NEURON simulation environment

The NEURON simulation environment is used in laboratories and classrooms around the world for building and using computational models of neurons and networks of neurons.

https://www.neuron.yale.edu/neuron/

Kernel: Python 3 (system-wide)

CoCalc Setup

important unset DISPLAY, otherwise gui is loading and neron crashes

In [1]:

import os
if 'DISPLAY' in os.environ:
    del os.environ['DISPLAY']

Add the library location to the search path

In [2]:

import sys
sys.path.insert(0, '/usr/local/nrn/lib/python/')

First Steps

see https://neuron.yale.edu/neuron/static/docs/neuronpython/firststeps.html

In [3]:

from neuron import h, __version__
__version__

In [4]:

soma = h.Section(name='soma')

In [5]:

h.psection()

In [6]:

soma.insert('pas')

In [7]:

print("type(soma) = {}".format(type(soma)))
print("type(soma(0.5)) ={}".format(type(soma(0.5))))

In [8]:

mech = soma(0.5).pas
print(dir(mech))

In [9]:

print(mech.g)

In [10]:

print(soma(0.5).pas.g)

In [11]:

asyn = h.AlphaSynapse(soma(0.5))

In [12]:

print("asyn.e = {}".format(asyn.e))
print("asyn.gmax = {}".format(asyn.gmax))
print("asyn.onset = {}".format(asyn.onset))
print("asyn.tau = {}".format(asyn.tau))

In [13]:

asyn.onset = 20
asyn.gmax = 1

In [14]:

h.psection()

In [15]:

v_vec = h.Vector()  # Membrane potential vector
t_vec = h.Vector()  # Time stamp vector
v_vec.record(soma(0.5)._ref_v)
t_vec.record(h._ref_t)

In [16]:

h.load_file('stdrun.hoc')
h.tstop = 40.0
h.run()

In [17]:

from matplotlib import pyplot
pyplot.figure(figsize=(8, 4))  # Default figsize is (8,6)
pyplot.plot(t_vec, v_vec)
pyplot.xlabel('time (ms)')
pyplot.ylabel('mV')
pyplot.show()

In [0]: