Cable cell mechanisms

When decorating a cable cell, we use a mechanism type to describe a mechanism that is to be painted or placed on the cable cell.

class mechanism

Mechanisms describe physical processes, distributed over the membrane of the cell. Density mechanisms are associated with regions of the cell, whose dynamics are a function of the cell state and their own state where they are present. Point mechanisms are defined at discrete locations on the cell, which receive events from the network. A third, specific type of density mechanism, which describes ionic reversal potential behaviour, can be specified for cells or the whole model.

The mechanism type is a simple wrapper around a mechanism mechanism.name and a dictionary of named parameters.

Mechanisms have two types of parameters:

  • global parameters: a scalar value that is the same for all instances of a mechanism.

  • range parameters: the value of range parameters is defined for each instance of the mechanism on a cell. For density mechanisms, this means one value for each control volume on which it is present.

The method for setting a parameter depends on its type. If global parameters change, we are effectively defining a new type of mechanism, so global parameter information is encoded in the name. Range parameters are set using a dictionary of name-value pairs.

import arbor

# hh dynamics with default parameters.
hh = arbor.mechanism('hh')

# A passive leaky channel with custom parameters
pas = arbor.mechanism('pas/e=-55.0', {'g': 0.02})

# Reversal potential using Nernst equation with GLOBAL parameter values
# for Faraday's constant and the target ion species, set with a '/' followed
# by comma-separated list of parameter after the base mechanism name.
rev = arbor.mechanism('nernst/F=96485,x=ca')

Mechanisms can be painted to a region. Different mechanisms can be painted on top of each other.

import arbor

# Create pas mechanism with default parameter values (set in NOMDL file).
m1 = arbor.mechanism('pas')

# Create default mechainsm with custom conductance (range).
m2 = arbor.mechanism('pas', {'g', 0.1})

# Create a new pas mechanism with that changes reversal potential (global).
m3 = arbor.mechanism('pas/e=-45')

# Create an instance of the same mechanism, that also sets conductance (range).
m4 = arbor.mechanism('pas/e=-45', {'g', 0.1})

# This is an equivalent to m4, using set method to specify range parameters.
m5 = arbor.mechanism('pas/e=-45')
m5.set('g', 0.1)

# Decorate the 'soma' with (multiple) mechanisms
decor.paint('"soma"', m1)
decor.paint('"soma"', m2) # Error: can't place the same mechanism on overlapping regions
decor.paint('"soma"', m3) # This is ok: m3 is a new, derived mechanism by virtue of
                          # having a different name, i.e. 'pas/e=-45' vs. 'pas'.
mechanism(name, params)

constructor for mechanism with name and range parameter overrides params, for example: arbor.mechanism(name='pas', params={'g': 0.01}).

Parameters
  • name (str) – name of mechanism.

  • params (dict[str, double]) – A dictionary of parameter values, with parameter name as key.

mechanism(name)

constructor for mechanism. The name can be either the name of a mechanism in the catalogue, e.g. arbor.mechanism('pas'), or an implicitly derived mechanism, e.g. arbor.mechanism('nernst/k').

set(name, value)

Set new value for a parameter.

Parameters
  • name (str) – name of the parameter.

  • value (float) – value of the parameter.

name: str

The name of the mechanism.

values
:type: dict

A dictionary of key-value pairs for the parameters.

class mechanism_info

Meta data about the fields and ion dependencies of a mechanism. The data is presented as read-only attributes.

import arbor
cat = arbor.default_catalogue()

# Get mechanism_info for the 'expsyn' mechanism.
mech = cat['expsyn']

# Query the mechanism_info for information about parameters.

print(mech.parameters.keys())
# dict_keys(['e', 'tau'])

print(mech.parameters['tau'].units)
# 'ms'

print(mech.parameters['tau'].default)
# 2.0
kind: string

String representation of the kind of the mechanism: density, point or reversal potential.

globals: dict[str, mechanism_field]

Global fields have one value common to an instance of a mechanism, are constant in time and set at instantiation.

parameters: dict[str, mechanism_field]

Parameter fields may vary across the extent of a mechanism, but are constant in time and set at instantiation.

state: dict[str, mechanism_field]

State fields vary in time and across the extent of a mechanism, and potentially can be sampled at run-time.

ions: dict[str, ion_dependency]

Ion dependencies.

linear: bool

True if a synapse mechanism has linear current contributions so that multiple instances on the same control volume can be coalesced.

post_events: bool

True if a synapse mechanism has a POST_EVENT procedure defined.

class ion_dependency

Meta data about a mechanism’s dependence on an ion species, presented as read-only attributes.

import arbor
cat = arbor.default_catalogue()

# Get ion_dependency for the 'hh' mechanism.
ions = cat['hh'].ions

# Query the ion_dependency.

print(ions.keys())
# dict_keys(['k', 'na'])

print(ions['k'].write_rev_pot)
# False

print(ions['k'].read_rev_pot)
# True
write_int_con: bool

If the mechanism contributes to the internal concentration of the ion species.

write_ext_con: bool

If the mechanism contributes to the external concentration of the ion species.

write_rev_pot: bool

If the mechanism calculates the reversal potential of the ion species.

read_rev_pot: bool

If the mechanism depends on the reversal potential of the ion species.

class mechanism_field

Meta data about a specific field of a mechanism, presented as read-only attributes.

units: string

The units of the field.

default: float

The default value of the field.

min: float

The minimum permissible value of the field.

max: float

The maximum permissible value of the field.

The mechanism_info type above presents read-only information about a mechanism that is available in a catalogue.

Mechanism catalogues

class catalogue

A mechanism catalogue is a collection of mechanisms that maintains:

  1. Collection of mechanism metadata indexed by name.

  2. A further hierarchy of derived mechanisms, that allow specialization of global parameters, ion bindings, and implementations.

__init__(catalogue=None)

Create an empty or copied catalogue.

Parameters

catalogue (catalogue) – catalogue to copy

Returns

empty or copied catalogue

Return type

catalogue

__contains__(name)

Test if mechanism with name is in the catalogue.

Note: This enables the following idiom

import arbor

if 'hh' in arbor.default_catalogue():
  print("Found HH mechanism.")
Parameters

name (str) – name of mechanism.

Returns

bool

is_derived(name)

Is name a derived mechanism or can it be implicitly derived?

Parameters

name (str) – name of mechanism.

Returns

bool

__getitem__(name)

Look up mechanism meta data with name.

import arbor

cat = arbor.default_catalogue()

# Print default value and units for gnabar parameter of hh.
print(cat['hh'].parameters['gnabar'])
Parameters

name (str) – name of mechanism.

Returns

mechanism metadata

Return type

mechanism_info

__iter___()

Return a list names of all the mechanisms in the catalogue.

Note: This enables the following idiom

import arbor

for name in arbor.default_catalogue():
  print(name)
Returns

py_mech_cat_iterator

extend(other, prefix)

Import another catalogue, possibly with a prefix. Will overwrite in case of name collisions.

import arbor

cat = arbor.default_catalogue()
cat.extend(arbor.allen_catalogue(), "")
Parameters
  • other (mechanism_catalogue) – reference to other catalogue.

  • prefix (str) – prefix for mechanism names in other

derive(name, parent, globals={}, ions={})

Derive a new mechanism with name from the mechanism parent.

If no parameters or ion renaming are specified with globals or ions, the method will attempt to implicitly derive a new mechanism from parent by parsing global and ions from the parent string.

import arbor

cat = arbor.default_catalogue()

# Use the value of the Faraday constant as published by CODATA in 1986,
# and bind to pottasium ion species.
cat.derive('krev',  'nernst', globals={'F': 96485.309}, ions={'x': 'k'})

# Derive a reversal potential mechanism for sodium from the one we defined
# for potasium, which will inherit the redefined Faraday constant.
cat.derive('narev', 'krev', ions={'k': 'na'})

# Alternatively, we can derive a mechanism with global parameters and ion renaming
# specified in the parent name string.
cat.derive('krev_imp', 'nernst/F=96485.309,k')
cat.derive('carev', 'krev_imp/ca')
Parameters
  • name (str) – name of new derived mechanism.

  • parent (str) – name of parent mechanism.

  • globals (dict[str, float]) – a dictionary mapping global parameter names to their values, if any.

  • ions (dict[str, str]) – a dictionary renaming ion species, if any.