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 Comput Neurosci 21:119-29 [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];
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netmod
parbulbNet
README *
cadecay.mod *
flushf.mod *
kA.mod *
kca.mod *
kfasttab.mod *
kM.mod *
kslowtab.mod *
lcafixed.mod *
nafast.mod *
nagran.mod *
nmdanet.mod *
bulb.hoc
calcisilag.hoc *
ddi_baseline.gnu *
ddi_baseline.ses *
experiment_ddi_baseline.hoc *
experiment_odour_baseline.hoc *
granule.tem *
init.hoc *
input.hoc *
input1 *
mathslib.hoc *
mitral.tem *
modstat
mosinit.hoc *
odour_baseline.gnu *
odour_baseline.ses *
par_batch1.hoc
par_bulb.hoc
par_calcisilag.hoc
par_experiment_ddi_baseline.hoc
par_granule.tem
par_init.hoc
par_input.hoc
par_mitral.tem
par_netpar.hoc
par_notes
parameters_ddi_baseline.hoc *
parameters_odour_baseline.hoc *
screenshot.png *
tabchannels.dat *
tabchannels.hoc *
test1.sh
                            
TITLE Calcium decay
: as described in Bhalla and Bower, J. Neurophysiol. 69:1948-1983 (1993)
: Andrew Davison, The Babraham Institute, 1998
: partially based on cadecay.mod by Alain Destexhe, Salk Institute 1995.

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

NEURON{
	SUFFIX cad
	USEION ca READ ica, cai WRITE cai
	RANGE ica, channel_flow, depth, B
	GLOBAL cai, tau, cainf
}

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

CONSTANT {
        FARADAY = 96154 (coul)
	:FARADAY = 93149 (coul)		: moles do not appear in units
					: note this value is chosen to fit with
					: Genesis
}

PARAMETER {
	dt (ms)
	depth = 1 	(um)		: shell within which cai is calculated
					: to match Bhalla and Bower 1993 set
					: depth = diam/4 for each compartment
	tau = 10 	(ms)		: cai decay constant
	cainf = 1e-5	(mM)		: baseline calcium concentration
	ica		(mA/cm2)
}

STATE {
	cai		(mM)
}

INITIAL {
	cai = cainf
}

ASSIGNED {
	channel_flow	(mM/ms)
	B		(mM cm2/ms/mA)
}

BREAKPOINT {
	SOLVE state METHOD cnexp
}

DERIVATIVE state {
	B = -(1e4)/(2*FARADAY*depth)
	channel_flow = B*ica
	if (channel_flow <= 0.0 ) { channel_flow = 0.0 }	: one way flow in channel
	cai' = channel_flow  - (cai - cainf)/tau
}
	






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