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 *
                            
objref compmap, allow, x

obfunc synaptic_compmap_construct () { local nrow, ncol  localobj f, s, tmpmap
/*
***************************************************************
Parameter, Description:
$1 thisno, maybe this double will be replaced in NEURON?
$2 num_postsynaptic_cells,  another double
// returned compmap(i,j), Matrix object=compartment #on postsyn cell j for ith presyn input
$3 num_presyninputs_perpostsyn_cell, a double 
$4 num_allowcomp, another double
$o5 allow, a Vector object of allowed postsyn compartments
$6 display, another double

c Construct a map of compartments at connections of one presynaptic
c cell to type to a postsynaptic cell type.
c compmap (i,j) = compartment number on postsynaptic cell j of its
c  i'th presynaptic input.
c display is an integer flag.  If display = 1, print compmap

        INTEGER thisno,
     &   num_postsynaptic_cells,
     &   num_presyninputs_perpostsyn_cell,
     &   compmap (num_presyninputs_perpostsyn_cell, 
     &                  num_postsynaptic_cells),
     &   num_allowcomp, allow(num_allowcomp)
c num_allowcomp = number of different allowed compartments
c allow = list of allowed compartments
        INTEGER i,j,k,l,m,n,o,p
        INTEGER display

        double precision seed, x(1)
***************************************************************
*/
//	print "arrived"
//	objref seed
	seed = new Vector()
        seed.append(377.e0)

        num_postsynaptic_cells = $2
	ncol=$2
        num_presyninputs_perpostsyn_cell = $3
	nrow=$3
	num_allowcomp = $4
	objref allow
	allow = $o5
	display = $6

	objref compmap
	compmap = new Matrix(num_presyninputs_perpostsyn_cell+1, num_postsynaptic_cells+1)
  if (!use_p2c_net_connections) {
//            map = 0
            k = 1
// print "num_postsynaptic_cells, num_presyninputs_perpostsyn_cell = ",num_postsynaptic_cells, num_presyninputs_perpostsyn_cell
// print "matrix size = ",compmap.nrow(),compmap.ncol()

        for ii = 1, num_postsynaptic_cells {
        for jj = 1, num_presyninputs_perpostsyn_cell {
            x = durand (seed, k, x)
// c This defines a compartment     
           LL = int ( x.x[0] * (num_allowcomp) ) + 1
//	 print "jj,ii: ",jj,ii, " LL=",LL
        if (LL > num_allowcomp) {
		print " unnexpected boundary issue in synaptic_compmap_construct()"
		LL = num_allowcomp
	}
// print allow.x(L)
           compmap.x[jj][ii] = allow.x[LL]

        }
        }

	thisno = $1
// c Possibly print out map when done.
       if ((display == 1) && (thisno == 0)) {
	print "SYNAPTIC COMPARTMENT MAP "
        for i = 1, num_postsynaptic_cells {
         printf("%6d %6d %6d\n", compmap.x(1,i), compmap.x(2,i), \
         compmap.x(num_presyninputs_perpostsyn_cell,i))               

        }
       }
  }else{
	// read from file created by port2colossus
	s = new String()
	sprint(s.s, "../../p2c/compmap/%s.dat", $s7)
//printf("%s %d %d\n", s.s, nrow, ncol)
	f = new File()
	f.ropen(s.s)
	tmpmap = new Matrix(ncol, nrow) // need to transpose
	tmpmap.scanf(f, ncol, nrow)
	tmpmap = tmpmap.transpose
	tmpmap.bcopy(0,0,nrow, ncol, 1, 1, compmap)
  }
       return compmap
}