bluepyemodel.model.model

Cell model creation.

Functions

create_cell_model(name, model_configuration)

Create a cell model based on a morphology, mechanisms and parameters

define_distributions(distributions_definition)

Create a list of ParameterScaler from a the definition of channel distributions

define_mechanisms(mechanisms_definition, ...)

Define a list of NrnMODMechanism from a definition dictionary

define_morphology(model_configuration[, ...])

Define a morphology object from a morphology file

define_parameters(parameters_definition, ...)

Define a list of NrnParameter from a definition dictionary

multi_locations(section_name, ...)

Define a list of locations from a section names.
create_cell_model(name, model_configuration, morph_modifiers=None, seclist_names=None, secarray_names=None, nseg_frequency=40)

Create a cell model based on a morphology, mechanisms and parameters

Parameters:

  • name (str) – name of the model

  • morphology (dict) – morphology from emodel api .get_morphologies()

  • model_configuration (NeuronModelConfiguration) – Configuration of the neuron model, containing the parameters their locations and the associated mechanisms.

  • morph_modifiers (list of str or list of list) –

    If str, name of the morph modifier to use from bluepyemodel.evaluation.modifiers. If List of morphology modifiers. Each modifier is defined by a list that includes the following elements: 1. The path to the file that contains the modifier. 2. The name of the function that applies the modifier. 3. Optionally, a “hoc_string” that represents the hoc code for the modifier. For example, morph_modifiers could be defined as follows:

    morph_modifiers = [["path_to_module",
                    "name_of_function",
                    "hoc_string"], ...].

    If the “hoc_string” is not provided, the system will search within the specified module for a string that matches the function name appended with “_hoc”. If None, the default modifier will replace the axon with a tappered axon initial segment (replace_axon_with_taper). If you do not wish to use any modifier, set the present argument to []. If ["bluepyopt_replace_axon"], the replace_axon function from bluepyopt.ephys.morphologies.NrnFileMorphology will be used and no other morph modifiers will be used.

Returns:

CellModel

define_distributions(distributions_definition, morphology=None)

Create a list of ParameterScaler from a the definition of channel distributions

Parameters:

distributions_definition (list) – definitions of the distributions

define_mechanisms(mechanisms_definition, mapping_multilocation)

Define a list of NrnMODMechanism from a definition dictionary

Parameters:

  • mechanisms_definition (list of MechanismConfiguration) – definition of the mechanisms

  • mapping_multilocation (dict) – mapping from multi-locations names to list of locations

Returns:

list of NrnMODMechanism

Return type:

list

define_morphology(model_configuration, do_set_nseg=True, nseg_frequency=40, morph_modifiers=None)

Define a morphology object from a morphology file

Parameters:

  • model_configuration (NeuronModelConfiguration) – configuration of the model

  • do_set_nseg (float) – set the length for the discretization of the segments

  • nseg_frequency (float) – frequency of nseg

  • morph_modifiers (list of str or list of list) –

    If str, name of the morph modifier to use from bluepyemodel.evaluation.modifiers. If List of morphology modifiers. Each modifier is defined by a list that includes the following elements: 1. The path to the file that contains the modifier. 2. The name of the function that applies the modifier. 3. Optionally, a “hoc_string” that represents the hoc code for the modifier. For example, morph_modifiers could be defined as follows:

    morph_modifiers = [["path_to_module",
                    "name_of_function",
                    "hoc_string"], ...].

    If the “hoc_string” is not provided, the system will search within the specified module for a string that matches the function name appended with “_hoc”. If None, the default modifier will replace the axon with a tappered axon initial segment (replace_axon_with_taper). If you do not wish to use any modifier, set the present argument to []. If ["bluepyopt_replace_axon"], the replace_axon function from bluepyopt.ephys.morphologies.NrnFileMorphology will be used and no other morph modifiers will be used.

Returns:

a morphology object

Return type:

bluepyopt.ephys.morphologies.NrnFileMorphology

define_parameters(parameters_definition, distributions, mapping_multilocation)

Define a list of NrnParameter from a definition dictionary

Parameters:

  • parameters_definition (list) – definitions of the parameters

  • distributions (list) – list of distributions in the form of ParameterScaler

  • mapping_multilocation (dict) – mapping from multi-locations names to list of locations

multi_locations(section_name, additional_multiloc_map)

Define a list of locations from a section names.

Parameters:

section_name (str) – name of section

Returns:

list of NrnSeclistLocation

Return type:

list