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