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]
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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 V1 L6 pyramidal corticothalamic GLU cell; Neocortex V1 L2/6 pyramidal intratelencephalic 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 V1 L6 pyramidal corticothalamic GLU cell; Neocortex V1 L2/6 pyramidal intratelencephalic 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
net
durand.hoc *
groucho.hoc
groucho_gapbld.hoc *
groucho_gapbld_mix.hoc *
groucho_traub.hoc
network_specification_interface.hoc *
serial_or_par_wrapper.hoc *
synaptic_compmap_construct.hoc *
synaptic_map_construct.hoc *
                            
// groucho_gapbld_mix.hoc
/*
****************************this is one big comment ************************
! 15 Nov. 2003, variation of groucho_gapbld.f to allow for gj
! between 2 cell populations, eg suppyrRS and suppyrFRB, or
! tuftRS and tuftIB.  Structure of gjtable as before, with col. 1
! giving cell of 1st type and col. 3 giving coupled cell of 2nd type.

      SUBROUTINE GROUCHO_gapbld_mix (thisno, numcells1, numcells2,
     & numgj, gjtable, allowedcomps, num_allowedcomps, display)
c       Construct a gap-junction network for groucho.f
$1 thisno double
$2 numcells1 = number of cells in 1st population.
$3 numcells2 = number of cells in 2nd population.
$4 numgj = total number of gj to be formed between these populations.
// this is the output: gjtable = table of gj's: each row is a gj.  
   Entries are: cell A, compartment on cell A; cell B, compartment on cell B
$o5 allowedcomps = a list of compartments where gj allowed to form
$6 num_allowedcomps = number of compartments in a cell on which a gj 
$7 display
c    might form.
! IT IS ASSUMED THAT ALLOWEDCOMPS AND NUM_ALLOWEDCOMPS SAME FOR
! THE 2 POPULATIONS.
c display is an integer flag.  If display = 1, print gjtable

        INTEGER thisno, numcells1, numcells2, numgj, gjtable(numgj,4),
     &    num_allowedcomps, allowedcomps(num_allowedcomps)
        INTEGER i,j,k,l,m,n,o,p, ictr /0/
c ictr keeps track of how many gj have been "built"
        INTEGER display

        double precision seed, x1(1), x2(1), y(2)
****************************this is one big comment ************************
*/
objref gjtable,x1, x2, y1
obfunc groucho_gapbld_mix() { // see note above for arguments:
	thisno  = $1
	numcells1 = $2
	numcells2 = $3
	numgj = $4
	allowedcomps = $o5
	num_allowedcomps = $6
	display = $7
//	print "Arrived at groucho_gapbld_mix with display = ",display

	seed = new Vector()
	seed.append(137.e0)
	objref gjtable
	gjtable = new Matrix(numgj+1, 4+1) // FORTRAN-like indicies start at 1

	ictr = 0

// 2
	while (ictr < numgj) {
		k = 1
	    not_unique = 1
	    while (not_unique) {
		x1 = durand (seed, k, x1) // durand returns vec c-style indicies
		x2 = durand (seed, k, x2)
// c This defines a candidate cell pair
                k = 2
		y = durand (seed, k, y)
// c This defines a candidate pair of compartments

		i = int ( x1.x[0] * numcells1 ) + 1
		j = int ( x2.x[0] * numcells2 ) + 1

// c Is the ORDERED cell pair (i,j) in the list so far?
// superfluous but true           if (ictr.eq.0) goto 1

		not_unique = 0
		for eL = 1, ictr {
		  if ((gjtable.x(eL,1) == i) && (gjtable.x(eL,3) == j)) {not_unique = 1}
		}
		if (one_tenth_ncell) {
			not_unique = 0
		}
	    } // loop replaces  if (p.eq.1) goto 2

// c Proceed with construction
// 1
	    ictr = ictr + 1
	    m = int ( y.x[0] * num_allowedcomps ) + 1
	    n = int ( y.x[1] * num_allowedcomps ) + 1

	    gjtable.x[ictr][1] = i
	    gjtable.x[ictr][3] = j
	    gjtable.x[ictr][2] = allowedcomps.x[m]
	    gjtable.x[ictr][4] = allowedcomps.x[n]

	} // loop replacing if (ictr.lt.numgj) goto 2

// c Possibly print out gjtable when done.
//	print "at end of groucho_gapbld_mix display = ",display,", thisno = ",thisno
	if ((display == 1) && (thisno == 0)) {
		print " MIX GJTABLE"
		for i = 1, numgj {
	          printf("%6d, %6d %6d %6d \n",gjtable.x(i,1), gjtable.x(i,2), \
                                       gjtable.x(i,3), gjtable.x(i,4))
		}
	}
//	print "successfully printed or not"
	return gjtable
}