introduce a specific type of noise

Anything that doesn't fit elsewhere.
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neurite
Posts: 13
Joined: Fri Jun 22, 2007 2:06 pm
Location: Boston University

introduce a specific type of noise

Post by neurite »

I would like to introduce a very specific type of noise to one of my channels. From the code below, I essentially need to add the variable 'dpz' to 'm' at very time step. I thought the code would work, but it doesn't. Please advise.

Code: Select all

NEURON {
	SUFFIX nap_ch
	USEION na READ ena WRITE ina
	RANGE gnabar, gna, ina
	GLOBAL m_inf
}

UNITS {
	(S) = (siemens)
	(mV) = (millivolt)
	(mA) = (milliamp)
}

PARAMETER { 

	gnabar = 0.0001 (S/cm2) 
	ena = 45 (mV)
}

ASSIGNED {
	v (mV)
	ina (mA/cm2)
	gna (S/cm2)
	m_inf
	
}

STATE { m }

BREAKPOINT {
	SOLVE states METHOD cnexp
	
	gna = gnabar * m
	ina = gna * (v - ena)
}


INITIAL {
	m = m_inf
}

DERIVATIVE states {
	rates(v)
	noise(m)
	UNITSOFF
	m' = (m_inf - m)/0.1 
	UNITSON
}



PROCEDURE rates(v (mV)) {
	
	m_inf = (1/(1+exp(-(v+50)/3.0 (mV))))
}

PROCEDURE noise(m) {

	LOCAL randflag, dpa, dpb, dpz

	:generate the random term
	srand ( time(NULL) )
	

	:generate randomflag between 0 and 1
	randflag = roundf(rand()/(2^31-1))
	
	if (randflag == 1){
		dpa = cos(2*(22/7)*rand()/(2^31-1))
	}
	
	if (randflag == 0){
		dpa = sin(2*(22/7)*rand()/(2^31-1))
	}


	dpb = -2*.001*(m_inf + m - 2*m_inf*m)/(300*.1)

	dpz = dpa*(dpb*log(rand()/(2^31-1)))^(1/2)

	m = m + dpz 
	
	if (m<0)
	{
             m=0
        }
           
        if (m>1)
	{
             m=1
        }
}

hines
Site Admin
Posts: 1599
Joined: Wed May 18, 2005 3:32 pm

Post by hines »

I assume you are using mswin since
on that machine you can only call
functions in the nrniv.exe file that
are listed in an export file and srand
and rand do not exist in the executable anyway. So you need to use either the built-in random generators, scop_rand, or Random
(for the latter, see src/nrnoc/netstim.mod for how to connect a hoc Random instance for use in a mod file) or else put a c implementation of a random function into a VERBATIM block in the mod file. There are examples of this in ModelDB. Search for drand48 or srand48.

neurite
Posts: 13
Joined: Fri Jun 22, 2007 2:06 pm
Location: Boston University

Post by neurite »

thanks for the pointer Michael, but it still doesn't really address the issue of adding an varying value to m at every time step.

patoorio
Posts: 81
Joined: Wed Jan 30, 2008 12:46 pm

Re: introduce a specific type of noise

Post by patoorio »

Why don't you just do something like

Code: Select all

DERIVATIVE states { 
rates(v) 
dpz=whatever-random-function-you-want
UNITSOFF 
m' = (m_inf - m + dpz)/0.1 
UNITSON 
} 
instead of 'manually' adding the random value in a separate procedure?

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