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]
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;
// Initialization of the simulation
//
// 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

load_file("nrngui.hoc")
load_file("vecevent.ses")
objref cvode,MFtoGCfile,MFtoGCfile1,MFtoGCfile2,MFtoGoCfile,pc1,IndexfileGoC
objref GoCtoGCfile,PFtoGoCfile,AxontoGoCfile,IndexfileGC
objref MFGoCtotalfile,MFGCtotalfile,PFGoCtotalfile,AxonGoCtotalfile
objref GoCcoordinatesfile, GCcoordinatesfile, MFcoordinatesfile, MFspikefile
objref GoCspiketimefile, cvector,GCspiketimefile, VMGoCfile, VMGCfile,BCSpikefile
objref PFtoSCfile, PFtoBCfile, PFSCtotalfile, PFBCtotalfile, BCgapfile,gapconfile,BCtoBCfile,SCSpikeFile
objref SCcoordinatesfile, BCcoordinatesfile,SCGapFile,SCtoSCFile
objref rand,timefile, Vtime, MFBundleCenter,MFBundleCenter_file
objref StellatePop , BasketPop


rand = new Random()
rand.uniform(-80,60)
pc1=new ParallelContext()
cvode = new CVode(0)
cvector = new Vector()
cvode.active(0)
use_mcell_ran4(1)
//cvode.use_local_dt(1)
st = pc1.time

// load global Parameters
xopen("Parameters.hoc")
//  model functions
xopen("utilities.hoc")
// conectivity rules and synaptic delay
xopen("enPassage.hoc")

// Create GoC Cell population
print "Reading Golgi cell template"


xopen("Golgi_template.hoc")
xopen("GolgiPopulation.hoc")

// Create GRC Cell population
print "Reading Granule cell template"

xopen("Granule_template.hoc")
//xopen("GranulePopulation.hoc")
xopen("GranulePopulation.hoc")


////Create the Mossy fiber input source
print "Creating network input"

xopen("MFPopulation.hoc")

if (MLplug==1){ // This part is reserved for future development

// Create Stellate Cell population
print "Reading Stellate cell template"
xopen("gap.hoc")
xopen("SC_template.hoc")
xopen("StellatePopulation.hoc")

// Create Basket Cell population
print "Reading Basket cell template"

xopen("BC1_Template.hoc")

//xopen("BC1_Template.hoc")
xopen("BasketPopulation1.hoc")
}

print "Cells populations created"
//print pc1.id

objref hines
hinest1 = startsw()
hinest2 = startsw()
hines = new FInitializeHandler(2, "hinest1=startsw() hinest2=startsw() hines1()")
proc hines1() {
        dt = step_time
        printf("%d t=%g dt=%g dreal=%g treal=%g\n", \
                pc1.id, t, dt, startsw()-hinest2, startsw()-hinest1)
              //  if(pc1.gid_exists(5)){
              //        print "Vm",pc1.gid2cell(5).soma.v(0.5)
              //    }
        hinest2 = startsw()
        cvode.event(t + 1, "hines1()")
}


//print pc1.id
//Create the network connections
print"Creating Network Connections"

xopen("netconMFtoGoC.hoc")
xopen("netconMFtoGC.hoc")
xopen("netconGoCtoGC.hoc")
xopen("netconGCtoGoC.hoc")
if (MLplug==1){ // This part is reserved for future development
    xopen("netconPFtoSC.hoc")
    xopen("netconPFtoBC.hoc")
}
print "Connectivity pattern created"
objref vmgoc_vec[GolgiPop.GoCcoordinates.nrow], vmgc_vec[GranulePop.GCcoordinates.nrow]
//pc1 = new ParallelContext()

proc vm_record(){

for rank=0, pc1.nhost-1 { // host 0 first, then 1, 2, etc.

pc1.barrier()
  if (rank==pc1.id) {

            // Granule cells connections
            for (i=pc1.id; i < GranulePop.GCcoordinates.nrow-1; i +=pc1.nhost) {
                vmgc_vec[i] = new Vector()
                vmgc_vec[i].record(&pc1.gid2cell(i+GolgiPop.GoCcoordinates.nrow).soma.v(.5),step_record)
            }

            // Golgi cells connections
            for (j=pc1.id; j < GolgiPop.GoCcoordinates.nrow-1; j +=pc1.nhost) {
                vmgoc_vec[j] = new Vector()
                vmgoc_vec[j].record(&pc1.gid2cell(j).soma.v(.5),step_record)
            }

    }
}

}


proc savedata(){

MFtoGCfile = new File()
MFtoGCfile1 = new File()
MFtoGCfile2 = new File()
MFtoGoCfile = new File()
GoCtoGCfile = new File()
PFtoGoCfile = new File()
AxontoGoCfile = new File()
MFGoCtotalfile = new File()
MFGCtotalfile = new File()
PFGoCtotalfile = new File()
AxonGoCtotalfile = new File()
MFcoordinatesfile = new File()
GoCcoordinatesfile = new File()
GCcoordinatesfile = new File()
GoCspiketimefile = new File()
GCspiketimefile = new File()
MFspikefile = new File()
VMGoCfile = new File()
VMGCfile = new File()
PFtoSCfile = new File()
PFtoBCfile = new File()
PFSCtotalfile = new File()
PFBCtotalfile = new File()
SCcoordinatesfile = new File()
BCcoordinatesfile = new File()
BCSpikefile = new File()
BCgapfile = new File()
gapconfile = new File()
BCtoBCfile = new File()
SCSpikeFile = new File()
SCGapFile = new File()
SCtoSCFile = new File()
//MFcoordinates = new File()

//MFBundleCenter_file = new File()


if (pc1.id==0){
    MFtoGCfile.wopen("MFtoGC.bin")
    MFtoGCfile1.wopen("MFtoGC1.dat")
    MFtoGCfile2.wopen("MFtoGC2.bin")
    MFtoGoCfile.wopen("MFtoGoC.bin")
    GoCtoGCfile.wopen("GoCtoGC.bin")
    PFtoGoCfile.wopen("PFtoGoC.bin")
    AxontoGoCfile.wopen("AxontoGoC.bin")
    MFGoCtotalfile.wopen("MFGoCtotal.bin")
    MFGCtotalfile.wopen("MFGCtotal.bin")
    PFGoCtotalfile.wopen("PFGoCtotal.bin")
    AxonGoCtotalfile.wopen("AxonGoCtotal.bin")
    MFcoordinatesfile.wopen("MFcoordinates.dat")
    GoCcoordinatesfile.wopen("GoCcoordinates.dat")
    GCcoordinatesfile.wopen("GCcoordinates.dat")
    GoCspiketimefile.wopen("GoCspiketime.bin")
    GCspiketimefile.wopen("Gspiketime.bin")
    MFspikefile.wopen("MFspiketime.bin")
    PFtoSCfile.wopen("PFtoSC.bin")
    PFtoBCfile.wopen("PFtoBC.bin")
    PFSCtotalfile.wopen("PFSCtotal.bin")
    PFBCtotalfile.wopen("PFBCtotal.bin")
    VMGoCfile.wopen("VMGoC.bin")
    VMGCfile.wopen("VMGC.bin")
    SCcoordinatesfile.wopen("SCcoordinates.dat")
    BCcoordinatesfile.wopen("BCcoordinates.dat")
    BCSpikefile.wopen("BCSpike.bin")
    BCgapfile.wopen("BCgap.bin")
    BCtoBCfile.wopen("BCtoBC.bin")
    gapconfile.wopen("gapcon.dat")
    SCSpikeFile.wopen("SCSpike.bin")
    SCGapFile.wopen("SCGap.bin")
    SCtoSCFile.wopen("SCtoSC.bin")

    //MFcoordinates.wopen("MFc.dat")
    //MFBundleCenter_file.wopen("MFBundleCenter.dat")


    enPassage[0].MFGoCtotal.vwrite(MFGoCtotalfile)
    enPassage[0].MFGCtotal.vwrite(MFGCtotalfile)
    enPassage[0].PFtotal.vwrite(PFGoCtotalfile)
    enPassage[0].Axontotal.vwrite(AxonGoCtotalfile)
    enPassage[0].PFSCtotal.vwrite(PFSCtotalfile)
    enPassage[0].PFBCtotal.vwrite(PFBCtotalfile)


    //MossyPop.MFBundleCenter.fprint(0,MFBundleCenter_file,"%f\t")


    MossyPop.MFcoordinates.fprint(0,MFcoordinatesfile,"%f\t")

    MFtoGCfile.close("MFtoGC.bin")
    MFtoGCfile1.close("MFtoGC1.dat")
    MFtoGCfile2.close("MFtoGC2.bin")
    MFtoGoCfile.close("MFtoGoC.bin")
    GoCtoGCfile.close("GoCtoGC.bin")
    PFtoGoCfile.close("PFtoGoC.bin")
    AxontoGoCfile.close("AxontoGoC.bin")
    MFGoCtotalfile.close("MFGoCtotal.bin")
    MFGCtotalfile.close("MFGCtotal.bin")
    PFGoCtotalfile.close("PFGoCtotal.bin")
    AxonGoCtotalfile.close("AxonGoCtotal.bin")
    MFcoordinatesfile.close("MFcoordinates.dat")
    GoCcoordinatesfile.close("GoCcoordinates.dat")
    GCcoordinatesfile.close("GCcoordinates.dat")
    GoCspiketimefile.close("GoCspiketime.bin")
    GCspiketimefile.close("Gspiketime.bin")
    MFspikefile.close("MFspiketime.bin")
    PFtoSCfile.close("PFtoSC.bin")
    PFtoBCfile.close("PFtoBC.bin")
    PFSCtotalfile.close("PFSCtotal.bin")
    PFBCtotalfile.close("PFBCtotal.bin")
    SCcoordinatesfile.close("SCcoordinates.dat")
    BCcoordinatesfile.close("BCcoordinates.dat")
    BCSpikefile.close("BCSpike.bin")
    BCgapfile.close("BCgap.bin")
    BCtoBCfile.close("BCtoBC.bin")
    gapconfile.close("gapcon.dat")
    SCSpikeFile.close("SCSpike.bin")
    SCGapFile.close("SCGap.bin")
    SCtoSCFile.close("SCtoSC.bin")

    //MFBundleCenter_file.close("MFBundleCenter.dat")

    VMGoCfile.close("VMGoC.bin")
    VMGCfile.close("VMGC.bin")

}
print "Saving data on host", pc1.id
for rank=0, pc1.nhost-1 { // host 0 first, then 1, 2, etc.
pc1.barrier()
  if (rank==pc1.id) {

        MFtoGCfile.aopen("MFtoGC.bin")
        MFtoGCfile1.aopen("MFtoGC1.dat")
        MFtoGCfile2.aopen("MFtoGC2.bin")
        MFtoGoCfile.aopen("MFtoGoC.bin")
        GoCtoGCfile.aopen("GoCtoGC.bin")
        PFtoGoCfile.aopen("PFtoGoC.bin")
        AxontoGoCfile.aopen("AxontoGoC.bin")
        GoCspiketimefile.aopen("GoCspiketime.bin")
        GCspiketimefile.aopen("Gspiketime.bin")
        MFspikefile.aopen("MFspiketime.bin")
        GoCcoordinatesfile.aopen("GoCcoordinates.dat")
        GCcoordinatesfile.aopen("GCcoordinates.dat")
        VMGCfile.aopen("VMGC.bin")
        VMGoCfile.aopen("VMGoC.bin")
        PFtoSCfile.aopen("PFtoSC.bin")
        PFtoBCfile.aopen("PFtoBC.bin")
        BCtoBCfile.aopen("BCtoBC.bin")
        BCgapfile.aopen("BCgap.bin")
        SCcoordinatesfile.aopen("SCcoordinates.dat")
        BCcoordinatesfile.aopen("BCcoordinates.dat")
        BCSpikefile.aopen("BCSpike.bin")
        gapconfile.aopen("gapcon.dat")
        SCSpikeFile.aopen("SCSpike.bin")
        SCGapFile.aopen("SCGap.bin")
        SCtoSCFile.aopen("SCtoSC.bin")
            // Granule cells connections
            for (i=pc1.id; i < GranulePop.GCcoordinates.nrow-1; i +=pc1.nhost) {
                pc1.gid2cell(i+GolgiPop.GoCcoordinates.nrow).spiketime.vwrite(GCspiketimefile)
                pc1.gid2cell(i+GolgiPop.GoCcoordinates.nrow).MFID.vwrite(MFtoGCfile)
                pc1.gid2cell(i+GolgiPop.GoCcoordinates.nrow).MFI.vwrite(MFtoGCfile2)
                pc1.gid2cell(i+GolgiPop.GoCcoordinates.nrow).MFT.fprint(MFtoGCfile1,"%f\t")
                pc1.gid2cell(i+GolgiPop.GoCcoordinates.nrow).GoCID.vwrite(GoCtoGCfile)

                GCx=GranulePop.GCcoordinates.x[i][0]
                GCy=GranulePop.GCcoordinates.x[i][1]
                GCz=GranulePop.GCcoordinates.x[i][2]
                GCcoordinatesfile.printf("%f\t %f\t %f\n",GCx,GCy,GCz)
//              vmgc_vec[i].vwrite(VMGCfile)

            }

            // Golgi cells connections
            for (j=pc1.id; j < GolgiPop.GoCcoordinates.nrow-1; j +=pc1.nhost) {
                pc1.gid2cell(j).spikecount.vwrite(GoCspiketimefile)
                pc1.gid2cell(j).MFID.vwrite(MFtoGoCfile)
                pc1.gid2cell(j).PFID.vwrite(PFtoGoCfile)
                pc1.gid2cell(j).AxonID.vwrite(AxontoGoCfile)
                pc1.gid2cell(j).setv(rand.repick())

                GoCx=GolgiPop.GoCcoordinates.x[j][0]
                GoCy=GolgiPop.GoCcoordinates.x[j][1]
                GoCz=GolgiPop.GoCcoordinates.x[j][2]
                GoCcoordinatesfile.printf("%f\t %f\t %f\n",GoCx,GoCy,GoCz)
//              vmgoc_vec[j].vwrite(VMGoCfile)

            }

        if (MLplug==1){ // This part is reserved for future development


            // Stellate cells connections
            if (pc1.id ==0) {
            for (i=pc1.id; i < StellatePop.SCcoordinates.nrow; i +=1) {
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow).PFID.vwrite(PFtoSCfile)
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow).gapid.vwrite(SCGapFile)
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow).SCID.vwrite(SCtoSCFile)
                SCx=StellatePop.SCcoordinates.x[i][0]
                SCy=StellatePop.SCcoordinates.x[i][1]
                SCz=StellatePop.SCcoordinates.x[i][2]
                SCcoordinatesfile.printf("%f\t %f\t %f\n",SCx,SCy,SCz)
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow).spikecount.vwrite(SCSpikeFile)

            }

            // Basket cells connections

            for (i=pc1.id; i < BasketPop.BCcoordinates.nrow; i +=1) {
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow+StellatePop.SCcoordinates.nrow).PFID.vwrite(PFtoBCfile)
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow+StellatePop.SCcoordinates.nrow).gapid.vwrite(BCgapfile)
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow+StellatePop.SCcoordinates.nrow).BCID.vwrite(BCtoBCfile)

                BCx=BasketPop.BCcoordinates.x[i][0]
                BCy=BasketPop.BCcoordinates.x[i][1]
                BCz=BasketPop.BCcoordinates.x[i][2]
                BCcoordinatesfile.printf("%f\t %f\t %f\n",BCx,BCy,BCz)
                pc1.gid2cell(i+GranulePop.GCcoordinates.nrow+GolgiPop.GoCcoordinates.nrow+MossyPop.MFcoordinates.nrow+StellatePop.SCcoordinates.nrow).spikecount.vwrite(BCSpikefile)

            }
            enPassage[0].gapcon.fprint(0,gapconfile,"%e\t")
        }


        }

            // MF input pattern
            if (pc1.id==0){ // generate MF Population only in host=0
                for i=0,MossyPop.MFcoordinates.nrow-1 {
                MossyPop.VecList.object(i).vwrite(MFspikefile)
                }
            }


    MFtoGCfile.close("MFtoGC.bin")
    MFtoGCfile1.close("MFtoGC1.dat")
    MFtoGCfile2.close("MFtoGC2.bin")
    MFtoGoCfile.close("MFtoGoC.bin")
    GoCtoGCfile.close("GoCtoGC.bin")
    PFtoGoCfile.close("PFtoGoC.bin")
    AxontoGoCfile.close("AxontoGoC.bin")
    GoCspiketimefile.close("GoCspiketime.bin")
    GCspiketimefile.close("Gspiketime.bin")
    MFspikefile.close("MFspiketime.bin")
    GoCcoordinatesfile.close("GoCcoordinates.dat")
    GCcoordinatesfile.close("GCcoordinates.dat")
    VMGCfile.close("VMGC.bin")
    VMGoCfile.close("VMGoC.bin")
    PFtoSCfile.close("PFtoSC.bin")
    PFtoBCfile.close("PFtoBC.bin")
    BCtoBCfile.close("BCtoBC.bin")
    SCcoordinatesfile.close("SCcoordinates.dat")
    BCcoordinatesfile.close("BCcoordinates.dat")
    BCSpikefile.close("BCSpike.bin")
    BCgapfile.close("BCgap.bin")
    SCSpikeFile.close("SCSpike.bin")
    SCGapFile.close("SCGap.bin")
    SCtoSCFile.close("SCtoSC.bin")

  }
}
pc1.barrier() // wait for all hosts to get to this point


} // end proc



tstop=stoptime

objref vecgf, vecg1,vecgf1
objref savv, savt, mat1,mat2
if (pc1.id == 0) {

vecgf = new Vector()
vecg1 = new Vector()
vecgf1 = new Vector()
vecgf.record(&pc1.gid2cell(10754).soma.v(0.5))
vecg1.record(&t)
vecgf1.record(&pc1.gid2cell(10786).soma.v(0.5))


}







vm_record()



{pc1.set_maxstep(10)}
stdinit()
//run()

{pc1.psolve(tstop)}

if (pc1.id ==0) {

savv = new File()
savt = new File()
mat1 = new Matrix(1+(tstop/0.025),2)
mat1.setcol(0, vecg1)
mat1.setcol(1,vecgf)
mat2 = new Matrix(1+(tstop/0.025),2)
mat2.setcol(0, vecg1)
mat2.setcol(1,vecgf1)

savv.wopen("cell3somav.dat")
savt.wopen("cell3somat.dat")
savv.close("cell3somav.dat")
savt.close()
savv.aopen("cell3somav.dat")
savt.aopen("cell3somat.dat")

//mat1.fprint(savv)
//vecgf.vwrite(savv)
mat1.fprint(savv,"%f\t")
mat2.fprint(savt,"%f\t")
savv.close()
savt.close()

}

savedata()


{pc1.runworker()}
{pc1.done()}
printf("Time = %4g\t on host =%4g \n", pc1.time - st,pc1.id)


//quit()




Loading data, please wait...