www.neuron.yale.edu

Code: Select all

begintemplate tpTCN 
	external newseed, grDur, stimulatortime
	public soma,vcell,gnoise,electrode,stimulator
	create soma
	objref vcell,gnoise,electrode,stimulator
	
	proc init() { 
		access soma
		soma {
			
			nseg = 1
			diam = 76.58
			L = 100
			cm = 1
			
			insert hh2	
			ena = 50
			ek = -100
			vtraub_hh2 = -52
			gnabar_hh2 = 0.01	
			gkbar_hh2 = 0.01 	
			
			insert itGHK
			cai = 2.4e-4 
			cao = 2 
			eca = 120 
			shift_itGHK = -1	
			gcabar_itGHK = 0.0002
			qm_itGHK = 2.5
			qh_itGHK = 2.5
			pcabar_itGHK = 8e-5
			
			insert cad
			depth_cad = 0.1
			kt_cad = 0 
			kd_cad = 1e-4
			taur_cad = 5
			cainf_cad = 2.4e-4	
			
			insert pas
			g_pas = 3.79e-5
			e_pas = -76.5
			cm = 0.88
			Ra = 173
			
			gnoise = new Gfluct(0.5) 
			gnoise.g_e0 = 0.0711
			gnoise.std_e = 0.005 
			gnoise.g_i0 = 0.1
			gnoise.std_i = 0.02
			gnoise.tau_e = 3 
			gnoise.tau_i = 10
			gnoise.E_e = 0
			gnoise.E_i = -75
			gnoise.new_seed(newseed())
			
			electrode = new PointProcessManager(0) 
			electrode.pp=new IClamp(0)
			electrode.pp.del=0
			electrode.pp.dur=grDur
			electrode.pp.amp=0 
		}
		
		vcell = new Vector()
		vcell.record(&soma.v(0.5))
		
		stimulator=new VectorPlay(1)
		stimulator.vy = new Vector(grDur+1) 
		stimulator.vx = stimulatortime 
		stimulator.vy.play(&electrode.pp.amp, stimulator.vx)
	}
endtemplate tpTCN

Code: Select all

rowsTCN=30
colsTCN=rowsTCN 
slabsTCN=2
objref TCN[colsTCN][rowsTCN][slabsTCN] 
for col=0, colsTCN-1 for row=0, rowsTCN-1 for slab=0, slabsTCN-1 {
	TCN[col][row][slab] = new tpTCN()
	TCN[col][row][slab].gnoise.g_e0 = .05
	print "created TCN[",col,"][",row,"][",slab,"]"
}

Code: Select all

t i
0 0
3.1 0
3.1 1
4.1 1
4.1 0
5 0

Code: Select all

template that defines cell class
create cell instances
attach IClamps
set up Vector play

Code: Select all

1.  create a program that does this
  template that defines cell class
  create cell instances
and test it

2.  add code that attaches IClamps and run a new test

3.  add code that sets up Vector play and run a new test

Code: Select all

proc run() {
	stdinit()
	while (t<grDur) {
		record voltage for all cells
		set amp for all cells
		fadvance()
	}
	record voltage for all cells
}

Code: Select all

COMMENT
isin.mod
Delivers sinusoidal current i = amp*sin(f*(t - del) + phi)
starting at t==del and ending at t==del+dur
where f is frequency in radians/s and phi is phase in radians
3/13/2009 NTC
ENDCOMMENT

NEURON {
  POINT_PROCESS Isin
  RANGE del, dur, f, phi, amp, i
  ELECTRODE_CURRENT i
}

UNITS {
  (nA) = (nanoamp)
  PI = (pi) (1)
  (Radian) = (1)
}

PARAMETER {
  del (ms)           : time at which current starts
  dur (ms) <0, 1e9>  : duration
  f (Radian/s) <0, 1e9> : frequency in radians/s
  phi (Radian)       : phase shift in radians
  amp (nA)
}

ASSIGNED {
  i (nA)
  on (1)
}

INITIAL {
  i = 0
  on = 0
  net_send(del, 1)
}

FUNCTION fsin(t (ms)) {
  fsin = sin(f*(t - del)/(1000) + phi)
}

BREAKPOINT {
  i = on*amp*fsin(t)
}

NET_RECEIVE (w) {
  : ignore any but self-events with flag == 1
  if (flag == 1) {
    if (on == 0) {
      : turn it on
      on = 1
      : prepare to turn it off
      net_send(dur, 1)
    } else {
      : turn it off
      on = 0
    }
  }
}