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];
/
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
                            
// init.hoc
// Olfactory bulb network model: initialisation file
// Andrew Davison, The Babraham Institute, 2000.

if (!name_declared("thresh")) {
	thresh = 0 // just need to declare, see parameters*.hoc for real value
}

objref exptBox, ctrlBox
strdef filename
quitmodel = 0

exptBox = new VBox()
exptBox.intercept(1)
  xpanel("Experiments")
    xlabel("Choose an experiment:")
    xradiobutton("Response to olfactory nerve shock (Fig. 2)", "run_experiment(\"ddi_baseline\")")
    xradiobutton("Response to odour stimulus (Fig. 8)","run_experiment(\"odour_baseline\")")
  xpanel()
  xpanel("Controls",1)
    xbutton("Quit","quit()")
  xpanel()
exptBox.intercept(0)
exptBox.map("Olfactory bulb network model",0,80,-1,-1)

proc run_experiment() {
  exptBox.unmap()
  ctrlBox = new VBox()
  ctrlBox.intercept(1)
    xpanel("Progress")
    xlabel("The network is being created. This may take some time.")
    xpanel()
  ctrlBox.intercept(0)
  ctrlBox.map("Olfactory bulb network model",0,80,-1,-1)
  xopen("mathslib.hoc")			// mathematical procedures
if (pnm.myid == 0)  print "Reading channel tables"
  xopen("tabchannels.hoc")		// channel tables
if (pnm.myid == 0)  print "Reading mitral cell template"
  xopen("par_mitral.tem")		// mitral cell template
if (pnm.myid == 0)  print "Reading granule cell template"
  xopen("par_granule.tem")		// granule cell template
if (pnm.myid == 0)  print "Reading parameters"
  sprint(filename,"parameters_%s.hoc",$s1)
  xopen(filename)                       // model parameters
if (pnm.myid == 0)  print "Creating network"
  xopen("par_bulb.hoc")			// model set-up
if (pnm.myid == 0)  print "Reading input procedures"
  xopen("par_input.hoc")		// define procedures to set-up input
if (pnm.myid == 0)  print "Setting-up experiment"
  sprint(filename,"par_experiment_%s.hoc",$s1)
  xopen(filename)                       // which parameters to record
  ctrlBox.unmap()
  ctrlBox = new VBox()
  ctrlBox.intercept(1)
  xpanel("Instructions")
    xlabel("* To run the simulation, click on [Init & Run].")
    xlabel("* When the simulation is complete, click on [Save Results].")
    xlabel("* If you wish to run a different experiment, you will have")
    xlabel("   to quit NEURON and restart.")
  xpanel()
  xpanel("Controls",1)
    xbutton("Quit","quit()")
    xlabel(" ")
    xbutton("Save results","print_results()")
  xpanel()
  ctrlBox.intercept(0)
  ctrlBox.map("Olfactory bulb network model",0,80,-1,-1)
  
/*
  print "Initialisation complete"
  print ""
  print "To run the simulation, click on [Init & Run]."
  print "When the simulation is complete, click on [Save Results]."
  print "If you have gnuplot (http://www.gnuplot.info) installed"
  print "on your computer, you can produce a figure by running"
  print "gnuplot with the file ", $s1, ".gnu"
*/
}


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