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add the petab files for Liu_IFACPapersOnLine2025
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@EchoRLiu
EchoRLiu committed Dec 4, 2024
1 parent 429dd0f commit 5b900e0
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183 changes: 183 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.xml
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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="baseline_model" id="baseline_model">
<listOfParameters>
<parameter id="U" constant="false"/>
<parameter id="rho" value="0.01" constant="true"/>
<parameter id="I" value="0" constant="false"/>
<parameter id="kappa" value="0.01" constant="true"/>
<parameter id="psi" value="0.01" constant="true"/>
<parameter id="V" constant="false"/>
<parameter id="alpha" value="0.01" constant="true"/>
<parameter id="beta" value="0.01" constant="true"/>
<parameter id="delta" value="0.01" constant="true"/>
<parameter id="u_2" constant="true"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="U">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> kappa </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<apply>
<minus/>
<apply>
<divide/>
<ci> kappa </ci>
<cn type="integer"> 400 </cn>
</apply>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<exp/>
<apply>
<minus/>
<ci> rho </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
</math>
</initialAssignment>
<initialAssignment symbol="V">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> u_2 </ci>
</math>
</initialAssignment>
<initialAssignment symbol="u_2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> 1 </cn>
<cn type="integer"> 1000000000 </cn>
</apply>
</math>
</initialAssignment>
</listOfInitialAssignments>
<listOfRules>
<rateRule variable="U">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> rho </ci>
<ci> U </ci>
<apply>
<minus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<apply>
<plus/>
<ci> U </ci>
<ci> I </ci>
</apply>
<ci> kappa </ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> psi </ci>
<ci> V </ci>
<ci> U </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="I">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> rho </ci>
<ci> I </ci>
<apply>
<minus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<apply>
<plus/>
<ci> U </ci>
<ci> I </ci>
</apply>
<ci> kappa </ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> psi </ci>
<ci> V </ci>
<ci> U </ci>
</apply>
</apply>
<apply>
<times/>
<ci> alpha </ci>
<ci> I </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="V">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<minus/>
<apply>
<times/>
<ci> alpha </ci>
<ci> beta </ci>
<ci> I </ci>
</apply>
<apply>
<times/>
<ci> psi </ci>
<ci> V </ci>
<ci> U </ci>
</apply>
</apply>
<apply>
<times/>
<ci> delta </ci>
<ci> V </ci>
</apply>
</apply>
</math>
</rateRule>
</listOfRules>
<listOfEvents>
<event id="_E0" useValuesFromTriggerTime="true">
<trigger initialValue="true" persistent="true">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<lt/>
<ci> U </ci>
<cn type="e-notation"> 1 <sep/> -8 </cn>
</apply>
</math>
</trigger>
<listOfEventAssignments>
<eventAssignment variable="U">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn type="integer"> 0 </cn>
</math>
</eventAssignment>
</listOfEventAssignments>
</event>
</listOfEvents>
</model>
</sbml>
13 changes: 13 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/baseline_model.yaml
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format_version: 1
parameter_file: parameters.tsv
problems:
- condition_files:
- conditions.tsv
measurement_files:
- measurements_scaled.tsv
observable_files:
- observables.tsv
sbml_files:
- baseline_model.xml
visualization_files:
- visualizations.tsv
3 changes: 3 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/conditions.tsv
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conditionId conditionName u_2
vvDD vvDD 1000000000.0
ctrl ctrl 0.0
101 changes: 101 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/measurements_scaled.tsv
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observableId simulationConditionId measurement time
tumor_num vvDD 451.73401707247393 0
tumor_num vvDD 477.41006706423315 0
tumor_num vvDD 509.5051295539299 0
tumor_num vvDD 554.4382170395085 0
tumor_num vvDD 852.9222981937005 0
tumor_num vvDD 1016.607116891161 0
tumor_num vvDD 1058.3306981277697 0
tumor_num vvDD 1084.006748119529 0
tumor_num vvDD 1241.2725543190497 0
tumor_num vvDD 1263.7390980618388 0
tumor_num vvDD 679.6089607493324 1
tumor_num vvDD 817.6177294550338 1
tumor_num vvDD 535.1811795456891 1
tumor_num vvDD 824.0367419529714 1
tumor_num vvDD 1055.1211918788 1
tumor_num vvDD 926.740941920006 1
tumor_num vvDD 1571.8516979629405 1
tumor_num vvDD 1331.1387292902025 1
tumor_num vvDD 1481.9855229917855 1
tumor_num vvDD 968.4645231566146 1
tumor_num vvDD 406.80092958689744 2
tumor_num vvDD 483.82907956217286 2
tumor_num vvDD 294.4682108729532 2
tumor_num vvDD 885.0173606833995 2
tumor_num vvDD 291.25870462398325 2
tumor_num vvDD 814.4082232060639 2
tumor_num vvDD 958.836004409705 2
tumor_num vvDD 1119.3113168581956 2
tumor_num vvDD 1132.1493418540751 2
tumor_num vvDD 1000.5595856463136 2
tumor_num vvDD 355.4488296033791 3
tumor_num vvDD 349.0298171054393 3
tumor_num vvDD 220.64956714664766 3
tumor_num vvDD 194.97351715488847 3
tumor_num vvDD 252.74462963634662 3
tumor_num vvDD 422.84846083174693 3
tumor_num vvDD 772.6846419694551 3
tumor_num vvDD 464.5720420683534 3
tumor_num vvDD 785.5226669653348 3
tumor_num vvDD 339.40129835853173 3
tumor_num vvDD 50.545735951247316 4
tumor_num vvDD 101.89783593476568 4
tumor_num vvDD 76.2217859430065 4
tumor_num vvDD 53.75524220021722 4
tumor_num vvDD 191.76401090591855 4
tumor_num vvDD 262.3731483832563 4
tumor_num vvDD 589.7427857781752 4
tumor_num vvDD 345.8203108564694 4
tumor_num vvDD 631.4663670147839 4
tumor_num vvDD 374.7058670971985 4
tumor_num ctrl 349.1039275702164 0
tumor_num ctrl 370.50979635893606 0
tumor_num ctrl 407.93829872021803 0
tumor_num ctrl 552.3499369974998 0
tumor_num ctrl 632.5786249293225 0
tumor_num ctrl 657.550182543784 0
tumor_num ctrl 945.4762838668787 0
tumor_num ctrl 985.5848518293386 0
tumor_num ctrl 1244.9967188123485 0
tumor_num ctrl 1343.9454339282627 0
tumor_num ctrl 508.3483427091911 1
tumor_num ctrl 323.8108084590962 1
tumor_num ctrl 516.3654354989194 1
tumor_num ctrl 917.5146511614834 1
tumor_num ctrl 965.6460879171242 1
tumor_num ctrl 830.874501593137 1
tumor_num ctrl 1345.400986797869 1
tumor_num ctrl 1404.2411339513233 1
tumor_num ctrl 1086.00067182176 1
tumor_num ctrl 1372.138106771691 1
tumor_num ctrl 648.8611786571674 2
tumor_num ctrl 343.986388512792 2
tumor_num ctrl 480.36360598998806 2
tumor_num ctrl 1250.5821141492872 2
tumor_num ctrl 1140.9304646390121 2
tumor_num ctrl 771.4696645965797 2
tumor_num ctrl 1400.3481076254745 2
tumor_num ctrl 1357.553698058382 2
tumor_num ctrl 1400.3423316220221 2
tumor_num ctrl 1592.8854066549445 2
tumor_num ctrl 612.8651251516885 3
tumor_num ctrl 441.73369491093814 3
tumor_num ctrl 449.7392356937657 3
tumor_num ctrl 1091.5802911552485 3
tumor_num ctrl 1265.4091150075299 3
tumor_num ctrl 959.3493729329441 3
tumor_num ctrl 1669.2210682609186 3
tumor_num ctrl 1441.9064524540886 3
tumor_num ctrl 1262.7232734028994 3
tumor_num ctrl 1749.461308199642 3
tumor_num ctrl 705.2811803647304 4
tumor_num ctrl 416.469455817074 4
tumor_num ctrl 496.70391975234486 4
tumor_num ctrl 1499.550966893223 4
tumor_num ctrl 1357.8136182136711 4
tumor_num ctrl 1026.0423760760882 4
tumor_num ctrl 1531.6539940728533 4
tumor_num ctrl 1700.1226867227788 4
tumor_num ctrl 1470.1280053147707 4
tumor_num ctrl 1876.6258001727879 4
2 changes: 2 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/observables.tsv
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observableId observableName observableFormula noiseFormula noiseDistribution observableTransformation
tumor_num tumor_number U + I sqrt(sigma_a^2 + (sigma_b * (U + I))^2) normal lin
9 changes: 9 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/parameters.tsv
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parameterId parameterName parameterScale lowerBound upperBound nominalValue estimate parameterType
rho rho log10 0.42 1.66 1 1
kappa kappa log10 100.0 100000.0 1 1
psi psi log10 1e-10 0.01 1 1
beta beta log10 1.0 10000.0 1 1
alpha alpha log10 0.0001 1000.0 1 1
delta delta log10 0.01 100.0 1 1
sigma_a sigma_a log10 10.0 100000.0 1 1
sigma_b sigma_b log10 0.0001 100.0 1 1
2 changes: 2 additions & 0 deletions Benchmark-Models/Liu_IFACPapersOnLine2025/visualizations.tsv
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plotId plotTypeData plotTypeSimulation xValues xLabel yValues yLabel legendEntry
plot1 MeanAndSD ScatterPlot condition Condition tumor_num Tumor Number Model

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