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Project: Testing 18.04
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Kernel: Python 3 (system-wide)

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

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

Add the library location to the search path

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

from neuron import h, __version__
__version__
'7.7.2'
soma = h.Section(name='soma')

h.psection()
soma { nseg=1 L=100 Ra=35.4 /*location 0 attached to cell 0*/ /* First segment only */ insert morphology { diam=500} insert capacitance { cm=1} }
1.0
soma.insert('pas')
soma
print("type(soma) = {}".format(type(soma)))
print("type(soma(0.5)) ={}".format(type(soma(0.5))))
type(soma) = <class 'nrn.Section'> type(soma(0.5)) =<class 'nrn.Segment'> 
mech = soma(0.5).pas
print(dir(mech))
['__class__', '__delattr__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__next__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', 'e', 'g', 'i', 'is_ion', 'name', 'segment'] 
print(mech.g)
0.001 
print(soma(0.5).pas.g)
0.001 
asyn = h.AlphaSynapse(soma(0.5))

print("asyn.e = {}".format(asyn.e))
print("asyn.gmax = {}".format(asyn.gmax))
print("asyn.onset = {}".format(asyn.onset))
print("asyn.tau = {}".format(asyn.tau))
asyn.e = 0.0 asyn.gmax = 0.0 asyn.onset = 0.0 asyn.tau = 0.1 
asyn.onset = 20
asyn.gmax = 1

h.psection()
soma { nseg=1 L=100 Ra=35.4 /*location 0 attached to cell 0*/ /* First segment only */ insert morphology { diam=500} insert capacitance { cm=1} insert pas { g_pas=0.001 e_pas=-70} insert AlphaSynapse { onset=20 tau=0.1 gmax=1 e=0} }
1.0
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)
Vector[1]
h.load_file('stdrun.hoc')
h.tstop = 40.0
h.run()
0.0
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()
Image in a Jupyter notebook