Model of the cerebellar granular network (Sudhakar et al 2017)

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Accession:232023
"The granular layer, which mainly consists of granule and Golgi cells, is the first stage of the cerebellar cortex and processes spatiotemporal information transmitted by mossy fiber inputs with a wide variety of firing patterns. To study its dynamics at multiple time scales in response to inputs approximating real spatiotemporal patterns, we constructed a large-scale 3D network model of the granular layer. ..."
Reference:
1 . Sudhakar SK, Hong S, Raikov I, Publio R, Lang C, Close T, Guo D, Negrello M, De Schutter E (2017) Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer. PLoS Comput Biol 13:e1005754 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum golgi cell;
Channel(s): I A; I Calcium; I K; I K,Ca; I Na,t; I h; I Na,p; I T low threshold;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Glutamate; Gaba;
Simulation Environment: NEURON;
Model Concept(s): Spatio-temporal Activity Patterns; Oscillations; Synchronization; Winner-take-all;
Implementer(s): Hong, Sungho [shhong at oist.jp]; Guo, Daqing [dqguo at uestc.edu.cn]; Raikov, Ivan [ivan.g.raikov at gmail.com]; Publio, Rodrigo [publio at oist.jp]; De Schutter, Erik [erik at oist.jp];
Search NeuronDB for information about:  AMPA; NMDA; Gaba; I Na,p; I Na,t; I T low threshold; I A; I K; I h; I K,Ca; I Calcium; Gaba; Glutamate;
// Template for inhibitory connections between cerebellar Golgi cells
//
// Written by Shyam Kumar Sudhakar, Ivan Raikov, Tom Close, Rodrigo Publio, Daqing Guo, and Sungho Hong
// Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Japan
// Supervisor: Erik De Schutter
//
// Correspondence: Sungho Hong (shhong@oist.jp)
//
// September 16, 2017

begintemplate GoCtoGoC

external GolgiPop, step_time, numAxonGolgi, numGABAGoC, GoC_GoC_inh_con, GoC_GoC_gap_con, vGoCtoGoCgapsources, vGoCtoGoCgaptargets, vGoCtoGoCgapdistances, gseed
external GoC_GoC_gap_A1, GoC_GoC_gap_A2, GoC_GoC_gap_x0, GoC_GoC_gap_dx, GoC_GoC_gap_beta, GoC_GoC_gap_lambda
external BoltzmannPDF, ExpPDF,CV_gmax
objref par_gaps,pc,r,Golgigap,vGoCtoGoCgapsourcefinal, vGoCtoGoCgaptargetfinal, vGoCtoGoCgapdistancefinal
public vGoCtoGoCgaptargetfinal, vGoCtoGoCgapsourcefinal, vGoCtoGoCgapdistancefinal

objref  inhNCelem


func gap_create() {localobj pc

    pc = $o5

    // for each gap junction create two unique global id in all hosts
    gap_src_gid += 2

    if (pc.gid_exists($1)) {
	gap_create1($1, $2, gap_src_gid + 1, gap_src_gid, pc,$6)
    }
    if (pc.gid_exists($3)) {
	gap_create1($3, $4, gap_src_gid, gap_src_gid + 1, pc,$6)
    }
    return 1
}


proc gap_create1() {local loc localobj pc, c, g,rn

    pc = $o5

    c = pc.gid2obj($1)
    rn = new Random(gseed)
    rn.uniform(0,1)
    loc = rn.discunif(0,3)

    c.dend[loc] {

	g = new gap(.5)
        g.g = $6

        par_gaps.append(g)


	pc.target_var(&g.vgap, $3)
	pc.source_var(&v(.5), $4)
    }
}


proc init() { local i,j,dist,a,b,axonid,tgaps,disgap,g localobj nc,cell,receptor,r1,r2
    inhNCelem = new List()
    r = new Random(gseed)
    r1 = new Random(gseed)
    r.uniform(0,1)
    r2 = new Random(gseed)
    Golgigap = new Matrix(GolgiPop.nCells,GolgiPop.nCells)
    numGoC = GolgiPop.nCells

    par_gaps=new List()
    mGABA = 330e-6
    SDGABA = mGABA*CV_gmax
    del = 20
    thresh = -10

    pc = new ParallelContext()


    if (GoC_GoC_inh_con == 1) {

        for (i=pc.id; i < numGoC; i +=pc.nhost) {

	    cell = pc.gid2cell(i+GolgiPop.startindex)

	    // Connect GoC axons to GoC somas

	    if(cell.GoCID.size() >= 1) { // At least 1 GoC connection

        for j=0, cell.GoCID.size()-1 {
  		    axonid = cell.GoCID.x(j)
          dendno=r2.discunif(0,3)
  		    receptor = cell.gaba.object(dendno)

  		    nc = pc.gid_connect(axonid,receptor)

  		    if (cell.GoCdel.x(j)<=step_time){
                          nc.delay = step_time + step_time/10
  		    }else{
                          nc.delay=cell.GoCdel.x(j)
  		    }

  		    w=r1.normal(mGABA,SDGABA*SDGABA)
  		    nc.weight=w
            inhNCelem.append(nc)
        }

	    }

        }
    }

    // Vary extra GABA with CV_gmax
    for j=0, cell.gabaML.count()-1 {
        mGABA1 = cell.gabaML.object(j).g
        SDGABA1 = 0.01*mGABA1
        w = r1.normal(mGABA1, SDGABA1*SDGABA1)
        cell.gabaML.object(j).g = w
    }


    if (GoC_GoC_gap_con == 1) {

        vGoCtoGoCgapsourcefinal  = new Vector()
        vGoCtoGoCgaptargetfinal  = new Vector()
        vGoCtoGoCgapdistancefinal = new Vector()

        tgaps=0
        for k=0,vGoCtoGoCgapsources.size()-1 {

            // Connect GoC gap junctions

            dist = vGoCtoGoCgapdistances.x[k]

            prob = BoltzmannPDF(dist, GoC_GoC_gap_A1, GoC_GoC_gap_A2, GoC_GoC_gap_x0, GoC_GoC_gap_dx) / 100

            a  = vGoCtoGoCgapsources.x[k]
            b  = vGoCtoGoCgaptargets.x[k]

            // Check if this gap junction has already been created
            if (Golgigap.x[b][a]==1 || Golgigap.x[a][b]==1) {
                continue
            }

       	    Golgigap.x[a][b] = 1

            if (r.repick() <= prob) {

	        pre  = vGoCtoGoCgapsources.x[k]
	        post = vGoCtoGoCgaptargets.x[k]

	        tgaps=tgaps+1

                vGoCtoGoCgapsourcefinal.append(pre)
                vGoCtoGoCgaptargetfinal.append(post)
                vGoCtoGoCgapdistancefinal.append(vGoCtoGoCgapdistances.x[k])

                g = ExpPDF(dist,GoC_GoC_gap_beta,GoC_GoC_gap_lambda) / 1000 // convert to microsiemens

                //printf("Gap junction: dist = %g prob = %g g = %g\n", dist, prob, g)

                gap_create (pre, 0, post, 0, pc, g)

            }
        }
    }

pc.barrier()

printf("\nNumber of gap objects on host %d is %d\n",pc.id, par_gaps.count())
printf("Total gap junctions = %d", tgaps)


} // end init

endtemplate GoCtoGoC

objref ncGoCtoGoC[1]
ncGoCtoGoC[0] = new GoCtoGoC()