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Python + NEURON
Interpreter
Neuron specific syntax
Range Variable
Mechanism

Compiled
Interpreter
Interpreter
Neuron specific syntax
Compiled
Installation
$ nrniv −python
$ nrniv −python
>>> from neuron import h
>>> print h
>>> h(’’’
. strdef s
. s = "hello"
. func square() { return $1*$1 }
. ’’’)
>>> h(’’’
. strdef s
. s = "hello"
. func square() { return $1*$1 }
. ’’’)
>>> print h.x, h.s, h.square(4)
>>> v = h.Vector(4).indgen().add(10)
>>> print v, len(v), v.size(), v.x[2], v[2]
>>> v = h.Vector(4).indgen().add(10)
>>> print v, len(v), v.size(), v.x[2], v[2]
>>> v.printf()
>>> for x in v: print x
>>>
>>> import numpy
>>> na = numpy.arange(0, 10, 0.00001) # 0.0131
>>> v = h.Vector(na) # 0.0197
>>> v.size()
>>> nb = numpy.array(v) # 0.0125
>>> nb[999999]
>>> b = list(v) # 0.0717
>>> for i in xrange(0, len(nb)):
. v.x[i] = na[i]
. # 3.7497
>>> def callback(a = 1, b = 2):
. print "callback: a=%d b=%d" % (a, b)
>>> fih = h.FInitializeHandler(callback)
>>> h.finitialize()
>>> def callback(a = 1, b = 2):
. print "callback: a=%d b=%d" % (a, b)
>>> fih = h.FInitializeHandler(callback)
>>> h.finitialize()
>>> fih = h.FInitializeHandler((callback,\
. (4, 5)))
>>> h.finitialize()
>>>
# assume hh soma model
vvec = h.Vector()
vvec.record(soma(.5)._ref_v, sec=soma)
# assume hh soma model
vvec = h.Vector()
vvec.record(soma(.5)._ref_v, sec=soma)
tvec = h.Vector()
tvec.record(h._ref_t, sec=soma)
# assume hh soma model
vvec = h.Vector()
vvec.record(soma(.5)._ref_v, sec=soma)
tvec = h.Vector()
tvec.record(h._ref_t, sec=soma)
g = h.Graph()
g.size(0, 5, −80, 40)
vvec.line(g, tvec)
>>> from neuron import h
>>> soma = h.Section(name = ’soma’)
>>> axon = h.Section()
>>> axon.connect(soma, 1)
>>> axon.nseg = 5
>>> h.topology()
‘−−−−| PySec_2b371cd17190(0−1) >>> axon.L = 1000
>>> axon.diam = 1
>>> for sec in h.allsec():
. sec.cm = 1
. sec.Ra = 100
. sec.insert(’hh’)
>>> axon.gnabar_hh = .1
>>> axon(.5).hh.gnabar = .09
>>> for seg in axon:
. print seg.x, seg.hh.gnabar
>>> stim = h.IClamp(.5, sec=soma)
>>> stim.delay = .5
>>> stim.dur = .1
>>> stim.amp = .4

Source: http://www.andrewdavison.info/media/slides/CodeJam3_Hines_NEURON.pdf

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