Synchrony by synapse location (McTavish et al. 2012)

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Accession:144054
This model considers synchrony between mitral cells induced via shared granule cell interneurons while taking into account the spatial constraints of the system. In particular, since inhibitory inputs decay passively along the lateral dendrites, this model demonstrates that an optimal arrangement of the inhibitory synapses will be near the cell bodies of the relevant mitral cells.
Reference:
1 . McTavish TS, Migliore M, Shepherd GM, Hines ML (2012) Mitral cell spike synchrony modulated by dendrodendritic synapse location. Front Comput Neurosci 6:3 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell;
Channel(s): I Na,t; I A; I K;
Gap Junctions:
Receptor(s): GabaB; AMPA; NMDA;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Synchronization; Olfaction;
Implementer(s): McTavish, Thomas S [thomas.mctavish at yale.edu];
Search NeuronDB for information about:  Olfactory bulb main mitral GLU cell; Olfactory bulb main interneuron granule MC GABA cell; GabaB; AMPA; NMDA; I Na,t; I A; I K;
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mctavish_syncbylocation
src
ampanmda.mod
fi.mod
kamt.mod
kdrmt.mod
naxn.mod
ThreshDetect.mod *
allsynhinton.hoc *
analysis.py
animtest.py
antest.ses *
bulbspikes.py
clear.hoc
connect.hoc
control.ses
default.hoc
granule.hoc *
hinton.hoc
init.hoc *
iterator.hoc *
lptiter.hoc
mgrs.hoc
michele_movie.hoc
mitral.hoc
mosinit.hoc
net.hoc
param.hoc
params.py
parinit.hoc
pattern.hoc
perfrun.hoc
show.hoc
showw.hoc
somesyn.hoc *
sortspike *
split.hoc
start.hoc
start.ses
stimodors.hoc
subset.hoc
subset_control.ses *
synweightsnapshot.py
viewspikes.hoc
viewspikes1.hoc
weight_movie.hoc
weightsave.hoc
                            
// iterator over this cpu subset using lpt whole cell algorithm
// assuming a specified complexity for mitral and granule

objref lptiter_gidvec, pc
{load_file("loadbal.hoc")}
{load_file("mitral.hoc")}
{load_file("granule.hoc")}
{load_file("split.hoc")}

proc cxhelp() {localobj cell, lb, pc
	lb = new LoadBalance()
	cell = new Granule()
	cell.soma cxgranule = lb.cell_complexity()
	cell = new GranuleSpine()
	cell.neck cxspine = lb.cell_complexity()
	cell = new Mitral()
	cell.soma cxmitral = lb.cell_complexity()
	cell.secden[0] disconnect()
	cell.secden[1] disconnect()
	cell.secden[0] cxsecden = lb.cell_complexity()
	cell.soma cxmainum_mitral = lb.cell_complexity()
	lb.mt[1].select("FastInhib")
	cxfi = lb.m_complex_[1].x(lb.mt[1].selected())
	lb.mt[1].select("AmpaNmda")
	cxampa = lb.m_complex_[1].x(lb.mt[1].selected())
	lb.mt[1].select("ThreshDetect")
	cxtd = lb.m_complex_[1].x(lb.mt[1].selected())
	
	pc = new ParallelContext()
	if (1 && pc.id == 0) {
		printf("cxgranule=%g\n", cxgranule)
		printf("cxspine=%g\n", cxspine)
		printf("cxmitral=%g\n", cxmitral)
		printf("cxsecden=%g\n", cxsecden)
		printf("cxmainum_mitral=%g\n", cxmainum_mitral)
		printf("cxfi=%g\n", cxfi)
		printf("cxampa=%g\n", cxampa)
		printf("cxtd=%g\n", cxtd)
	}
	pc.gid_clear()
}
if (1) {
	cxhelp()
}else{
	cxgranule=216
	cxspine = 23
	cxmitral=1475
	cxsecden=602
	cxmainum_mitral=273
	cxfi=3
	cxampa=4
	cxtd=1
}
cxcpu = 0 // to be computed by lptiter_set

iterator cell_gids() { local i
	if (object_id(lptiter_gidvec) == 0) { lptiter_set() }
	for i=0, lptiter_gidvec.size-1 {
		$&1 = lptiter_gidvec.x[i]
		$&2 = i
		iterator_statement
	}
}

proc lptiter_set() {local i  localobj ldbal, cx, p, gid
	// gid and cx are parallel
	if (is_split) {
		// mitrals are split into three pieces
		// the main piece is given the standard whole
		// cell gid and consists of the soma, axon, primary
		// and tuft. The other two pieces are the left
		// and right secondary dendrite and have a
		// gid = mgid + splitbit*(secondary_index + 1)
		gid = new Vector(num_mitral*3 + num_granule)
		cx = gid.c
		for i=0, num_mitral-1 {
			gid.x[i] = i
			gid.x[num_mitral + i] = i + splitbit
			gid.x[2*num_mitral + i] = i + 2*splitbit
		}
		for i=0, num_granule-1 {
			gid.x[3*num_mitral + i] = num_mitral + i
		} 
		for i=0, gid.size-1 {
			cx.x[i] = fcx(gid.x[i])
		}
	}else{
		// for whole cells
		gid = new Vector(ncell)
		cx = new Vector(ncell)
		// for whole cells
		gid.indgen().add(num_mitral_begin)
		cx.fill(cxmitral, 0, num_mitral-1)
		if (num_granule > 0) {
			cx.fill(cxgranule, num_mitral, ncell - 1)
		}
		for i=0, num_mitral-1 {
			cx.x[i] += (cxfi + cxtd)*(how_many_syn_on_secden(i, 0) + how_many_syn_on_secden(i,1))
		}
		for i=num_mitral, ncell-1 {
			cx.x[i] += (cxtd+cxampa)*how_many_syn_on_granule(i-num_mitral)
		}
	}
	p = lptiter_lpt(cx, pnm.nhost, 0)
	lptiter_gidvec = p.c.indvwhere("==", pnm.myid)
	cx.index(cx, lptiter_gidvec)
	cxcpu = cx.sum
	lptiter_gidvec.index(gid, lptiter_gidvec)
//	printf("cxcpu=%g\n", cxcpu)
//	for i=0, lptiter_gidvec.size-1 { printf("%d %d\n", pnm.myid, lptiter_gidvec.x[i])}
}

// complexity of piece given the piece gid
func fcx() {
	if ($1 >= 2*splitbit) { //left mitral secden
		return cxsecden + (cxtd+cxfi)*how_many_syn_on_secden(basegid($1), 1)
	}else if ($1 >= splitbit) { // right mitral secden
		return cxsecden + (cxtd+cxfi)*how_many_syn_on_secden(basegid($1), 0)
	}else if ($1 >= num_mitral ) { // granule
		$1 -= num_mitral
		return cxgranule + (cxspine+cxtd+cxampa)*how_many_syn_on_granule($1)
	}else{ // main mitral
		return cxmainum_mitral
	}
}

// from loadbal.hoc
// least processing time algorithm
// $o1 is vector of weights  $2 is number of partitions
// return is vector of partition indices parallel to weights
obfunc lptiter_lpt() {local i, j  localobj wx, ix, pw
	if ($3) {
		print $o1.size, " piece weights"
		$o1.printf
	}
	wx = $o1.sortindex.reverse
	ix = new Vector($o1.size)
	pw = new Vector($2)
	for i=0, $o1.size-1 {
		j = wx.x[i]
		w = $o1.x[j]
		ip = pw.min_ind
		pw.x[ip] += w
		ix.x[j] = ip
	}
	if ($3) {
		print $2, " partition complexities"
		pw.printf
	}
	if (pw.mean) {
		thread_cxbal_ = pw.max/(pw.mean)
	}else{
		thread_cxbal_ = 1
	}
	return ix
}


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