bluepyopt.ephys.protocols

Protocol classes

class bluepyopt.ephys.protocols.ArbSweepProtocol(name=None, stimuli=None, recordings=None, use_labels=False)[source]

Arbor Sweep protocol

Constructor

Parameters:

  • name (str) – name of this object

  • stimuli (list of Stimuli) – Stimulus objects used in the protocol

  • recordings (list of Recordings) – Recording objects used in the protocol

  • use_labels (bool) – Add stimuli/recording locations to label dict

instantiate_iclamp_stimuli(decor, use_labels=False)[source]

Instantiate iclamp stimuli

instantiate_locations(label_dict)[source]

Instantiate protocol (stimuli/recordings) locations on label_dict

instantiate_recordings(cell_model, use_labels=False)[source]

Instantiate recordings

instantiate_synaptic_stimuli(cell_model, use_labels=False)[source]

Instantiate synaptic stimuli

run(cell_model, param_values, sim=None, isolate=None, timeout=None)[source]

Instantiate protocol

subprotocols()[source]

Return subprotocols

property total_duration

Total duration

exception bluepyopt.ephys.protocols.ArbSweepProtocolException(message)[source]

All exceptions generated by ArbSweepProtocol

Constructor

class bluepyopt.ephys.protocols.Protocol(name=None)[source]

Class representing a protocol (stimulus and recording).

Constructor

Parameters:

name (str) – name of the feature

class bluepyopt.ephys.protocols.SequenceProtocol(name=None, protocols=None)[source]

A protocol consisting of a sequence of other protocols

Constructor

Parameters:

  • name (str) – name of this object

  • protocols (list of Protocols) – subprotocols this protocol consists of

run(cell_model, param_values, sim=None, isolate=None, timeout=None)[source]

Instantiate protocol

subprotocols()[source]

Return subprotocols

class bluepyopt.ephys.protocols.StepProtocol(name=None, step_stimulus=None, holding_stimulus=None, recordings=None, cvode_active=None, deterministic=False)[source]

Protocol consisting of step and holding current

Constructor

Parameters:

  • name (str) – name of this object

  • step_stimulus (list of Stimuli) – Stimulus objects used in protocol

  • recordings (list of Recordings) – Recording objects used in the protocol

  • cvode_active (bool) – whether to use variable time step

  • deterministic (bool) – whether to force all mechanism to be deterministic

property step_delay

Time stimulus starts

property step_duration

Time stimulus starts

class bluepyopt.ephys.protocols.SweepProtocol(name=None, stimuli=None, recordings=None, cvode_active=None, deterministic=False)[source]

Sweep protocol

Constructor

Parameters:

  • name (str) – name of this object

  • stimuli (list of Stimuli) – Stimulus objects used in the protocol

  • recordings (list of Recordings) – Recording objects used in the protocol

  • cvode_active (bool) – whether to use variable time step

  • deterministic (bool) – whether to force all mechanism to be deterministic

adjust_stochasticity()[source]

Decorator method to adjust the stochasticity of the mechanisms

destroy(sim=None)[source]

Destroy protocol

instantiate(sim=None, cell_model=None)[source]

Instantiate

run(cell_model, param_values, **kwargs)[source]

Inner function

subprotocols()[source]

Return subprotocols

property total_duration

Total duration

exception bluepyopt.ephys.protocols.SweepProtocolException(message)[source]

All exceptions generated by SweepProtocol

Constructor