<parameter id="u_2" constant="true"/>
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</listOfParameters>
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<listOfInitialAssignments>
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<initialAssignment symbol="U">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<divide/>
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<ci> kappa </ci>
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<apply>
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<plus/>
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<cn type="integer"> 1 </cn>
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<apply>
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<times/>
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<apply>
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<minus/>
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<apply>
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<divide/>
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<ci> kappa </ci>
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<cn type="integer"> 400 </cn>
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</apply>
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<cn type="integer"> 1 </cn>
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</apply>
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<apply>
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<exp/>
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<apply>
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<minus/>
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<ci> rho </ci>
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</apply>
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</apply>
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</apply>
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</apply>
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</apply>
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</math>
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</initialAssignment>
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<initialAssignment symbol="V">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> u_2 </ci>
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</math>
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</initialAssignment>
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<initialAssignment symbol="u_2">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<cn type="integer"> 1 </cn>
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<cn type="integer"> 1000000000 </cn>
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</apply>
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</math>
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</initialAssignment>
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</listOfInitialAssignments>
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<listOfRules>
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<rateRule variable="U">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> rho </ci>
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<ci> U </ci>
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<apply>
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<minus/>
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<cn type="integer"> 1 </cn>
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<apply>
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<divide/>
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<apply>
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<plus/>
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<ci> U </ci>
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<ci> I </ci>
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</apply>
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<ci> kappa </ci>
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</apply>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> psi </ci>
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<ci> V </ci>
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<ci> U </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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<rateRule variable="I">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<plus/>
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<apply>
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<times/>
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<ci> rho </ci>
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<ci> I </ci>
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<apply>
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<minus/>
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<cn type="integer"> 1 </cn>
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<apply>
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<divide/>
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<apply>
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<plus/>
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<ci> U </ci>
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<ci> I </ci>
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</apply>
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<ci> kappa </ci>
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</apply>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> psi </ci>
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<ci> V </ci>
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<ci> U </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> alpha </ci>
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<ci> I </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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<rateRule variable="V">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> alpha </ci>
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<ci> beta </ci>
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<ci> I </ci>
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</apply>
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<apply>
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<times/>
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<ci> psi </ci>
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<ci> V </ci>
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<ci> U </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> delta </ci>
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<ci> V </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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</listOfRules>
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<listOfEvents>
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<event id="_E0" useValuesFromTriggerTime="true">
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<trigger initialValue="true" persistent="true">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<lt/>
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<ci> U </ci>
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<cn type="e-notation"> 1 <sep/> -8 </cn>
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</apply>
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</math>
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</trigger>
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<listOfEventAssignments>
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<eventAssignment variable="U">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<cn type="integer"> 0 </cn>
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</math>
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</eventAssignment>
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</listOfEventAssignments>
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</event>
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</listOfEvents>
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</model>
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</sbml>

‎Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml‎

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format_version: 1
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parameter_file: parameters.tsv
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problems:
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- condition_files:
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- conditions.tsv
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measurement_files:
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- measurements_scaled.tsv
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observable_files:
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- observables.tsv
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sbml_files:
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- baseline_model.xml
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visualization_files:
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- visualizations.tsv

‎Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv‎

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conditionId conditionName u_2
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vvDD vvDD 1000000000.0
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ctrl ctrl 0.0

‎Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv‎

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

‎Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv‎

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observableId observableName observableFormula noiseFormula noiseDistribution observableTransformation
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tumor_num tumor_number U + I sqrt(sigma_a^2 + (sigma_b * (U + I))^2) normal lin

‎Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv‎

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parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType
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rho rho log10 0.42 1.66 1 1
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kappa kappa log10 100.0 100000.0 1 1
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psi psi log10 1e-10 0.01 1 1
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beta beta log10 1.0 10000.0 1 1
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alpha alpha log10 0.0001 1000.0 1 1
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delta delta log10 0.01 100.0 1 1
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sigma_a sigma_a log10 10.0 100000.0 1 1
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sigma_b sigma_b log10 0.0001 100.0 1 1

‎Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv‎

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plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel legendEntry
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plot1 MeanAndSD ScatterPlot condition Condition tumor_num Tumor Number Model

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