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];
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netmod
parscalebush
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
myfit.mod
na.mod
nafRT03.mod *
nap.mod
napRT03.mod *
NMDA.mod *
nstim.mod
stats.mod
vecst.mod
batch.hoc
bg
bg_cvode.inc
boltz_cvode.inc
geneval_cvode.inc
geom.hoc
init.hoc
netcon.inc
network.hoc
nqsnet.hoc
nspike.dat
params.hoc
parnetwork.hoc
parnqsnet.hoc
perfrun.hoc
prebatch_.hoc
run.hoc
spkplt.hoc *
x_vs_nspike.hoc
                            
: $Id: netcon.inc,v 1.1 2006/02/08 11:09:26 hines Exp $

COMMENT
USAGE: for most receptors
 *****************************************************************************
    NEURON {
      POINT_PROCESS NAME
    }

    PARAMETER {
      Cdur	= 1.08	(ms)		: transmitter duration (rising phase)
      Alpha	= 1	(/ms mM)	: forward (binding) rate
      Beta	= 0.02	(/ms)		: backward (unbinding) rate
      Erev	= -80	(mV)		: reversal potential
    }
    
    INCLUDE "netcon.inc"
 *****************************************************************************

USAGE: for NMDA receptor
 *****************************************************************************
    NEURON{ POINT_PROCESS NMDA
      RANGE B 
    }

    PARAMETER {
      mg        = 1.    (mM)     : external magnesium concentration
      Cdur	= 1.	(ms)	 : transmitter duration (rising phase)
      Alpha	= 4.	(/ms mM) : forward (binding) rate
      Beta	= 0.0067 (/ms)	 : backward (unbinding) rate 1/150
      Erev	= 0.	(mV)	 : reversal potential
    }

    ASSIGNED { B }

    INCLUDE "netcon.inc"
    : EXTRA BREAKPOINT MUST BE BELOW THE INCLUDE
    BREAKPOINT {
      rates(v)
      g = g * B : but don't really need to readjust conductance
      i = i * B : i = g*(v - Erev)
    }

    PROCEDURE rates(v(mV)) {
      TABLE B
      DEPEND mg
      FROM -100 TO 80 WITH 180
      B = 1 / (1 + Exp1(0.062 (/mV) * -v) * (mg / 3.57 (mM)))
    }
 *****************************************************************************
ENDCOMMENT

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

NEURON {
  RANGE g, Erev, fflag
  NONSPECIFIC_CURRENT i
  GLOBAL Cdur, Alpha, Beta, Rinf, Rtau
}

UNITS {
  (nA) = (nanoamp)
  (mV) = (millivolt)
  (umho) = (micromho)
  (mM) = (milli/liter)
}

PARAMETER {
  fflag = 0
}

ASSIGNED {
  v		(mV)		: postsynaptic voltage
  i 		(nA)		: current = g*(v - Erev)
  g 		(umho)		: conductance
  Rinf				: steady state channels open
  Rtau		(ms)		: time constant of channel binding
  synon
}

STATE {Ron Roff}

INITIAL {
  Rinf = Alpha / (Alpha + Beta)
  Rtau = 1 / (Alpha + Beta)
  synon = 0
}

BREAKPOINT {
  SOLVE release METHOD cnexp
  g = (Ron + Roff)*1(umho)
  i = g*(v - Erev)
}

DERIVATIVE release {
  Ron' = (synon*Rinf - Ron)/Rtau
  Roff' = -Beta*Roff
}

: following supports both saturation from single input and
: summation from multiple inputs
: if spike occurs during CDur then new off time is t + CDur
: ie. transmitter concatenates but does not summate
: Note: automatic initialization of all reference args to 0 except first

NET_RECEIVE(weight, on, nspike, r0, t0 (ms)) {
  : flag is an implicit argument of NET_RECEIVE and  normally 0
  if (t>0) { : bug fix so that init doesn't send a false event
    if (flag == 0) { : a spike, so turn on if not already in a Cdur pulse
      nspike = nspike + 1
      if (!on) {
        r0 = r0*Exp1(-Beta*(t - t0))
        t0 = t
        on = 1
        synon = synon + weight
        Ron = Ron + r0
        Roff = Roff - r0
      }
      : come again in Cdur with flag = current value of nspike
      net_send(Cdur, nspike)
    }
    if (flag == nspike) { : if this associated with last spike then turn off
      r0 = weight*Rinf + (r0 - weight*Rinf)*Exp1(-(t - t0)/Rtau)
      t0 = t
      synon = synon - weight
      Ron = Ron - r0
      Roff = Roff + r0
      on = 0
    }
  }
}

FUNCTION Exp1(x) {   
  if (x < -100) {
    Exp1  = 0
  } else if (x > 100) {
    Exp1 = exp(100)
  } else{
    Exp1 = exp(x)
  }
}

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