emodelrunner.cell

Custom Cell class.

Classes

CellModelCustom(name[, morph, mechs, ...])

Cell model class.

class emodelrunner.cell.CellModelCustom(name, morph=None, mechs=None, params=None, gid=0, add_synapses=False, fixhp=False)[source]

Bases: CellModel

Cell model class.

name

name of the model

Type

str

morphology

underlying Morphology of the cell

Type

bluepyopt.ephys.morphologies.Morphology

mechanisms

Mechanisms associated with the cell

Type

list of bluepyopt.ephys.mechanisms.Mechanisms

params

Parameters of the cell model

Type

collections.OrderedDict of bluepyopt.Parameters

icell

Cell instantiation in simulator

Type

neuron cell

param_values

contains values of the optimized parameters

Type

dict

gid

cell’s ID

Type

int

seclist_names

Names of the lists of sections

Type

list of strings

secarray_names

Names of the sections

Type

list of strings

add_synapses

set to True to add synapses to the cell

Type

bool

fixhp

to uninsert SK_E2 for hyperpolarization

Type

bool

static connectable_empty_cell_template(template_name, seclist_names=None, secarray_names=None)[source]

Create a hoc script of an empty cell with an additional connection function.

Parameters
  • template_name (str) – name of the cell model

  • seclist_names (list of strings) – Names of the lists of sections

  • secarray_names (list of strings) – Names of the sections

Returns

hoc script describing an empty cell model with connection function

Return type

str

create_custom_hoc(param_values, ignored_globals=(), template_path='templates/cell_template.jinja2', disable_banner=False, syn_dir=None, syn_hoc_filename=None, syn_temp_name='hoc_synapses')[source]

Create hoc code for this model.

Parameters
  • param_values (dict) – contains values of the optimized parameters

  • ignored_globals (iterable str) – HOC coded is added for each NrnGlobalParameter that exists, to test that it matches the values set in the parameters. This iterable contains parameter names that aren’t checked

  • template_path (str) – path to the jinja2 template

  • disable_banner (bool) – if not True: a banner is added to the hoc file

  • syn_dir (str) – directory where the synapse data /files are

  • syn_hoc_filename (str) – file name of synapse hoc file

  • syn_temp_name (str) – synapse class name in hoc

Returns

hoc script describing this cell model

Return type

str

static create_empty_cell(name, sim, seclist_names=None, secarray_names=None)[source]

Create an empty cell in Neuron.

Parameters
  • template_name (str) – name of the cell model

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

  • seclist_names (list of strings) – Names of the lists of sections

  • secarray_names (list of strings) – Names of the sections

Returns

Cell instantiation in simulator

freeze_params(param_values)[source]

Freeze params and return list of params to unfreze afterwards.

Parameters

param_values (dict) – contains values of the optimized parameters

Returns

names of the newly frozen parameters

Return type

list

get_replace_axon()[source]

Return appropriate replace_axon str.

Returns

hoc script defining the replacement axon

Return type

str

instantiate(sim=None)[source]

Instantiate model in simulator.

Parameters

sim (bluepyopt.ephys.NrnSimulator) – neuron simulator

remove_point_process_mechs()[source]

Return mechanisms without point process mechanisms.

Returns

list of Mechanisms without the point process mechanisms