Parametric computation and persistent gamma in a cortical model (Chambers et al. 2012)

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Accession:144579
Using the Traub et al (2005) model of the cortex we determined how 33 synaptic strength parameters control gamma oscillations. We used fractional factorial design to reduce the number of runs required to 4096. We found an expected multiplicative interaction between parameters.
Reference:
1 . Chambers JD, Bethwaite B, Diamond NT, Peachey T, Abramson D, Petrou S, Thomas EA (2012) Parametric computation predicts a multiplicative interaction between synaptic strength parameters that control gamma oscillations. Front Comput Neurosci 6:53 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Axon; Synapse; Channel/Receptor; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex V1 interneuron basket PV GABA cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s): I A; I K; I K,leak; I K,Ca; I Calcium; I_K,Na;
Gap Junctions: Gap junctions;
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Parameter sensitivity;
Implementer(s): Thomas, Evan [evan at evan-thomas.net]; Chambers, Jordan [jordandchambers at gmail.com];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; Neocortex L2/3 pyramidal GLU cell; Neocortex V1 interneuron basket PV GABA cell; GabaA; AMPA; NMDA; I A; I K; I K,leak; I K,Ca; I Calcium; I_K,Na; Gaba; Glutamate;
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FRBGamma
hoc
balcomp.hoc *
defvar.hoc *
lbcreate.hoc *
mscreate.hoc *
parlib.hoc
parlib_traub.hoc
parlib2.hoc
traubcon.hoc *
traubcon_net.hoc *
                            
objref netstims, netstim_netcons, netstim_randoms
netstims = new List()
netstim_netcons = new List()
netstim_randoms = new List()
netstim_random_seedoffset = ranseedbase + pnm.ncell // increment by number of Cells
splitbit = 2^28

func targetcomp_exists() {local spgid
	if (load_balance_phase == 3 || load_balance_phase == 7) {
		spgid = thishost_gid($1)
		if (spgid < 0) { return -1 }
		if (pc.gid_exists(spgid)) {
			if (section_exists("comp", $2, pc.gid2obj(spgid))) {
				return spgid
			}
		}
	}else{
		if (pc.gid_exists($1)) {
			return $1
		}
	}
	return -1
}

func target_exists() {local spgid
	if (load_balance_phase == 3 || load_balance_phase == 7) {
		spgid = thishost_gid($1)
		if (spgid < 0) { return -1 }
		if (pc.gid_exists(spgid)) {
			return spgid
		}
	}else{
		if (pc.gid_exists($1)) {
			return $1
		}
	}
	return -1
}

proc par_netstim_create() {local gid  localobj cell, syn, nc, ns, r
	if (!use_ectopic) { return }
	if ((gid = targetcomp_exists($1, $2)) >= 0) {
		cell = pc.gid2obj(gid)
		cell.comp[$2] {syn = new PulseSyn(.5)}
		syn.amp = $3
		ns = new S_NetStim()
		ns.pp.interval = $4
		netstims.append(ns)
		nc = new NetCon(ns.pp, syn)
		netstim_netcons.append(nc)
		nc.delay = 0
		r = new Random()
		r.negexp(1)
//		r.Isaac64(netstim_random_seedoffset + netstim_base_)
		r.MCellRan4(netstim_random_seedoffset + 1000*netstim_base_)
		ns.pp.noiseFromRandom(r)
		netstim_randoms.append(r)
	}
	netstim_base_ += 1
}

begintemplate gGap
proc init() {
	execerror("gGap not available. use gGapPar instead.", "")
}
endtemplate gGap

objref par_gaps
par_gaps = new List()
gap_src_gid = 2

objref rangap
if (one_tenth_ncell) {
	rangap = new Random()
	rangap.MCellRan4(1)
	rangap.uniform(0,1)
	ranfrac=.1
}

proc par_gap_create() { local gid
	if (!use_gap) { return }
	if (object_id(rangap)) {
		if (rangap.repick() > ranfrac) { return }
	}
	gap_src_gid += 2
	if ((gid = targetcomp_exists($1, $2)) >= 0) {
		par_gap_create1(gid, $2, gap_src_gid + 1, gap_src_gid, $5)
	}
	if ((gid = targetcomp_exists($3, $4)) >= 0) {
		par_gap_create1(gid, $4, gap_src_gid, gap_src_gid + 1, $5)
	}
}
proc par_gap_create1() {localobj c, g
	c = pc.gid2obj($1)
	c.comp[$2] {
		g = new gGapPar(.5)
		par_gaps.append(g)
		pc.target_var(g, &g.vgap, $3)
		pc.source_var(&v(.5), $4)
		g.g = $5
	}
}

icdel0_ = 0
cdel0_ = 0

func nc_append() {local targid, comp  localobj cell, syn, s
	targid = target_exists($2)
	if ($5 <= 0) {
//		if (targid >= 0) {
//			print pc.id, $1, $2, targid, $3, $4, $5, " ", pc.gid2obj(targid)
//		}
		if (icdel0_ == 0) if ((pc.gid_exists($1)!=0) != (targid != 0)) {
if (pmesg) print "Notice: Requesting an interprocessor connection delay of 0"
			icdel0_ = 1
		}
		if (cdel0_ == 0) {
if (pmesg) print "Notice: Requesting a connection delay of 0. Setting those to 1ms."
			cdel0_ = 1
		}
		$5 = 1
	}
	if ($5 < mindelay_) if (pc.gid_exists($1) == 0) if (targid >= 0) {
		mindelay_ = $5
	}

	if (targid >= 0) {
		cell = pc.gid2cell(targid)
		syn = cell.synlist.object($3)
		s = new String()
		classname(syn, s.s)
		if (strcmp(s.s, "GABAA") == 0) {
			syn.e = vgaba.x[cell.type]
		}
		// for debugging :need to switch the debug lines in
		// ampa.mod, traub_nmda.mod, and gabaa.mod
	    if (0) {
		syn.get_loc
		comp = -1
		sscanf(secname(), "%*[^0-9]%*d%*[^0-9]%d",&comp)
		pop_section()
		syn.srcgid = $1
		syn.targid = $2
		syn.synid = $3
		syn.comp = comp
	    }
	}
	if (targid >= 0) {
		return pnm.nc_append($1, targid, $3, $4, $5)
	}else{
		return -1
	}
}

proc set_const_curr_inj() {local i, gid  localobj c, clmp
	if (!use_inject) { return }
	for i = 1, $2 if ((gid = targetcomp_exists($1+i, 1)) >= 0) {
		c = pc.gid2obj(gid)
		c.comp[1] clmp = new IClamp_const(0.5)
		clmp.amp = $o3.x[i]
		iclamp_const_list.append(clmp)
	}
}

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