emodelrunner.protocols.synplas_protocols¶

Protocol creation functions & custom protocol classes for Synplas packages.

Functions

fastforward_synapses(cell_model)

Enable synapse fast-forwarding.

Classes

`SweepProtocolCustom`([name, stimuli, ...])	SweepProtocol with ability of synapse fastforwarding.
`SweepProtocolPairSim`([name, stimuli, ...])	Sweep protocol for pair simulation with fastforwarding.

class emodelrunner.protocols.synplas_protocols.SweepProtocolCustom(name=None, stimuli=None, recordings=None, cvode_active=None, fastforward=None)[source]¶

Bases: SweepProtocol

SweepProtocol with ability of synapse fastforwarding.

name¶

name of this object.

Type:: str

stimuli¶

Stimulus objects used in the protocol The list must be of size 2 and contain first the list for the presynaptic stimuli and then the list for the postsynaptic stimuli.

Type:: list of 2 lists of Stimuli

recordings¶

Recording objects used in the protocol. The list must be of size 2 and contain first the list for the presynaptic recording and then the list for the postsynaptic recording.

Type:: list of 2 lists of Recordings

cvode_active¶

whether to use variable time step

Type:: bool

fastforward¶

Time after which the synapses are fasforwarded. Leave None for no fastforward.

Type:: float

class emodelrunner.protocols.synplas_protocols.SweepProtocolPairSim(name=None, stimuli=None, recordings=None, cvode_active=None, fastforward=None)[source]¶

Bases: Protocol

Sweep protocol for pair simulation with fastforwarding.

name¶

name of this object.

Type:: str

stimuli¶

Stimulus objects used in the protocol The list must be of size 2 and contain first the list for the presynaptic stimuli and then the list for the postsynaptic stimuli.

Type:: list of 2 lists of Stimuli

recordings¶

Recording objects used in the protocol. The list must be of size 2 and contain first the list for the presynaptic recording and then the list for the postsynaptic recording.

Type:: list of 2 lists of Recordings

cvode_active¶

whether to use variable time step

Type:: bool

fastforward¶

Time after which the synapses are fasforwarded. Leave None for no fastforward.

Type:: float

destroy(sim=None)[source]¶

Destroy protocol.

Parameters:: sim (bluepyopt.ephys.NrnSimulator) – neuron simulator

instantiate(sim=None, pre_icell=None, post_icell=None)[source]¶

Instantiate.

Parameters:

sim (bluepyopt.ephys.NrnSimulator) – neuron simulator
pre_icell (neuron cell) – presynaptic cell instantiation in simulator
post_icell (neuron cell) – postsynaptic cell instantiation in simulator

run(precell_model, postcell_model, pre_param_values, post_param_values, sim=None, isolate=None, timeout=None)[source]¶

Instantiate protocol.

Parameters:

precell_model (bluepyopt.ephys.models.CellModel) – the presynaptic cell model
postcell_model (bluepyopt.ephys.models.CellModel) – the postsynaptic cell model
pre_param_values (dict) – optimized parameters of the presynaptic cell model
post_param_values (dict) – optimized parameters of the postsynaptic cell model
sim (bluepyopt.ephys.NrnSimulator) – neuron simulator
isolate (bool) – whether to isolate the run in a process with a timeout to avoid bad cells running for too long
timeout (float) – maximum real time (s) the cells are allowed to run when isolated

Returns:

list of 2 dicts containing the responses of both the cells

Has the structure [presynaptic response dict, postsynaptic response dict]

subprotocols()[source]¶

Return subprotocols.

Returns:: a dict containing the object

property total_duration¶

Total duration.

Returns:: total duration
Return type:: float

emodelrunner.protocols.synplas_protocols.fastforward_synapses(cell_model)[source]¶

Enable synapse fast-forwarding.

Parameters:: cell_model (emodelrunner.cell.CellModelCustom) – the cell whose synapses are to be fast-forwarded