Translating network models to parallel hardware in NEURON (Hines and Carnevale 2008)

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Accession:96444
Shows how to move a working network model written in NEURON from a serial processor to a parallel machine in such a way that the final result will produce numerically identical results on either serial or parallel hardware.
Reference:
1 . Hines ML, Carnevale NT (2008) Translating network models to parallel hardware in NEURON. J Neurosci Methods 169:425-55 [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): Simplified Models; Methods;
Implementer(s): Carnevale, Ted [Ted.Carnevale at Yale.edu]; Hines, Michael [Michael.Hines at Yale.edu];
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HinesCarnevaleJNM2007
ring
cell.hoc
ringpar.hoc
ringser.hoc
                            
begintemplate B_BallStick
public is_art
public init, topol, basic_shape, subsets, geom, biophys, geom_nseg, biophys_inhomo
public synlist, x, y, z, position, connect2target

public soma, dend
public all

objref synlist

proc init() {
  topol()
  subsets()
  geom()
  biophys()
  geom_nseg()
  synlist = new List()
  synapses()
  x = y = z = 0 // only change via position
}

create soma, dend

proc topol() { local i
  connect dend(0), soma(1)
  basic_shape()
}
proc basic_shape() {
  soma {pt3dclear() pt3dadd(0, 0, 0, 1) pt3dadd(15, 0, 0, 1)}
  dend {pt3dclear() pt3dadd(15, 0, 0, 1) pt3dadd(105, 0, 0, 1)}
}

objref all
proc subsets() { local i
  objref all
  all = new SectionList()
    soma all.append()
    dend all.append()

}
proc geom() {
  forsec all {  }
  soma {  /*area = 500 */ L = diam = 12.6157  }
  dend {  L = 200  diam = 1  }
}
external lambda_f
proc geom_nseg() {
  forsec all { nseg = int((L/(0.1*lambda_f(100))+.9)/2)*2 + 1  }
}
proc biophys() {
  forsec all {
    Ra = 100
    cm = 1
  }
  soma {
    insert hh
      gnabar_hh = 0.12
      gkbar_hh = 0.036
      gl_hh = 0.0003
      el_hh = -54.3
  }
  dend {
    insert pas
      g_pas = 0.001
      e_pas = -65
  }
}
proc biophys_inhomo(){}
proc position() { local i
  soma for i = 0, n3d()-1 {
    pt3dchange(i, $1-x+x3d(i), $2-y+y3d(i), $3-z+z3d(i), diam3d(i))
  }
  x = $1  y = $2  z = $3
}
obfunc connect2target() { localobj nc //$o1 target point process, optional $o2 returned NetCon
  soma nc = new NetCon(&v(1), $o1)
  nc.threshold = 10
  if (numarg() == 2) { $o2 = nc } // for backward compatibility
  return nc
}
objref syn_
proc synapses() {
  /* E0 */   dend syn_ = new ExpSyn(0.8)  synlist.append(syn_)
    syn_.tau = 2
  /* I1 */   dend syn_ = new ExpSyn(0.1)  synlist.append(syn_)
    syn_.tau = 5
    syn_.e = -80
}
func is_art() { return 0 }

endtemplate B_BallStick

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