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: geneval_cvode.inc,v 1.1 2006/02/08 11:09:26 hines Exp $  
TITLE Kevins Cvode modified Generalized Hodgkin-Huxley eqn Channel Model 

COMMENT

Each channel has activation and inactivation particles as in the original
Hodgkin Huxley formulation.  The activation particle mm and inactivation
particle hh go from on to off states according to kinetic variables alpha
and beta which are voltage dependent.
Allows exponential, sigmoid and linoid forms (flags 0,1,2)
See functions alpha() and beta() for details of parameterization

ENDCOMMENT

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

NEURON {
	RANGE gmax, g, i
	GLOBAL erev, Inf, Tau, vrest
} : end NEURON

CONSTANT {
	  FARADAY = 96489.0	: Faraday's constant
	  R= 8.31441		: Gas constant

} : end CONSTANT

UNITS {
	(mA) = (milliamp)
	(mV) = (millivolt)
	(umho) = (micromho)
} : end UNITS

COMMENT
** Parameter values should come from files specific to particular channels

PARAMETER {
	erev 		= 0    (mV)
	gmax 		= 0    (mho/cm^2)

	maflag 		= 0
	malphaA 	= 0
	malphaB		= 0
	malphaV0	= 0
	mbflag 		= 0
	mbetaA 		= 0
	mbetaB		= 0
	mbetaV0		= 0
	exptemp		= 0
	mq10		= 3
	mexp 		= 0

	haflag 		= 0
	halphaA 	= 0
	halphaB		= 0
	halphaV0	= 0
	hbflag 		= 0
	hbetaA 		= 0
	hbetaB		= 0
	hbetaV0		= 0
	hq10		= 3
	hexp 		= 0
} : end PARAMETER
ENDCOMMENT

PARAMETER {
  cao                (mM)
  cai                (mM)
  celsius			   (degC)
  dt 				   (ms)
  v 			       (mV)
}

ASSIGNED {
	i (mA/cm^2)		
	g (mho/cm^2)
	Inf[2]		: 0 = m and 1 = h
	Tau[2]		: 0 = m and 1 = h
} : end ASSIGNED 

STATE { m h }

INITIAL { 
 	mh(v)
	m = Inf[0] h = Inf[1]
}

BREAKPOINT {

  LOCAL hexp_val, index, mexp_val, mexp2

  SOLVE states METHOD cnexp

  hexp_val = 1
  mexp_val = 1

  : Determining h's exponent value
  if (hexp > 0) {
    FROM index=1 TO hexp {
      hexp_val = h * hexp_val
    }
  }

  : Determining m's exponent value
  if (mexp > 0) {
    FROM index = 1 TO mexp {
      mexp_val = m * mexp_val
    }
  } else if (mexp<0) {
    mexp2=-mexp
    FROM index = 1 TO mexp2 {
      mexp_val = Inf[0] * mexp_val
    }
  }

  :			       mexp			    hexp
  : Note that mexp_val is now = m      and hexp_val is now = h 
  g = gmax * mexp_val * hexp_val

  iassign()
} : end BREAKPOINT

: ASSIGNMENT PROCEDURES
: Must be given by a user routines in parameters.multi
: E.G.:
:   PROCEDURE iassign () { i = g*(v-erev) ina=i }
:   PROCEDURE iassign () { i = g*ghkca(v) ica=i }

:-------------------------------------------------------------------

DERIVATIVE states {
  mh(v)
  m' = (-m + Inf[0]) / Tau[0] 
  h' = (-h + Inf[1]) / Tau[1]
}

:-------------------------------------------------------------------
: NOTE : 0 = m and 1 = h
PROCEDURE mh (v) {
  LOCAL a, b, j, qq10[2]

  qq10[0] = mq10^((celsius-exptemp)/10.)	
  qq10[1] = hq10^((celsius-exptemp)/10.)	

  : Calculater Inf and Tau values for h and m
  FROM j = 0 TO 1 {
    a = alpha (v, j)
    b = beta (v, j)

    if (j==1 && hexp==0) { Tau[j] = 1. Inf[j] = 1.
    } else {
      Inf[j] = a / (a + b)
      Tau[j] = 1. / (a + b) / qq10[j]
    }
  }
} : end PROCEDURE mh (v)

:-------------------------------------------------------------------
FUNCTION alpha(v,j) {
  LOCAL flag, A, B, V0
  if (j==1 && hexp==0) {
	  alpha = 0
  } else {

     if (j == 1) {
	  A = halphaA B = halphaB V0 = halphaV0+vrest flag = haflag
     } else {
	  A = malphaA B = malphaB V0 = malphaV0+vrest flag = maflag
     }

     if (flag == 1) { :  EXPONENTIAL
	 alpha = A*exp((v-V0)/B)	
     } else if (flag == 2) { :  SIGMOID
	 alpha = A/(exp((v-V0)/B)+1)
     } else if (flag == 3) { :  LINOID
	 if(v == V0) {
           alpha = A*B
         } else {
           alpha = A*(v-V0)/(exp((v-V0)/B)-1) }
     }
}
} : end FUNCTION alpha (v,j)

:-------------------------------------------------------------------
FUNCTION beta (v,j) {
  LOCAL flag, A, B, V0
  if (j==1 && hexp==0) {
	  beta = 1
  } else {

     if (j == 1) {
	  A = hbetaA B = hbetaB V0 = hbetaV0+vrest flag = hbflag
     } else {
	  A = mbetaA B = mbetaB V0 = mbetaV0+vrest flag = mbflag
     }

    if (flag == 1) { :  EXPONENTIAL
	 beta = A*exp((v-V0)/B)
     } else if (flag == 2) { :  SIGMOID
	 beta = A/(exp((v-V0)/B)+1)
     } else if (flag == 3) { :  LINOID
	 if(v == V0) {
            beta = A*B 
         } else {
            beta = A*(v-V0)/(exp((v-V0)/B)-1) }
     }
}
} : end FUNCTION beta (v,j)

:-------------------------------------------------------------------
FUNCTION FRT(temperature) {
	FRT = FARADAY * 0.001 / R / (temperature + 273.15)
} : end FUNCTION FRT (temperature)

:-------------------------------------------------------------------
 FUNCTION ghkca (v) { : Goldman-Hodgkin-Katz eqn
       LOCAL nu, efun

       nu = v*2*FRT(celsius)
       if(fabs(nu) < 1.e-6) {
               efun = 1.- nu/2.
       } else {
               efun = nu/(exp(nu)-1.) }

       ghkca = -FARADAY*2.e-3*efun*(cao - cai*exp(nu))
 } : end FUNCTION ghkca()

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