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Add amici spline application example
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‎doc/example.rst‎

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example/conversion_reaction.ipynb
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example/synthetic_data.ipynb
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example/example_amici_splines_swameye/example_amici_splines_Swameye2003.ipynb

‎doc/example/example_amici_splines_swameye/Swameye_PNAS2003/swameye2003_conditions.tsv‎

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conditionId conditionName
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condition1

‎doc/example/example_amici_splines_swameye/Swameye_PNAS2003/swameye2003_measurements.tsv‎

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observableId simulationConditionId measurement time noiseParameters observableTransformation
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tSTAT5_au condition1 1.0000 0 0.084 lin
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tSTAT5_au condition1 0.9275 2 0.046 lin
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tSTAT5_au condition1 0.7923 4 0.038 lin
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tSTAT5_au condition1 0.7778 6 0.032 lin
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tSTAT5_au condition1 0.7053 8 0.033 lin
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tSTAT5_au condition1 0.6522 10 0.037 lin
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tSTAT5_au condition1 0.5894 12 0.039 lin
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tSTAT5_au condition1 0.5894 14 0.040 lin
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tSTAT5_au condition1 0.6377 16 0.030 lin
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tSTAT5_au condition1 0.6425 18 0.028 lin
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tSTAT5_au condition1 0.6908 20 0.030 lin
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tSTAT5_au condition1 0.6908 25 0.031 lin
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tSTAT5_au condition1 0.7585 30 0.032 lin
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tSTAT5_au condition1 0.8068 40 0.040 lin
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tSTAT5_au condition1 0.9275 50 0.046 lin
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tSTAT5_au condition1 0.9710 60 0.082 lin
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pSTAT5_au condition1 0.3315 2 0.050 lin
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pSTAT5_au condition1 0.8645 4 0.066 lin
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pSTAT5_au condition1 0.9635 6 0.070 lin
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pSTAT5_au condition1 0.9279 8 0.065 lin
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pSTAT5_au condition1 0.8162 10 0.051 lin
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pSTAT5_au condition1 0.7553 12 0.053 lin
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pSTAT5_au condition1 0.7680 14 0.051 lin
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pSTAT5_au condition1 0.8416 16 0.040 lin
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pSTAT5_au condition1 0.7680 18 0.040 lin
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pSTAT5_au condition1 0.8010 20 0.048 lin
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pSTAT5_au condition1 0.7832 25 0.052 lin
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pSTAT5_au condition1 0.8086 30 0.054 lin
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pSTAT5_au condition1 0.4888 40 0.055 lin
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pSTAT5_au condition1 0.2782 50 0.044 lin
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pSTAT5_au condition1 0.2553 60 0.071 lin
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pEpoR_au condition1 0.01713 0 lin
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pEpoR_au condition1 0.145 2 lin
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pEpoR_au condition1 0.2442 4 lin
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pEpoR_au condition1 0.7659 6 lin
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pEpoR_au condition1 1 8 lin
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pEpoR_au condition1 0.8605 10 lin
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pEpoR_au condition1 0.7829 12 lin
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pEpoR_au condition1 0.5705 14 lin
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pEpoR_au condition1 0.6217 16 lin
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pEpoR_au condition1 0.331 18 lin
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pEpoR_au condition1 0.3388 20 lin
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pEpoR_au condition1 0.3116 25 lin
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pEpoR_au condition1 0.05062 30 lin
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pEpoR_au condition1 0.02504 40 lin
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pEpoR_au condition1 0.01163 50 lin

‎doc/example/example_amici_splines_swameye/Swameye_PNAS2003/swameye2003_model.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
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<model id="swameye2003">
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<listOfUnitDefinitions>
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<unitDefinition id="time" name="time">
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<listOfUnits>
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<unit kind="second" exponent="1" scale="0" multiplier="60"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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<listOfCompartments>
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<compartment id="cyt" spatialDimensions="3" size="1.4" constant="true"/>
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<compartment id="nuc" spatialDimensions="3" size="0.45" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species id="pEpoR" compartment="cyt" initialConcentration="0.0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="STAT5" compartment="cyt" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="pSTAT5" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="pSTAT5_pSTAT5" compartment="cyt" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="npSTAT5_npSTAT5" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_1" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_2" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_3" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_4" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_5" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_6" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_7" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_8" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="nSTAT5_9" compartment="nuc" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="k1" value="1.95" constant="true"/>
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<parameter id="k2" value="0.11" constant="true"/>
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<parameter id="k3" value="98400" constant="true"/>
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<parameter id="k4" value="1.49" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction id="reaction1" reversible="false">
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<listOfReactants>
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<speciesReference species="STAT5" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="pSTAT5" stoichiometry="1"/>
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</listOfProducts>
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<listOfModifiers>
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<modifierSpeciesReference species="pEpoR"/>
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</listOfModifiers>
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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> cyt </ci>
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<ci> k1 </ci>
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<ci> STAT5 </ci>
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<ci> pEpoR </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="reaction2" reversible="false">
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<listOfReactants>
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<speciesReference species="pSTAT5" stoichiometry="2"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="pSTAT5_pSTAT5" stoichiometry="1"/>
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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> cyt </ci>
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<ci> k2 </ci>
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<apply>
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<power/>
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<ci> pSTAT5 </ci>
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<cn type="integer"> 2 </cn>
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</apply>
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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="reaction3" reversible="false">
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<listOfReactants>
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<speciesReference species="pSTAT5_pSTAT5" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="npSTAT5_npSTAT5" stoichiometry="1"/>
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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> cyt </ci>
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<ci> k3 </ci>
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<ci> pSTAT5_pSTAT5 </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="reaction4_01" reversible="false">
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<listOfReactants>
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<speciesReference species="npSTAT5_npSTAT5" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_1" stoichiometry="2"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> npSTAT5_npSTAT5 </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="reaction4_02" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_1" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_2" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_1 </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="reaction4_03" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_2" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_3" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_2 </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="reaction4_04" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_3" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_4" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_3 </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="reaction4_05" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_4" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_5" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_4 </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="reaction4_06" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_5" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_6" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_5 </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="reaction4_07" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_6" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_7" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_6 </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="reaction4_08" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_7" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_8" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_7 </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="reaction4_09" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_8" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="nSTAT5_9" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_8 </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="reaction4_10" reversible="false">
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<listOfReactants>
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<speciesReference species="nSTAT5_9" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="STAT5" stoichiometry="1"/>
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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> nuc </ci>
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<ci> k4 </ci>
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<ci> nSTAT5_9 </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>

‎doc/example/example_amici_splines_swameye/Swameye_PNAS2003/swameye2003_observables.tsv‎

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observableId observableFormula observableTransformation noiseFormula noiseDistribution
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tSTAT5_au scale_tSTAT5 * (STAT5 + pSTAT5 + 2 * pSTAT5_pSTAT5) lin noiseParameter1_tSTAT5_au normal
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pSTAT5_au scale_pSTAT5 * (pSTAT5 + 2 * pSTAT5_pSTAT5) lin noiseParameter1_pSTAT5_au normal
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pEpoR_au pEpoR lin sigma_pEpoR_abs + sigma_pEpoR_rel * pEpoR normal

‎doc/example/example_amici_splines_swameye/Swameye_PNAS2003/swameye2003_parameters.tsv‎

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parameterId parameterScale lowerBound upperBound nominalValue estimate
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k1 log10 0.001 100000 1.95 1
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k2 log10 0.001 100000 0.11 1
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k3 log10 0.001 1000000 98400 1
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k4 log10 0.001 100000 1.49 1
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scale_tSTAT5 log10 0.01 100 0.95 1
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scale_pSTAT5 log10 0.01 100 1.25 1
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sigma_pEpoR_abs log10 0.001 1 0.0274 0
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sigma_pEpoR_rel log10 0.001 1 0.10 0

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