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add individual based age of infection model in the subfolder
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Benchmark-Models/Liu_IFACPapersOnLine2025/individual-based/conditions.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| conditionId conditionName u_2 xi_i_k | ||
| vvDD_1 vvDD_1 1000000000.0 xi_v_1 | ||
| vvDD_2 vvDD_2 1000000000.0 xi_v_2 | ||
| vvDD_3 vvDD_3 1000000000.0 xi_v_3 | ||
| vvDD_4 vvDD_4 1000000000.0 xi_v_4 | ||
| vvDD_5 vvDD_5 1000000000.0 xi_v_5 | ||
| vvDD_6 vvDD_6 1000000000.0 xi_v_6 | ||
| vvDD_7 vvDD_7 1000000000.0 xi_v_7 | ||
| vvDD_8 vvDD_8 1000000000.0 xi_v_8 | ||
| vvDD_9 vvDD_9 1000000000.0 xi_v_9 | ||
| vvDD_10 vvDD_10 1000000000.0 xi_v_10 | ||
| ctrl_1 ctrl_1 0.0 xi_c_1 | ||
| ctrl_2 ctrl_2 0.0 xi_c_2 | ||
| ctrl_3 ctrl_3 0.0 xi_c_3 | ||
| ctrl_4 ctrl_4 0.0 xi_c_4 | ||
| ctrl_5 ctrl_5 0.0 xi_c_5 | ||
| ctrl_6 ctrl_6 0.0 xi_c_6 | ||
| ctrl_7 ctrl_7 0.0 xi_c_7 | ||
| ctrl_8 ctrl_8 0.0 xi_c_8 | ||
| ctrl_9 ctrl_9 0.0 xi_c_9 | ||
| ctrl_10 ctrl_10 0.0 xi_c_10 |
369 changes: 369 additions & 0 deletions
369
...els/Liu_IFACPapersOnLine2025/individual-based/individual_based_age_of_infection_model.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,369 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2"> | ||
| <model metaid="individual_based_age_of_infection_model" id="individual_based_age_of_infection_model"> | ||
| <listOfParameters> | ||
| <parameter id="U" constant="false"/> | ||
| <parameter id="rho" value="0.01" constant="true"/> | ||
| <parameter id="I_1" value="0" constant="false"/> | ||
| <parameter id="I_2" value="0" constant="false"/> | ||
| <parameter id="I_3" value="0" constant="false"/> | ||
| <parameter id="I_4" value="0" constant="false"/> | ||
| <parameter id="I_5" 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="phi" value="0.01" constant="true"/> | ||
| <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="xi_i_k" value="1" 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> | ||
| <apply> | ||
| <times/> | ||
| <cn type="integer"> 400 </cn> | ||
| <ci> xi_i_k </ci> | ||
| </apply> | ||
| </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_1 </ci> | ||
| <ci> I_2 </ci> | ||
| <ci> I_3 </ci> | ||
| <ci> I_4 </ci> | ||
| <ci> I_5 </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_1"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <minus/> | ||
| <apply> | ||
| <plus/> | ||
| <apply> | ||
| <times/> | ||
| <ci> rho </ci> | ||
| <ci> I_1 </ci> | ||
| <apply> | ||
| <minus/> | ||
| <cn type="integer"> 1 </cn> | ||
| <apply> | ||
| <divide/> | ||
| <apply> | ||
| <plus/> | ||
| <ci> U </ci> | ||
| <ci> I_1 </ci> | ||
| <ci> I_2 </ci> | ||
| <ci> I_3 </ci> | ||
| <ci> I_4 </ci> | ||
| <ci> I_5 </ci> | ||
| </apply> | ||
| <ci> kappa </ci> | ||
| </apply> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> psi </ci> | ||
| <ci> V </ci> | ||
| <ci> U </ci> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_1 </ci> | ||
| </apply> | ||
| </apply> | ||
| </math> | ||
| </rateRule> | ||
| <rateRule variable="I_2"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <minus/> | ||
| <apply> | ||
| <plus/> | ||
| <apply> | ||
| <times/> | ||
| <ci> rho </ci> | ||
| <ci> I_2 </ci> | ||
| <apply> | ||
| <minus/> | ||
| <cn type="integer"> 1 </cn> | ||
| <apply> | ||
| <divide/> | ||
| <apply> | ||
| <plus/> | ||
| <ci> U </ci> | ||
| <ci> I_1 </ci> | ||
| <ci> I_2 </ci> | ||
| <ci> I_3 </ci> | ||
| <ci> I_4 </ci> | ||
| <ci> I_5 </ci> | ||
| </apply> | ||
| <ci> kappa </ci> | ||
| </apply> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_1 </ci> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_2 </ci> | ||
| </apply> | ||
| </apply> | ||
| </math> | ||
| </rateRule> | ||
| <rateRule variable="I_3"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <minus/> | ||
| <apply> | ||
| <plus/> | ||
| <apply> | ||
| <times/> | ||
| <ci> rho </ci> | ||
| <ci> I_3 </ci> | ||
| <apply> | ||
| <minus/> | ||
| <cn type="integer"> 1 </cn> | ||
| <apply> | ||
| <divide/> | ||
| <apply> | ||
| <plus/> | ||
| <ci> U </ci> | ||
| <ci> I_1 </ci> | ||
| <ci> I_2 </ci> | ||
| <ci> I_3 </ci> | ||
| <ci> I_4 </ci> | ||
| <ci> I_5 </ci> | ||
| </apply> | ||
| <ci> kappa </ci> | ||
| </apply> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_2 </ci> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_3 </ci> | ||
| </apply> | ||
| </apply> | ||
| </math> | ||
| </rateRule> | ||
| <rateRule variable="I_4"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <minus/> | ||
| <apply> | ||
| <plus/> | ||
| <apply> | ||
| <times/> | ||
| <ci> rho </ci> | ||
| <ci> I_4 </ci> | ||
| <apply> | ||
| <minus/> | ||
| <cn type="integer"> 1 </cn> | ||
| <apply> | ||
| <divide/> | ||
| <apply> | ||
| <plus/> | ||
| <ci> U </ci> | ||
| <ci> I_1 </ci> | ||
| <ci> I_2 </ci> | ||
| <ci> I_3 </ci> | ||
| <ci> I_4 </ci> | ||
| <ci> I_5 </ci> | ||
| </apply> | ||
| <ci> kappa </ci> | ||
| </apply> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_3 </ci> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_4 </ci> | ||
| </apply> | ||
| </apply> | ||
| </math> | ||
| </rateRule> | ||
| <rateRule variable="I_5"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <minus/> | ||
| <apply> | ||
| <plus/> | ||
| <apply> | ||
| <times/> | ||
| <ci> rho </ci> | ||
| <ci> I_5 </ci> | ||
| <apply> | ||
| <minus/> | ||
| <cn type="integer"> 1 </cn> | ||
| <apply> | ||
| <divide/> | ||
| <apply> | ||
| <plus/> | ||
| <ci> U </ci> | ||
| <ci> I_1 </ci> | ||
| <ci> I_2 </ci> | ||
| <ci> I_3 </ci> | ||
| <ci> I_4 </ci> | ||
| <ci> I_5 </ci> | ||
| </apply> | ||
| <ci> kappa </ci> | ||
| </apply> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> phi </ci> | ||
| <ci> I_4 </ci> | ||
| </apply> | ||
| </apply> | ||
| <apply> | ||
| <times/> | ||
| <ci> alpha </ci> | ||
| <ci> I_5 </ci> | ||
| </apply> | ||
| </apply> | ||
| </math> | ||
| </rateRule> | ||
| <rateRule variable="V"> | ||
| <math xmlns="http://www.w3.org/1998/Math/MathML"> | ||
| <apply> | ||
| <minus/> | ||
| <apply> | ||
| <minus/> | ||
| <apply> | ||
| <times/> | ||
| <ci> beta </ci> | ||
| <ci> alpha </ci> | ||
| <ci> I_5 </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> |
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