sbmlsim.examples.experiments.covid.experiments

Submodules

• sbmlsim.examples.experiments.covid.experiments.bertozzi2020
• sbmlsim.examples.experiments.covid.experiments.carcione2020
• sbmlsim.examples.experiments.covid.experiments.cuadros2020

Package Contents

Classes

Bertozzi2020	Generic simulation experiment.
Cuadros2020	Generic simulation experiment.
Carcione2020	Generic simulation experiment.

class sbmlsim.examples.experiments.covid.experiments.Bertozzi2020(sid=None, base_path=None, data_path=None, ureg=None, **kwargs)

Bases: sbmlsim.experiment.SimulationExperiment

Generic simulation experiment.

Consists of models, datasets, simulations, tasks, results, processing, figures

Parameters:

• sid (str) –

• base_path (pathlib.Path) –

• data_path (pathlib.Path) –

• ureg (sbmlsim.units.UnitRegistry) –

models()

Define model definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.model.AbstractModel]

simulations()

Define simulation definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.simulation.TimecourseSim]

tasks()

Define task definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.task.Task]

figures()

Figure definition.

Selections accessed in figures and analyses must be registered beforehand via datagenerators.

Most figures do not require access to concrete data, but only abstract data concepts.

Return type:

Dict[str, sbmlsim.plot.Figure]

class sbmlsim.examples.experiments.covid.experiments.Cuadros2020(sid=None, base_path=None, data_path=None, ureg=None, **kwargs)

Bases: sbmlsim.experiment.SimulationExperiment

Generic simulation experiment.

Consists of models, datasets, simulations, tasks, results, processing, figures

Parameters:

• sid (str) –

• base_path (pathlib.Path) –

• data_path (pathlib.Path) –

• ureg (sbmlsim.units.UnitRegistry) –

models()

Define model definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.model.AbstractModel]

simulations()

Define simulation definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.simulation.TimecourseSim]

tasks()

Define task definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.task.Task]

figures()

Figure definition.

Selections accessed in figures and analyses must be registered beforehand via datagenerators.

Most figures do not require access to concrete data, but only abstract data concepts.

Return type:

Dict[str, sbmlsim.plot.Figure]

class sbmlsim.examples.experiments.covid.experiments.Carcione2020(sid=None, base_path=None, data_path=None, ureg=None, **kwargs)

Bases: sbmlsim.experiment.SimulationExperiment

Generic simulation experiment.

Consists of models, datasets, simulations, tasks, results, processing, figures

Parameters:

• sid (str) –

• base_path (pathlib.Path) –

• data_path (pathlib.Path) –

• ureg (sbmlsim.units.UnitRegistry) –

models()

Define model definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.model.AbstractModel]

tasks()

Define task definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.task.Task]

simulations()

Define simulation definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.simulation.TimecourseSim]

figures()

Figure definition.

Selections accessed in figures and analyses must be registered beforehand via datagenerators.

Most figures do not require access to concrete data, but only abstract data concepts.

Return type:

Dict[str, sbmlsim.plot.Figure]

figure_plot_1()