Parallel network simulations with NEURON (Migliore et al 2006)

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Accession:64229
The NEURON simulation environment has been extended to support parallel network simulations. The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters.
Reference:
1 . Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
/
netmod
parbush
data
AMPA.mod *
arhRT03.mod *
cadecay.mod
cadRT03.mod
cah.mod
calRT03.mod
catRT03.mod *
GABAa.mod *
GABAb.mod *
intf.mod
k2RT03.mod *
kahpRT03.mod
kaRT03.mod *
kca.mod *
kcRT03.mod
kdr.mod
kdrp.mod
kdrRT03.mod *
kmRT03.mod *
misc.mod
na.mod
nafRT03.mod *
nap.mod
napRT03.mod *
NMDA.mod *
nstim.mod
vecst.mod
batch_.hoc
bg_cvode.inc
boltz_cvode.inc
geneval_cvode.inc
modstat
netcon.inc
test1.sh
xtmp
                            
: $Id: kca.mod,v 1.1 2006/02/08 11:09:26 hines Exp $
TITLE Calcium-dependent potassium conductance
: Paul Bush 4.1.92  No warranties expressed or implied.
: Rate constants are not temperature sensitive

INDEPENDENT {t FROM 0 TO 1 WITH 10 (ms)}

NEURON {
	SUFFIX kca
	USEION ca READ cai
	USEION k WRITE ik
	RANGE gmax, g, i, o_rate, c_rate, o
	GLOBAL erev, cadep, maxc_rate, cainit
}

UNITS {
	(molar) = (1/liter)
	(mM)	= (millimolar)
	(mA)	= (milliamp)
	(mV) = (millivolt)
}

PARAMETER {
	gmax = 0.015	(mho/cm2)
	erev = -90	(mV)
	cadep = 2
	maxc_rate = 0.1 (1/ms)
	cai		(mM)
	v		(mV)
	o_rate = 0	(1/ms)
	c_rate = 0	(1/ms)
	cainit = 5e-5	(mM)
}

ASSIGNED { 
	ik	(mA/cm2) 
	i	(mA/cm2)
        g       (mho/cm^2)
	o		: fraction of channels open
}

STATE {
	c		: fraction of channels closed
}

BREAKPOINT {

	rates(cai)
	SOLVE state METHOD cnexp
	o = 1-c
        g = gmax*o
	i = g*(v-erev) ik=i 
}

DERIVATIVE state {

	c' = c_rate - (c_rate + o_rate)*c
}

PROCEDURE rates(cai) {	: calculate rate constants

	TABLE o_rate, c_rate DEPEND cainit, cadep, maxc_rate FROM cainit TO 0.1 WITH 200

	o_rate = (cai - cainit) * cadep
	if (o_rate > 0) { c_rate = 1/o_rate
		if (c_rate > maxc_rate) { c_rate = maxc_rate }
			}
	else { c_rate = maxc_rate  }
}


INITIAL {
    rates(cai)
    o = o_rate/(o_rate+c_rate)
    c = 1-o
}





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