sbmlsim.examples.experiments.repressilator.repressilator

Example simulation experiment.

Module Contents

Classes

RepressilatorExperiment

Simple repressilator experiment.

Functions

run_repressilator_experiments(output_path)

Run the repressilator simulation experiments.

class sbmlsim.examples.experiments.repressilator.repressilator.RepressilatorExperiment(sid=None, base_path=None, data_path=None, ureg=None, **kwargs)[source]

Bases: sbmlsim.experiment.SimulationExperiment

Simple repressilator experiment.

Parameters
  • sid (str) –

  • base_path (pathlib.Path) –

  • data_path (pathlib.Path) –

  • ureg (sbmlsim.units.UnitRegistry) –

models(self)[source]

Define model definitions.

The child classes fill out the information.

Return type

Dict[str, Union[pathlib.Path, sbmlsim.model.AbstractModel]]

tasks(self)[source]

Define task definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.task.Task]

simulations(self)[source]

Define simulation definitions.

The child classes fill out the information.

Return type

Dict[str, sbmlsim.simulation.AbstractSim]

sim_scans(self)[source]
Return type

Dict[str, sbmlsim.simulation.AbstractSim]

datagenerators(self)[source]

Data to plot and analyze.

Returns

Return type

None

figures(self)[source]

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]

sbmlsim.examples.experiments.repressilator.repressilator.run_repressilator_experiments(output_path)[source]

Run the repressilator simulation experiments.

Parameters

output_path (pathlib.Path) –

Return type

pathlib.Path