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
                            
// parameters_ddi_baseline.hoc
// Olfactory bulb network model: parameters file
//   for dendrodendritic inhibition.
// Andrew Davison, The Babraham Institute, 2000.

nmitx       = 5			// 1st dimension of mitral cell array
nmity       = 5			// 2nd dimension of mitral cell array
nglom       = nmitx*nmity	// total number of mitral cells
g2m         = 10		// 
ngranx      = nmitx*g2m		// 1st dimension of granule cell array
ngrany      = nmity*g2m		// 2nd dimension of granule cell array
mitsep      = 1.0		// um	// mitral cell separation
gransep     = mitsep/g2m	// granule cell separation
seed        = 0			// seed for random number generator
rmax        = ngranx*0.5	// maximum range of synaptic connections
synpermit   = 200		// synapses per mitral cell
thresh      = -10       // mV	// threshold for detecting spikes
edelay      = 1.8       // ms	// time delay of mitral->granule synapses
conducdel   = 0		// ms	// conduction delay in secondary dendrites
idelay      = 0.6       // ms	// time delat of granule->mitral synapses
AMPAweight  = 1e-3	// uS	// }
NMDAweight  = 7e-4	// uS	// } synaptic conductances
iweight     = 6e-4	// uS	// }
maxinput    = 1.0	// nA	// measure of `odour intensity'
nof         = 10        	// number of `odour features'
diffglom    = 0			// } 0 - cells are in the same glomerulus
				// } 1 - cells are in different glomeruli
NMDArisetime = 30	// ms	// rise-time of NMDA conductance
NMDAdecay    = 343      // ms   // NMDA decay time constant
NMDArise     = 52       // ms   // NMDA rise time constant
mgconc 	    = 0		// mM	// external magnesium ion concentration
strdef fileroot
sprint(fileroot,"ddi_baseline")	// root for output filenames
odournumber = 1			// odour file
inputnumber = 1			// fixed input file
tstop	    = 1500	// ms	// total simulation time
ttrans	    = 0		// ms   // when calculating statistics, ignore
				// spikes occuring before this time
cvode.active(0)
dt 	    = 0.05	//ms

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