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Add test case with estimated initial conditions specified via the conditions table
Closes #62
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‎petabtests/cases/v1.0.0/sbml/0011/0011.py

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This case tests initial concentrations in the condition table.
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For species `B`, the initial concentration is specified in the condition
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table, while for `A` it is given via an assignment rule in the SBML model.
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table, while for `A` it is given via an initial assignment in the SBML model.
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## Model
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‎petabtests/cases/v1.0.0/sbml/0011/README.md

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This case tests initial concentrations in the condition table.
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For species `B`, the initial concentration is specified in the condition
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table, while for `A` it is given via an assignment rule in the SBML model.
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table, while for `A` it is given via an initial assignment in the SBML model.
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## Model
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‎petabtests/cases/v1.0.0/sbml/0019/0019.py

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from inspect import cleandoc
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import pandas as pd
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from petab.C import *
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from petabtests import PetabTestCase, analytical_a
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DESCRIPTION = cleandoc("""
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## Objective
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This case tests handling of initial concentrations that are specified
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in the conditions table. For species `A`, the initial concentration is
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estimated for species `B` the initial concentration is specified in the
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parameters table.
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## Model
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A simple conversion reaction `A <=> B` in a single compartment, following
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mass action kinetics.
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""")
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# problem --------------------------------------------------------------------
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condition_df = pd.DataFrame(data={
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CONDITION_ID: ['c0'],
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'A': ["initial_A"],
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'B': ["initial_B"],
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}).set_index([CONDITION_ID])
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measurement_df = pd.DataFrame(data={
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OBSERVABLE_ID: ['obs_a', 'obs_a'],
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SIMULATION_CONDITION_ID: ['c0', 'c0'],
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TIME: [0, 10],
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MEASUREMENT: [0.7, 0.1]
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})
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observable_df = pd.DataFrame(data={
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OBSERVABLE_ID: ['obs_a'],
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OBSERVABLE_FORMULA: ['A'],
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NOISE_FORMULA: [0.5]
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}).set_index([OBSERVABLE_ID])
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parameter_df = pd.DataFrame(data={
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PARAMETER_ID: ['k1', 'k2', 'initial_A', 'initial_B'],
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PARAMETER_SCALE: [LIN, LIN, LOG10, LIN],
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LOWER_BOUND: [0] * 4,
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UPPER_BOUND: [10] * 4,
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NOMINAL_VALUE: [0.8, 0.6, 1, 2],
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ESTIMATE: [1] * 3 + [0],
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}).set_index(PARAMETER_ID)
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# solutions ------------------------------------------------------------------
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simulation_df = measurement_df.copy(deep=True).rename(
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columns={MEASUREMENT: SIMULATION})
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simulation_df[SIMULATION] = [analytical_a(t, 1, 2, 0.8, 0.6)
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for t in simulation_df[TIME]]
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case = PetabTestCase(
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id=19,
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brief="Simulation. InitialAssignment to species overridden.",
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description=DESCRIPTION,
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model='conversion_modified.xml',
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condition_dfs=[condition_df],
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observable_dfs=[observable_df],
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measurement_dfs=[measurement_df],
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simulation_dfs=[simulation_df],
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parameter_df=parameter_df,
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)

‎petabtests/cases/v1.0.0/sbml/0019/README.md

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# PEtab test case 0019
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## Objective
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This case tests handling of initial concentrations that are specified
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in the conditions table. For species `A`, the initial concentration is
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estimated for species `B` the initial concentration is specified in the
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parameters table.
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## Model
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A simple conversion reaction `A <=> B` in a single compartment, following
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mass action kinetics.

‎petabtests/cases/v1.0.0/sbml/0019/_0019.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.tsv
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observable_files:
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- _observables.tsv
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sbml_files:
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- _model.xml

‎petabtests/cases/v1.0.0/sbml/0019/_0019_solution.yaml

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chi2: 5.98367121577545
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llh: -3.44341831317718
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simulation_files:
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- _simulations.tsv
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tol_chi2: 0.001
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tol_llh: 0.001
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tol_simulations: 0.001

‎petabtests/cases/v1.0.0/sbml/0019/_conditions.tsv

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conditionId A B
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c0 initial_A initial_B

‎petabtests/cases/v1.0.0/sbml/0019/_measurements.tsv

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observableId simulationConditionId time measurement
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obs_a c0 0 0.7
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obs_a c0 10 0.1

‎petabtests/cases/v1.0.0/sbml/0019/_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="conversion_reaction_0" name="Conversion Reaction 0">
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<listOfUnitDefinitions>
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<unitDefinition id="volume" name="volume">
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<listOfUnits>
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<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="substance" name="substance">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
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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="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
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</compartment>
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</listOfCompartments>
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<listOfSpecies>
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<species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
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</species>
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<species id="B" name="B" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
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</species>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="a0" name="a0" value="1" constant="true">
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</parameter>
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<parameter id="k1" name="k1" value="0" constant="true">
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</parameter>
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<parameter id="k2" name="k2" value="0" constant="true">
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</parameter>
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</listOfParameters>
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<listOfInitialAssignments>
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<initialAssignment symbol="A">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> a0 </ci>
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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="fwd" name="fwd" reversible="false">
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<listOfReactants>
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<speciesReference species="A" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="B" 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> compartment </ci>
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<ci> k1 </ci>
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<ci> A </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="rev" name="rev" reversible="false">
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<listOfReactants>
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<speciesReference species="B" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="A" 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> compartment </ci>
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<ci> k2 </ci>
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<ci> B </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>

‎petabtests/cases/v1.0.0/sbml/0019/_observables.tsv

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observableId observableFormula noiseFormula
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obs_a A 0.5

‎petabtests/cases/v1.0.0/sbml/0019/_parameters.tsv

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parameterId parameterScale lowerBound upperBound nominalValue estimate
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k1 lin 0 10 0.8 1
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k2 lin 0 10 0.6 1
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initial_A log10 0 10 1.0 1
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initial_B lin 0 10 2.0 0

‎petabtests/cases/v1.0.0/sbml/0019/_simulations.tsv

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observableId simulationConditionId time simulation
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obs_a c0 0 1.0
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obs_a c0 10 1.2857140481346516

‎petabtests/cases/v1.0.0/sbml/0019/conversion_modified.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="conversion_reaction_0" name="Conversion Reaction 0">
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<listOfUnitDefinitions>
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<unitDefinition id="volume" name="volume">
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<listOfUnits>
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<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="substance" name="substance">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
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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="compartment" name="compartment" spatialDimensions="3" size="1" constant="true">
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</compartment>
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</listOfCompartments>
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<listOfSpecies>
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<species id="A" name="A" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
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</species>
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<species id="B" name="B" compartment="compartment" initialConcentration="1" boundaryCondition="false" constant="false">
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</species>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="a0" name="a0" value="1" constant="true">
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</parameter>
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<parameter id="k1" name="k1" value="0" constant="true">
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</parameter>
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<parameter id="k2" name="k2" value="0" constant="true">
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</parameter>
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</listOfParameters>
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<listOfInitialAssignments>
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<initialAssignment symbol="A">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> a0 </ci>
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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="fwd" name="fwd" reversible="false">
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<listOfReactants>
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<speciesReference species="A" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="B" 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> compartment </ci>
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<ci> k1 </ci>
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<ci> A </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="rev" name="rev" reversible="false">
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<listOfReactants>
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<speciesReference species="B" stoichiometry="1"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="A" 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> compartment </ci>
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<ci> k2 </ci>
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<ci> B </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>

‎petabtests/cases/v1.0.0/sbml/README.md

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Simulation. Preequilibration and RateRules. One state reinitialized, one not (NaN in condition table). InitialAssignment to species overridden.
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# [0019](0019/)
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Simulation. InitialAssignment to species overridden.
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‎petabtests/cases/v2.0.0/sbml/0020/0020.py

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from inspect import cleandoc
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import pandas as pd
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from petab.C import *
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from petabtests import PetabTestCase, analytical_a
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DESCRIPTION = cleandoc("""
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## Objective
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This case tests handling of initial concentrations that are specified
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in the conditions table. For species `A`, the initial concentration is
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estimated for species `B` the initial concentration is specified in the
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parameters table.
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## Model
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A simple conversion reaction `A <=> B` in a single compartment, following
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mass action kinetics.
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""")
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# problem --------------------------------------------------------------------
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condition_df = pd.DataFrame(data={
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CONDITION_ID: ['c0'],
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'A': ["initial_A"],
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'B': ["initial_B"],
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}).set_index([CONDITION_ID])
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measurement_df = pd.DataFrame(data={
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OBSERVABLE_ID: ['obs_a', 'obs_a'],
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SIMULATION_CONDITION_ID: ['c0', 'c0'],
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TIME: [0, 10],
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MEASUREMENT: [0.7, 0.1]
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})
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observable_df = pd.DataFrame(data={
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OBSERVABLE_ID: ['obs_a'],
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OBSERVABLE_FORMULA: ['A'],
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NOISE_FORMULA: [0.5]
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}).set_index([OBSERVABLE_ID])
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parameter_df = pd.DataFrame(data={
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PARAMETER_ID: ['k1', 'k2', 'initial_A', 'initial_B'],
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PARAMETER_SCALE: [LIN, LIN, LOG10, LIN],
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LOWER_BOUND: [0] * 4,
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UPPER_BOUND: [10] * 4,
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NOMINAL_VALUE: [0.8, 0.6, 1, 2],
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ESTIMATE: [1] * 3 + [0],
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}).set_index(PARAMETER_ID)
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# solutions ------------------------------------------------------------------
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simulation_df = measurement_df.copy(deep=True).rename(
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columns={MEASUREMENT: SIMULATION})
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simulation_df[SIMULATION] = [analytical_a(t, 1, 2, 0.8, 0.6)
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for t in simulation_df[TIME]]
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case = PetabTestCase(
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id=20,
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brief="Simulation. InitialAssignment to species overridden.",
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description=DESCRIPTION,
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model='conversion_modified.xml',
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condition_dfs=[condition_df],
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observable_dfs=[observable_df],
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measurement_dfs=[measurement_df],
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simulation_dfs=[simulation_df],
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parameter_df=parameter_df,
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)

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