NEURON

Configuration options

Adaptive time step integration

The default integration method used by the pyNN.neuron backend uses a fixed time step, specified by the timestep argument to the setup() function.

NEURON also supports use of variable time step methods, which can improve simulation speed:

setup(use_cvode=True)

If using cvode, there are two more optional parameters:

setup(cvode=True,
      rtol=0.001, # specify relative error tolerance
      atol=1e-4)  # specify absolute error tolerance

If not specified, the default values are rtol = 0 and atol = 0.001. For full details, see the CVode documentation

Todo

native_rng_baseseed is added to MPI.rank to form seed for SpikeSourcePoisson, etc., but I think it would be better to add a seed parameter to SpikeSourcePoisson

Todo

Population.get_data() does not yet handle cvode properly.

Using native cell models

A native NEURON cell model is described using a Python class (which may wrap a Hoc template). For this class to work with PyNN, there are a small number of requirements:

• the __init__() method should take just **parameters as its argument.

• instances should have attributes:

  • source: a reference to the membrane potential which will be

    monitored for spike emission, e.g. self.soma(0.5)._ref_v

  • source_section: the Hoc Section in which source is located.

  • parameter_names: a tuple of the names of attributes/properties of

    the class that correspond to parameters of the model.

  • traces: an empty dict, used for recording.

  • recording_time: should be False initially.

• there must be a memb_init() method, taking no arguments.

Here is an example, which uses the nrnutils package for conciseness:

from nrnutils import Mechanism, Section

class SimpleNeuron(object):

    def __init__(self, **parameters):
        hh = Mechanism('hh', gl=parameters['g_leak'], el=-65,
                       gnabar=parameters['gnabar'], gkbar=parameters['gkbar'])
        self.soma = Section(L=30, diam=30, mechanisms=[hh])
        self.soma.add_synapse('ampa', 'Exp2Syn', e=0.0, tau1=0.1, tau2=5.0)

        # needed for PyNN
        self.source_section = self.soma
        self.source = self.soma(0.5)._ref_v
        self.parameter_names = ('g_leak', 'gnabar', 'gkbar')
        self.traces = {}
        self.recording_time = False

    def _set_gnabar(self, value):
        for seg in self.soma:
            seg.hh.gnabar = value
    def _get_gnabar(self):
        return self.soma(0.5).hh.gnabar
    gnabar = property(fget=_get_gnabar, fset=_set_gnabar)

    # ... gkbar and g_leak properties defined similarly

    def memb_init(self):
        for seg in self.soma:
            seg.v = self.v_init

For each cell model, you must also define a cell type:

from pyNN.neuron import NativeCellType

class SimpleNeuronType(NativeCellType):
    default_parameters = {'g_leak': 0.0002, 'gkbar': 0.036, 'gnabar': 0.12}
    default_initial_values = {'v': -65.0}
    recordable = ['soma(0.5).v', 'soma(0.5).ina']
    units = {'soma(0.5).v' : 'mV', 'soma(0.5).ina': 'nA'}
    receptor_types = ['soma.ampa']
    model = SimpleNeuron

The requirement to explicitly list all variables you might wish to record in the recordable attribute is a temporary inconvenience, which will be removed in a future version.

It is now straightforward to use this cell type in PyNN:

from pyNN.neuron import setup, run, Population, Projection, AllToAllConnector, StaticSynapse
setup()
p1 = Population(10, SimpleNeuronType(g_leak=0.0003))
p1.record('soma(0.5).ina')
syn = StaticSynapse(weight=0.01, delay=0.5)
prj = Projection(p1, p1, AllToAllConnector(), syn, receptor_type='soma.ampa')
run(100.0)
output = p1.get_data()

If your model relies on other NMODL mechanisms, call the load_mechanisms() function with the path to the directory containing the .mod files.