Parametric computation and persistent gamma in a cortical model (Chambers et al. 2012)

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Accession:144579
Using the Traub et al (2005) model of the cortex we determined how 33 synaptic strength parameters control gamma oscillations. We used fractional factorial design to reduce the number of runs required to 4096. We found an expected multiplicative interaction between parameters.
Reference:
1 . Chambers JD, Bethwaite B, Diamond NT, Peachey T, Abramson D, Petrou S, Thomas EA (2012) Parametric computation predicts a multiplicative interaction between synaptic strength parameters that control gamma oscillations. Front Comput Neurosci 6:53 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Axon; Synapse; Channel/Receptor; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex V1 interneuron basket PV GABA cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I A; I K; I K,leak; I K,Ca; I Calcium; I_K,Na;
Gap Junctions: Gap junctions;
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Parameter sensitivity;
Implementer(s): Thomas, Evan [evan at evan-thomas.net]; Chambers, Jordan [jordandchambers at gmail.com];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex V1 interneuron basket PV GABA cell; GabaA; AMPA; NMDA; I A; I K; I K,leak; I K,Ca; I Calcium; I_K,Na; Gaba; Glutamate;
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FRBGamma
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: $Id: rand.mod,v 1.1.1.1 2006/05/17 21:28:53 hines Exp $
COMMENT
$Header: /home/cvsroot/nrntraub/mod/rand.mod,v 1.1.1.1 2006/05/17 21:28:53 hines Exp $

Author: Stephen Fisher
Date:   December 1992
Email:  fisher@james.psych.yale.edu

Misc. random routines:
	fseed(seed)
		- set seed
		- return seed

	n_rand()
		- uniform distribution (0.0 <= rand < 1.0)

	fran(low, high)
		- returns random number between low and high

	u_rand()
		- uniform distribution (0.0 <= rand <= 1.0)

	norm()
		- gaussian distribution around 0

	pois(mean)
		- poisson distribution

	poisrand(mean)
		- integer poisson distribution using scop

** Note that with a SUFFIX equal to "nothing" these functions do not
have a suffix in hoc.  Thus to call norm() in hoc use simply type
"norm()" <- without the quotes.
ENDCOMMENT
					       
INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}

NEURON {
	SUFFIX nothing
}

VERBATIM
#include <stdlib.h>
#include <math.h>

#if 0
#include <values.h> /* contains MAXLONG */
#endif

/* Michael Hines fix for cygwin on mswin */
#if !defined(MAXLONG)
#include <limits.h>
#define MAXLONG LONG_MAX
#endif
/* some machines do not have drand48 and srand48 so use the implementation
at the end of this file */
extern double my_drand48();
extern void my_srand48();
#undef drand48
#undef srand48
#define drand48 my_drand48
#define srand48 my_srand48

extern double drand48();
#define random()                drand48()*MAXLONG
#define initstate(c1,c2,c3)     srand48(c1)

static long state2[32] = {
	470594912, 650447616, 310934240, 695012864, 850358912,
61088076, 481306752, 786902080, 224042800, 805177664, 938284096,
145937936, 622867968, 160207584, 977329216, 716234240, 127727624,
415316352, 870137472, 18664444, 330872224, 93728752, 914779200,
736261248, 643647616, 755802688, 213052336, 410240448, 218974736,
109419280, 178026128, 689569664
};
ENDVERBATIM



FUNCTION fseed(seed) {
VERBATIM
    initstate((unsigned)_lseed,(char *)state2,32);
	_lfseed = _lseed;
ENDVERBATIM
}


FUNCTION n_rand() { : 0.0 <= n_rand < 1.0
VERBATIM
    _ln_rand = ((double)random()) / (((double)MAXLONG) + 1.);
ENDVERBATIM
}


FUNCTION fran(l, h) { : returns random number between low and high
VERBATIM
{
	int low, high;
    double num, imax, *getarg();
    
	low = (int)_ll;
	high = (int)_lh;
    imax = high-low+1; /* the total number of numbers being used */
    _lfran = (double)(low + (int) (imax*n_rand()));  
}
ENDVERBATIM
}


FUNCTION u_rand() { : uniform distribution (0.0 <= rand <= 1.0)
VERBATIM
    _lu_rand = (((double)random()) / ((double)MAXLONG));
ENDVERBATIM
}
    

FUNCTION norm() { : gaussian distribution around 0
VERBATIM
{
    static int iset = 0;
    static float gset;
    float fac, r , v1, v2;
    double sqrt();

    if (iset == 0) {
        do {
	    	v1 = 2.0 * n_rand() - 1.0;
		    v2 = 2.0 * n_rand() - 1.0;
		    r = v1 * v1 + v2 * v2;
	    } while (r >= 1.0);

        fac = (float)sqrt(-2.0 * log(r) / r);
        gset = v1 * fac;
        iset = 1;
        _lnorm = v2 * fac;

    } else {
        iset = 0;
        _lnorm = (double)gset;
    }
}
ENDVERBATIM
}


FUNCTION pois(mean) { : poisson distribution
VERBATIM
    _lpois = - _lmean * log(((double)random()+1.) / ((double)MAXLONG+1.));
ENDVERBATIM
}

FUNCTION poisint(mean) {
  poisint = poisrand(mean)
}

VERBATIM
/* http://www.mit.edu/afs/athena/activity/c/cgs/src/math/drand48/ */
/*
 Michael Hines removed  all code not used by srand48 and drand48,
 the code handling non-floating point processor machines, and the
 pdp-11 fragment. Global names have my_ prefix added.
*/


/*	@(#)drand48.c	2.2	*/
/*LINTLIBRARY*/
/*
 *	drand48, etc. pseudo-random number generator
 *	This implementation assumes unsigned short integers of at least
 *	16 bits, long integers of at least 32 bits, and ignores
 *	overflows on adding or multiplying two unsigned integers.
 *	Two's-complement representation is assumed in a few places.
 *	Some extra masking is done if unsigneds are exactly 16 bits
 *	or longs are exactly 32 bits, but so what?
 *	An assembly-language implementation would run significantly faster.
 */
#define N	16
#define MASK	((unsigned)(1 << (N - 1)) + (1 << (N - 1)) - 1)
#define LOW(x)	((unsigned)(x) & MASK)
#define HIGH(x)	LOW((x) >> N)
#define MUL(x, y, z)	{ long l = (long)(x) * (long)(y); \
		(z)[0] = LOW(l); (z)[1] = HIGH(l); }
#define CARRY(x, y)	((long)(x) + (long)(y) > MASK)
#define ADDEQU(x, y, z)	(z = CARRY(x, (y)), x = LOW(x + (y)))
#define X0	0x330E
#define X1	0xABCD
#define X2	0x1234
#define A0	0xE66D
#define A1	0xDEEC
#define A2	0x5
#define C	0xB
#define SET3(x, x0, x1, x2)	((x)[0] = (x0), (x)[1] = (x1), (x)[2] = (x2))
#define SEED(x0, x1, x2) (SET3(x, x0, x1, x2), SET3(a, A0, A1, A2), c = C)

static unsigned x[3] = { X0, X1, X2 }, a[3] = { A0, A1, A2 }, c = C;
static unsigned short lastx[3];
static void next();

double
my_drand48()
{
	static double two16m = 1.0 / (1L << N);

	next();
	return (two16m * (two16m * (two16m * x[0] + x[1]) + x[2]));
}

static void
next()
{
	unsigned p[2], q[2], r[2], carry0, carry1;

	MUL(a[0], x[0], p);
	ADDEQU(p[0], c, carry0);
	ADDEQU(p[1], carry0, carry1);
	MUL(a[0], x[1], q);
	ADDEQU(p[1], q[0], carry0);
	MUL(a[1], x[0], r);
	x[2] = LOW(carry0 + carry1 + CARRY(p[1], r[0]) + q[1] + r[1] +
		a[0] * x[2] + a[1] * x[1] + a[2] * x[0]);
	x[1] = LOW(p[1] + r[0]);
	x[0] = LOW(p[0]);
}

void
my_srand48(seedval)
long seedval;
{
	SEED(X0, LOW(seedval), HIGH(seedval));
}

#if 0
#ifdef DRIVER
/*
	This should print the sequences of integers in Tables 2
		and 1 of the TM:
	1623, 3442, 1447, 1829, 1305, ...
	657EB7255101, D72A0C966378, 5A743C062A23, ...
 */
#include <stdio.h>

main()
{
	int i;

	for (i = 0; i < 80; i++) {
		printf("%4d ", (int)(4096 * my_drand48()));
		printf("%.4X%.4X%.4X\n", x[2], x[1], x[0]);
	}
}
#endif
#endif
ENDVERBATIM