Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr 2012)

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Accession:141505
This model is an extension of a model (<a href="http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=138379">138379</a>) recently published in Frontiers in Computational Neuroscience. This model consists of 4700 event-driven, rule-based neurons, wired according to anatomical data, and driven by both white-noise synaptic inputs and a sensory signal recorded from a rat thalamus. Its purpose is to explore the effects of cortical damage, along with the repair of this damage via a neuroprosthesis.
Reference:
1 . Kerr CC, Neymotin SA, Chadderdon GL, Fietkiewicz CT, Francis JT, Lytton WW (2012) Electrostimulation as a prosthesis for repair of information flow in a computer model of neocortex IEEE Transactions on Neural Systems & Rehabilitation Engineering 20(2):153-60 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell;
Channel(s): I Chloride; I Sodium; I Potassium;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Deep brain stimulation; Information transfer; Brain Rhythms;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu]; Kerr, Cliff [cliffk at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; GabaA; AMPA; NMDA; Gaba; I Chloride; I Sodium; I Potassium; Gaba; Glutamate;
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neuroprosthesis
README
infot.mod *
intf6_.mod *
intfsw.mod *
misc.mod *
nstim.mod *
staley.mod *
stats.mod *
vecst.mod *
batch.hoc
boxes.hoc
bsmart.py
col.hoc
comparecausality.py
comparerasters.py
declist.hoc
decmat.hoc *
decnqs.hoc *
decvec.hoc
default.hoc *
drline.hoc *
filtutils.hoc
flexinput.hoc
grvec.hoc
infot.hoc *
init.hoc
intfsw.hoc
labels.hoc
local.hoc *
misc.h *
mosinit.hoc
network.hoc
nload.hoc
nqs.hoc
nqsnet.hoc
nrnoc.hoc
params.hoc
pyhoc.py
ratlfp.dat *
run.hoc
runsim
setup.hoc *
simctrl.hoc *
spkts.hoc *
staley.hoc *
stats.hoc *
stdgui.hoc *
syncode.hoc *
updown.hoc *
xgetargs.hoc *
                            
// $Id: nqsnet.hoc,v 1.65 2010/09/07 18:56:17 samn Exp $

print "Loading nqsnet..."

//      pre-id  post-id  pre#  post#   distance weight  syn-id   nc ptr  wt1 (eg AMPA+NMDA)
objref nq[2],sq[CTYPi][CTYPi],cp
obfunc mkcp0 () { localobj lo
  lo = new NQS("PRID","POID","STYP","PIJ","DIV","CONV","NSYN","NPRE")
  lo.useslist("PRID",CTYP) lo.useslist("POID",CTYP) lo.useslist("STYP",STYP)
  return lo
}

// CODE: PRID,POID,INCOL,COL1,COL2
obfunc mksp () { localobj lo
  lo=new NQS("CODE","PR","PO","DEL","WT0","WT1") // CODE==PRID(1),POID(2),COLA(3),COLB(4)
  lo.coddec("CODE")
  // lo.useslist("PRID",CTYP) lo.useslist("POID",CTYP) 
  return lo
}
sp=mksp()

//* Numbers and connectivity params

// layer return layer location with 'sublayer' defined by Inhib (+0.5) or other suffix
// E or I should be 1st letter of name, suffix letter will ideally dichotomize into late
// alphabet or early alphabet
func layer () { local x,in,la
  la=0
  if (sscanf(CTYP.o($1).s,"%c%d%c",&in,&x,&la)<2) return -1
  if (x==23) x=3 // layer 2/3
  if (in==73) x+=0.5 // ascii 73 is 'I'
  if (la>77) x+=0.2 // <='M'
  return x
}

//* routines
//** styp() sets synapse type based on presynaptic cell
func styp () { local pr,po
  pr=$1 po=$2
  if (pr==IN && po==IN) { return GA 
  } else if (pr==IN) { return IX
  } else if (pr==SU || pr==DP) { return EX
  } else if (pr==SM) { return AM
  } else if (strm(CTYP.o[pr].s,"^E")) { return EX
  } else if (strm(CTYP.o[pr].s,"^I")) { return IX
  } else printf("styp ERR %s->%s not classified",CTYP.object(pr).s,CTYP.object(po).s)
}

//** ellfld() place the cells inside an ellipse
// r for an ellipse = a*b/sqrt((a*sin(theta))^2 + (b*cos(theta))^2)
proc ellfld () { local a,b,ii,jj,p,seed localobj xv,yv,xo
  seed=239023229
  a=1 b=2
  p=allocvecs(xv,yv) vrsz(allcells*10,xv,yv)
  xv.setrnd(4,2*a,seed) yv.setrnd(4,2*b) xv.sub(a) yv.sub(b)
  jj=0
  for vtr2(&x,&y,xv,yv,&ii) {
    if (a*x^2+b*y^2<1) { ce.o(jj).xloc=x ce.o(jj).yloc=y jj+=1 }
    if (jj==ce.count) break
  }
  print ii,jj
  if (jj!=ce.count) print "Not filled"
  dealloc(p)
}

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