sbmlsim.examples.experiments.repressilator.repressilator_scans

Example simulation experiment.

Module Contents

Classes

RepressilatorScanExperiment

Simple repressilator experiment.

Functions

run_repressilator_experiments(output_path)

Run the repressilator simulation experiments.
class sbmlsim.examples.experiments.repressilator.repressilator_scans.RepressilatorScanExperiment(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()[source]

Define model definitions.

The child classes fill out the information.

Return type:

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

simulations()[source]

Define simulation definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.simulation.AbstractSim]

tasks()[source]

Define task definitions.

The child classes fill out the information.

Return type:

Dict[str, sbmlsim.task.Task]

sim_scans()[source]
Return type:

Dict[str, sbmlsim.simulation.AbstractSim]

data()[source]

Data used for plotting and analysis. Generates promises for results.

Returns:

Return type:

Dict[str, sbmlsim.data.Data]

figures()[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_scans.run_repressilator_experiments(output_path)[source]

Run the repressilator simulation experiments.

Parameters:

output_path (pathlib.Path) –

Return type:

pathlib.Path