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Bertozzi_PNAS2020: update to match Table 1 of paper (#222)
* refactor into paper parameters; change infection reaction to avoid copasi warning * add optimized parameters to parameters table * checklist; use `petab.v1` * delete notes; info is outdated or in #99 * change tests to python 3.11
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‎.github/workflows/tests.yml‎

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runs-on: ubuntu-latest
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python-version: [3.9]
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python-version: [3.11]
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steps:
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- name: Check out repository

‎Benchmark-Models/Bertozzi_PNAS2020/Bertozzi_PNAS2020.yaml‎

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‎Benchmark-Models/Bertozzi_PNAS2020/Bertozzi_PNAS2020_notes_on_model.txt‎

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‎Benchmark-Models/Bertozzi_PNAS2020/conditions.tsv‎

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conditionId N_ I0_ R0_ gamma_
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u_CA 39560000 I0_CA R0_CA gamma_CA
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u_NY 19540000 I0_NY R0_NY gamma_NY

‎Benchmark-Models/Bertozzi_PNAS2020/experimentalCondition_Bertozzi_PNAS2020.tsv‎

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‎Benchmark-Models/Bertozzi_PNAS2020/measurementData_Bertozzi_PNAS2020.tsv‎

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‎Benchmark-Models/Bertozzi_PNAS2020/measurements.tsv‎

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observableId simulationConditionId measurement time datasetId realDate
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y_I_CA u_CA 225 0 data_CA 2020-03-20
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y_I_CA u_CA 187 1 data_CA 2020-03-21
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y_I_CA u_CA 282 2 data_CA 2020-03-22
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y_I_CA u_CA 462 3 data_CA 2020-03-23
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y_I_CA u_CA 430 4 data_CA 2020-03-24
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y_I_CA u_CA 460 5 data_CA 2020-03-25
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y_I_CA u_CA 901 6 data_CA 2020-03-26
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y_I_CA u_CA 758 7 data_CA 2020-03-27
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y_I_CA u_CA 437 8 data_CA 2020-03-28
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y_I_CA u_CA 757 9 data_CA 2020-03-29
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y_I_CA u_CA 1286 10 data_CA 2020-03-30
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y_I_NY u_NY 2945 0 data_NY 2020-03-20
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y_I_NY u_NY 3400 1 data_NY 2020-03-21
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y_I_NY u_NY 4090 2 data_NY 2020-03-22
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y_I_NY u_NY 5084 3 data_NY 2020-03-23
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y_I_NY u_NY 4797 4 data_NY 2020-03-24
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y_I_NY u_NY 5160 5 data_NY 2020-03-25
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y_I_NY u_NY 7036 6 data_NY 2020-03-26
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y_I_NY u_NY 6999 7 data_NY 2020-03-27
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y_I_NY u_NY 7534 8 data_NY 2020-03-28
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y_I_NY u_NY 7237 9 data_NY 2020-03-29
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y_I_NY u_NY 7015 10 data_NY 2020-03-30

‎Benchmark-Models/Bertozzi_PNAS2020/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 id="Bertozzi_PNAS2020" name="Bertozzi_PNAS2020">
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
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<rdf:Description rdf:about="#benchmark_models_petab">
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<bqbiol:isDescribedBy>
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<rdf:Bag>
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<rdf:li rdf:resource="http://identifiers.org/doi/10.1073/pnas.2006520117"/>
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</rdf:Bag>
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</bqbiol:isDescribedBy>
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</rdf:Description>
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</rdf:RDF>
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</annotation>
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<listOfCompartments>
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<compartment id="compartment" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species id="I_" compartment="compartment" initialConcentration="0.1" boundaryCondition="false" constant="false" hasOnlySubstanceUnits="true"/>
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<species id="R_" compartment="compartment" initialConcentration="0" boundaryCondition="false" constant="false" hasOnlySubstanceUnits="true"/>
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<species id="S_" compartment="compartment" initialConcentration="0.9" boundaryCondition="false" constant="false" hasOnlySubstanceUnits="true"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="N_" value="1" constant="true"/>
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<parameter id="beta_N" value="0" constant="true"/>
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<parameter id="gamma_" value="0.1" constant="true"/>
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<parameter id="I0_" value="0.1" constant="true"/>
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<parameter id="R0_" value="0.1" constant="true"/>
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</listOfParameters>
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<listOfInitialAssignments>
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<initialAssignment symbol="I_">
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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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<ci> I0_ </ci>
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</apply>
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</math>
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</initialAssignment>
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<initialAssignment symbol="S_">
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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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<ci> N_ </ci>
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<ci> I0_ </ci>
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</apply>
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</math>
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</initialAssignment>
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<initialAssignment symbol="beta_N">
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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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<apply>
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<times/>
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<ci> R0_ </ci>
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<ci> gamma_ </ci>
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</apply>
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<ci> N_ </ci>
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</apply>
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</math>
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</initialAssignment>
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</listOfInitialAssignments>
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<listOfReactions>
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<reaction id="infection" reversible="false">
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<listOfReactants>
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<speciesReference species="S_" stoichiometry="1" constant="true"/>
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<speciesReference species="I_" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="I_" stoichiometry="2" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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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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<ci> beta_N </ci>
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<ci> I_ </ci>
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<ci> S_ </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction id="recovery" reversible="false">
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<listOfReactants>
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<speciesReference species="I_" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="R_" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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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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<ci> gamma_ </ci>
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<ci> I_ </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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</listOfReactions>
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</model>
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</sbml>

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