emodelrunner.create_cells

Functions to create cells.

Functions

create_cell(unopt_params_path, emodel, ...)

Create a cell.

create_cell_using_config(config)

Create a cell given configuration.

get_postcell(config[, fixhp, syn_setup_params])

Return the postcell for synapse plasticity run.

get_precell(config[, fixhp])

Return the precell for synapse plasticity pair simulation run.

emodelrunner.create_cells.create_cell(unopt_params_path, emodel, add_synapses, morph, gid, syn_mech_args=None, use_glu_synapse=False, fixhp=False, syn_setup_params=None, v_init=-80, celsius=34)[source]

Create a cell.

Parameters
  • unopt_params_path (str) – path to the unoptimized parameters json file

  • emodel (str) – name to give to the cell model

  • add_synapses (bool) – whether to add synapses to the cell

  • morph (ephys.morphologies.NrnFileMorphology) – morphology object

  • gid (int) – cell model ID

  • syn_mech_args (SynMechArgs) – synapse-related configuration

  • use_glu_synapse (bool) – whether to use GluSynapseCustom class for synapses

  • fixhp (bool) – to uninsert SK_E2 for hyperpolarization in cell model

  • syn_setup_params (dict) – contains extra parameters to setup synapses when using GluSynapseCustom

  • v_init (int) – initial voltage (mV)

  • celsius (int) – cell temperature (celsius)

Returns

cell model

Return type

CellModelCustom

emodelrunner.create_cells.create_cell_using_config(config)[source]

Create a cell given configuration.

Parameters

config (configparser.ConfigParser) – configuration

Raises

ValueError – raised when package_type is not supported

Returns

cell model

Return type

CellModelCustom

emodelrunner.create_cells.get_postcell(config, fixhp=False, syn_setup_params=None)[source]

Return the postcell for synapse plasticity run.

Parameters
  • config (configparser.ConfigParser) – configuration

  • fixhp (bool) – to uninsert SK_E2 for hyperpolarization in cell model

  • syn_setup_params (dict) – contains extra parameters to setup synapses when using GluSynapseCustom

Returns

post-synaptic cell model

Return type

CellModelCustom

emodelrunner.create_cells.get_precell(config, fixhp=False)[source]

Return the precell for synapse plasticity pair simulation run.

Args:

config (configparser.ConfigParser): configuration fixhp (bool): to uninsert SK_E2 for hyperpolarization in cell model

Returns

pre-synaptic cell model

Return type

CellModelCustom