sbmlsim.simulator.rr_worker

Classes for running simulations with SBML models.

Module Contents

Classes

SimulationWorkerRR

Worker running simulations with roadrunner.

Attributes

logger

sbmlsim.simulator.rr_worker.logger[source]
class sbmlsim.simulator.rr_worker.SimulationWorkerRR[source]

Worker running simulations with roadrunner.

Implements the timecourse simulation once which can be reused by the different simulators.

set_model(model_state)[source]

Set model for simulator and updates the integrator settings.

Parameters

model_state (str) –

Return type

None

set_timecourse_selections(selections=None)[source]

Set the timecourse selections.

If the selections are None the complee selections will be used.

Raises

RuntimeError

Parameters

selections (Optional[Iterator[str]]) –

Return type

None

get_timecourse_selections()[source]

Get timecourse selections.

Return type

List[str]

set_integrator_settings(**kwargs)[source]

Set integrator settings.

Keys are:

variable_step_size [boolean] stiff [boolean] absolute_tolerance [float] relative_tolerance [float]

Return type

sbmlsim.model.rr_model.roadrunner.Integrator

get_integrator_setting(key)[source]

Get integrator setting for given key.

Parameters

key (str) –

Return type

Any

_timecourse(simulation)[source]

Timecourse simulation.

Requires for all timecourse definitions in the timecourse simulation to be unit normalized. The changes have no units any more for parallel simulations. You should never call this function directly!

Parameters

simulation (sbmlsim.simulation.TimecourseSim) – Simulation definition(s)

Returns

DataFrame with results

Return type

pandas.DataFrame