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add reinitialization test
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‎petabtests/cases/v2.0.0/sbml/0021/0021.py

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case = PetabTestCase(
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id=21,
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brief="Simulation. Nothing special.",
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brief="Observable-dependent noise formula.",
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description=DESCRIPTION,
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model=DEFAULT_SBML_FILE,
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condition_dfs=[],

‎petabtests/cases/v2.0.0/sbml/0022/0022.py

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from inspect import cleandoc
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from petab.v2.C import *
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from petab.v2 import Problem
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from petabtests import (
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PetabTestCase,
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analytical_a,
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antimony_to_sbml_str,
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analytical_b,
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)
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from pathlib import Path
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DESCRIPTION = cleandoc("""
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## Objective
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This case tests simultaneous re-initialization of compartment size and
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contained species.
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## Model
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Two simple conversion reactions `A <=> B`, `a <=> b` in a single compartment,
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following mass action kinetics.
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`A` and `B` are species defined in terms of concentrations, `a` and `b` are
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`hasOnlySubstanceUnits=True` species defined in terms of amounts.
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The compartment size and the species amounts/concentrations are re-initialized
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at time 10. The assigned values are independent of the model state.
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At time 10, the conditions table changes:
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* The compartment size from 2 to 4.
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* The concentration of `A` to `5`. This implies that the amount of
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`A` is changed to `5 * 2 = 10` (concentration * compartment size).
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* The amount of `a` to `10`.
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This leads to the following model state at time 10:
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* The concentration of `A` is `10 / 4 = 2.5`
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(new amount divided by new volume).
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* The amount of `a` is `10`, unaffected by the compartment size change.
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* The concentration of `B` is `(2 * 2) / 4 = 1`
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(previous amount / new volume
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= previous concentration * previous volume / new volume).
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* The amount of `b` remains at `4`, unaffected by the compartment size change.
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""")
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# problem --------------------------------------------------------------------
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sbml_file = Path(__file__).parent / "model.xml"
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a_c0 = 2
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b_c0 = 1
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a_c10 = 2.5
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b_c10 = 1
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vol0 = 2
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vol_new = 10
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k1 = 2
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k2 = 1
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ant_model = f"""
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model petab_test_0022
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compartment default_compartment = {vol0}
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initial_conc_A = {a_c0}
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initial_conc_B = {b_c0}
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species A in default_compartment = initial_conc_A
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substanceOnly species a in default_compartment = initial_conc_A * default_compartment
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species B in default_compartment = initial_conc_B
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substanceOnly species b in default_compartment = initial_conc_B * default_compartment
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k1 = {k1}
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k2 = {k2}
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A' = k2 * B - k1 * A
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B' = - k2 * B + k1 * A
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a' = k2 * b - k1 * a
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b' = - k2 * b + k1 * a
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# the result of the PEtab reinitialization should be the same as with
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# the following event and no reinitialization:
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#
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# at time >= 10: A = 5, a = 5 * default_compartment, default_compartment = 4
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end
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"""
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sbml_file.write_text(antimony_to_sbml_str(ant_model))
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problem = Problem()
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problem.add_observable("obs_a", "a", noise_formula="1")
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problem.add_observable("obs_A", "A", noise_formula="1")
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problem.add_observable("obs_b", "b", noise_formula="1")
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problem.add_observable("obs_B", "B", noise_formula="1")
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problem.add_parameter("k1", lb=0, ub=10, nominal_value=k1, scale=LIN)
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problem.add_experiment("experiment1", 0, "", 10, "condition2")
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problem.add_condition(
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"condition2", "condition2", a=5 * vol0, A=5, default_compartment=vol_new
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)
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ts = [0, 5, 10, 15]
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for t in ts:
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problem.add_measurement("obs_a", "", t, 2)
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problem.add_measurement("obs_A", "", t, 2)
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problem.add_measurement("obs_b", "", t, 1)
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problem.add_measurement("obs_B", "", t, 1)
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# solutions ------------------------------------------------------------------
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simulation_df = problem.measurement_df.copy(deep=True).rename(
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columns={MEASUREMENT: SIMULATION}
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)
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simulation_df[SIMULATION] = [
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# a, A, b, B
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# t=0
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a_c0 * vol0,
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a_c0,
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b_c0 * vol0,
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b_c0,
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# t=5
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analytical_a(5, a_c0, b_c0, k1, k2) * vol0,
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analytical_a(5, a_c0, b_c0, k1, k2),
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analytical_b(5, a_c0, b_c0, k1, k2) * vol0,
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analytical_b(5, a_c0, b_c0, k1, k2),
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# t=10, re-initialize compartment size and contained species
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a_c10 * vol_new,
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a_c10,
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b_c10 * vol_new,
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b_c10,
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# t=15
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analytical_a(5, a_c10, b_c10, k1, k2) * vol_new,
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analytical_a(5, a_c10, b_c10, k1, k2),
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analytical_b(5, a_c10, b_c10, k1, k2) * vol_new,
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analytical_b(5, a_c10, b_c10, k1, k2),
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]
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case = PetabTestCase(
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id=22,
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brief="Simultaneous re-initialization of compartment size and contained species.",
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description=DESCRIPTION,
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model=sbml_file,
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experiment_dfs=[problem.experiment_df],
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condition_dfs=[problem.condition_df],
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observable_dfs=[problem.observable_df],
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measurement_dfs=[problem.measurement_df],
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simulation_dfs=[simulation_df],
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parameter_df=problem.parameter_df,
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)

‎petabtests/cases/v2.0.0/sbml/0022/README.md

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# PEtab test case 0022
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## Objective
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This case tests simultaneous re-initialization of compartment size and
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contained species.
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## Model
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Two simple conversion reactions `A <=> B`, `a <=> b` in a single compartment,
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following mass action kinetics.
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`A` and `B` are species defined in terms of concentrations, `a` and `b` are
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`hasOnlySubstanceUnits=True` species defined in terms of amounts.
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The compartment size and the species amounts/concentrations are re-initialized
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at time 10. The assigned values are independent of the model state.
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At time 10, the conditions table changes:
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* The compartment size from 2 to 4.
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* The concentration of `A` to `5`. This implies that the amount of
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`A` is changed to `5 * 2 = 10` (concentration * compartment size).
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* The amount of `a` to `10`.
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This leads to the following model state at time 10:
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* The concentration of `A` is `10 / 4 = 2.5`
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(new amount divided by new volume).
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* The amount of `a` is `10`, unaffected by the compartment size change.
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* The concentration of `B` is `(2 * 2) / 4 = 1`
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(previous amount / new volume
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= previous concentration * previous volume / new volume).
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* The amount of `b` remains at `4`, unaffected by the compartment size change.

‎petabtests/cases/v2.0.0/sbml/0022/_0022.yaml

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format_version: 2.0.0
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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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experiment_files:
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- _experiments.tsv
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measurement_files:
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- _measurements.tsv
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model_files:
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model_0:
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language: sbml
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location: _model.xml
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observable_files:
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- _observables.tsv

‎petabtests/cases/v2.0.0/sbml/0022/_0022_solution.yaml

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chi2: 1220.9443344556003
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llh: -625.1751837590749
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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/v2.0.0/sbml/0022/_conditions.tsv

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conditionId targetId operationType targetValue conditionName
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condition2 a setCurrentValue 10 ['condition2']
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condition2 A setCurrentValue 5 ['condition2']
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condition2 default_compartment setCurrentValue 10 ['condition2']

‎petabtests/cases/v2.0.0/sbml/0022/_experiments.tsv

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experimentId time conditionId
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experiment1 0
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experiment1 10 condition2

‎petabtests/cases/v2.0.0/sbml/0022/_measurements.tsv

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observableId experimentId time measurement
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obs_a 0 2
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obs_A 0 2
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obs_b 0 1
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obs_B 0 1
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obs_a 5 2
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obs_A 5 2
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obs_b 5 1
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obs_B 5 1
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obs_a 10 2
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obs_A 10 2
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obs_b 10 1
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obs_B 10 1
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obs_a 15 2
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obs_A 15 2
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obs_b 15 1
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obs_B 15 1

‎petabtests/cases/v2.0.0/sbml/0022/_model.xml

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<?xml version="1.0" encoding="UTF-8"?>
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<!-- Created by libAntimony version v2.15.0 with libSBML version 5.20.2. -->
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<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
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<model metaid="petab_test_0022" id="petab_test_0022">
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<listOfCompartments>
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<compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="2" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species id="A" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="a" compartment="default_compartment" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species id="B" compartment="default_compartment" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
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<species id="b" compartment="default_compartment" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter id="initial_conc_A" value="2" constant="true"/>
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<parameter id="initial_conc_B" value="1" constant="true"/>
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<parameter id="k1" value="2" constant="true"/>
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<parameter id="k2" value="1" constant="true"/>
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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> initial_conc_A </ci>
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</math>
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</initialAssignment>
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<initialAssignment symbol="a">
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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> initial_conc_A </ci>
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<ci> default_compartment </ci>
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</apply>
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</math>
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</initialAssignment>
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<initialAssignment symbol="B">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> initial_conc_B </ci>
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</math>
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</initialAssignment>
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<initialAssignment symbol="b">
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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> initial_conc_B </ci>
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<ci> default_compartment </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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<listOfRules>
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<rateRule variable="A">
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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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<apply>
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<times/>
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<ci> k2 </ci>
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<ci> B </ci>
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</apply>
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<apply>
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<times/>
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<ci> k1 </ci>
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<ci> A </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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<rateRule variable="a">
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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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<apply>
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<times/>
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<ci> k2 </ci>
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<ci> b </ci>
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</apply>
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<apply>
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<times/>
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<ci> k1 </ci>
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<ci> a </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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<rateRule variable="B">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<plus/>
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<apply>
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<times/>
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<apply>
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<minus/>
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<ci> k2 </ci>
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</apply>
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<ci> B </ci>
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</apply>
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<apply>
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<times/>
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<ci> k1 </ci>
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<ci> A </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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<rateRule variable="b">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<plus/>
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<apply>
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<times/>
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<apply>
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<minus/>
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<ci> k2 </ci>
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</apply>
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<ci> b </ci>
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</apply>
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<apply>
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<times/>
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<ci> k1 </ci>
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<ci> a </ci>
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</apply>
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</apply>
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</math>
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</rateRule>
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</listOfRules>
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</model>
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</sbml>

‎petabtests/cases/v2.0.0/sbml/0022/_observables.tsv

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observableId observableFormula noiseFormula
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obs_a a 1
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obs_A A 1
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obs_b b 1
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obs_B B 1

‎petabtests/cases/v2.0.0/sbml/0022/_parameters.tsv

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parameterId estimate nominalValue parameterScale lowerBound upperBound
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k1 1 2 lin 0 10

‎petabtests/cases/v2.0.0/sbml/0022/_simulations.tsv

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observableId experimentId time simulation
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obs_a 0 4.0
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obs_A 0 2.0
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obs_b 0 2.0
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obs_B 0 1.0
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obs_a 5 2.000000611804641
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obs_A 5 1.0000003059023206
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obs_b 5 3.999999388195359
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obs_B 5 1.9999996940976794
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obs_a 10 25.0
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obs_A 10 2.5
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obs_b 10 10.0
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obs_B 10 1.0
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obs_a 15 11.666670745364273
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obs_A 15 1.1666670745364274
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obs_b 15 23.33332925463573
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obs_B 15 2.333332925463573

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