emodelrunner.synapses.mechanism

Synapse Point Process Mechanisms.

Classes

NrnMODPointProcessMechanismCustom(name, ...)

Class containing all the synapses.

class emodelrunner.synapses.mechanism.NrnMODPointProcessMechanismCustom(name, synapses_data, synconf_dict, seed, rng_settings_mode, pre_mtypes=None, stim_params=None, comment='', use_glu_synapse=False, syn_setup_params=None)[source]

Bases: Mechanism

Class containing all the synapses.

synapses_data

synapse data

Type

list of dicts

synconf_dict

synapse configuration

Type

dict

seed

random number generator seed number

Type

int

rng_settings_mode

mode of the random number generator Can be “Random123” or “Compatibility”

Type

str

pre_mtypes

activate only synapses whose pre_mtype is in this list if None, all synapses are activated

Type

list of ints

stim_params

dict with pre_mtype as key, and netstim params list as item. netstim params list is [start, interval, number, noise]

Type

dict or None

use_glu_synapse

if True, instantiate synapses to use GluSynapse

Type

bool

syn_setup_params

contains extra parameters to setup synapses when using GluSynapseCustom

Type

dict

rng

random number generator of the simulator

Type

neuron Random

pprocesses

list of the synapses

Type

list of SynapseCustom or GluSynapseCustom

destroy(sim=None)[source]

Destroy mechanism instantiation.

Parameters

sim (bluepyopt.ephys.NrnSimulator) – neuron simulator

static get_cell_section_for_synapse(synapse, icell)[source]

Returns the cell section on which is the synapse.

Parameters
  • synapse (dict) – contains the synapse data

  • icell (neuron cell) – cell instantiation in simulator

Returns

neuron section where the synapse is attached

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

Instantiate the synapses.

In the process, fill the self.pprocesses list.

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

  • icell (neuron cell) – cell instantiation in simulator