sbmlsim.examples.experiments.covid.experiments

Submodules

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)[source]

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)[source]

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)[source]

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()