emodelrunner.synapses.synapse

Custom synapse-related classes.

Classes

SynapseCustom(sim, icell, synapse, section, ...)

Attach a synapse to the simulation.

SynapseMixin()

Class containing the synapse-related methods.

class emodelrunner.synapses.synapse.SynapseCustom(sim, icell, synapse, section, seed, rng_settings_mode, synconf_dict, start=None, interval=None, number=None, noise=None)[source]

Bases: SynapseMixin

Attach a synapse to the simulation.

seed

random number generator seed number

Type

int

rng_settins_mode

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

Type

str

section

cell location where the synapse is attached to

Type

neuron section

hsynapse

synapse instantion in simulator

Type

neuron ProbGABAAB_EMS or ProbAMPANMDA_EMS

delay

synapse delay

Type

float

weight

synapse weight

Type

float

pre_mtype

ID (but not gid) of the presynaptic cell

Type

int

start

force synapse to start firing at given value when using NetStim

Type

int/None

interval

force synapse to fire at given interval when using NetStim

Type

int/None

number

force synapse to fire N times when using NetStim

Type

int/None

noise

force synapse to have given noise when using NetStim

Type

int/None

class emodelrunner.synapses.synapse.SynapseMixin[source]

Bases: object

Class containing the synapse-related methods.

execute_synapse_configuration(synconf_dict, sid, sim, exec_all=False)[source]

Create a hoc file configuring synapse.

Parameters
  • synconf_dict (dict) – synapse configuration

  • sid (int) – synapse id

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

  • exec_all (bool) – whether to also execute commands with ‘*’

set_random_nmb_generator(sim, icell, sid)[source]

Sets the random number generator.

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

  • icell (neuron cell) – cell instantiation in simulator

  • sid (int) – synapse id

set_tau_r(sim, icell, sid)[source]

Set tau_r_GABAA using random nmb generator.

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

  • icell (neuron cell) – cell instantiation in simulator

  • sid (int) – synapse id