Basal ganglia network model of subthalamic deep brain stimulation (Hahn and McIntyre 2010)

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Accession:127388
Basal ganglia network model of parkinsonian activity and subthalamic deep brain stimulation in non-human primates from the article Instructions are provided in the README.txt file. Contact hahnp@ccf.org if you have any questions about the implementation of the model. Please include "ModelDB - BGnet" in the subject heading.
Reference:
1 . Hahn PJ, McIntyre CC (2010) Modeling shifts in the rate and pattern of subthalamopallidal network activity during deep brain stimulation. J Comput Neurosci 28:425-41 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Basal ganglia;
Cell Type(s): Subthalamus nucleus projection neuron; Globus pallidus neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Dopamine; Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Bursting; Parkinson's; Deep brain stimulation;
Implementer(s): Hahn, Philip [hahnp at ccf.org];
Search NeuronDB for information about:  Dopamine; Gaba; Glutamate;
//proc randomize(seedVal)
//proc zeroNet()
//proc saveSpikes(filename)
//proc recGidVm(mode/*0=setup, 1=get values*/)
//proc saveStims(filename)
//proc netStats(resultVec)
//proc updateAll()
//proc saveCON()



load_file("pBGburstSearch.hoc")


objref r, sc_r

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
proc randomize() {local seedVal	//$1 seedVal base
////////////////
seedVal = $1 + pnm.pc.id
r = new Random(seedVal)
sc_r = new scopRandom(.5)
sc_r.seed(seedVal)

print "pc.id() ", pnm.pc.id(), " using random seed ", seedVal

}


////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
proc zeroNet() {
////////////////
//Set all synaptic weights to zero

gmaxSTNGPe = 0
gmaxGPeGPe = 0
gmaxGPeSTN = 0
gmaxGPeGPi = 0
gmaxSTNGPi = 0
gmaxGPiTha = 0

CONupdateWeights()

gmaxCtxSTN = 0
gmaxStrGPe = 0
gmaxStrGPi = 0

INPupdateWeights()

}


////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
proc saveSpikes() { local i localobj f	//(s1:filename)
////////////////
//Save random seed and pnm spike time and id vectors to file with name passed in $s1

//pnm.gatherspikes()	should be called right after prun, calling twice produces error?

f =  new File()
f.wopen($s1)
print "seed=", seedVal
f.printf("%f\n", seedVal)
for i=0, pnm.spikevec.size-1 {
	f.printf("%f\t%f\n", pnm.spikevec.x[i], pnm.idvec.x[i])
}
f.close()

}



objref vmRecIds,vmL,vmI
vmRecIds = new Vector()	//global record id vector
vmL = new List()	//list containing record data vectors
vmI = new Vector()	//locally owned record id vector
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
proc setupVms() {local i	localobj vm
////////////////
//Called internally - prepare to record voltages for cell ids stored in vmRecIds, vecs stored locally will be collected by master in the same manner as pnm spikevec and idvec

vmL.remove_all()
vmI.resize(0)

if (pnm.pc.id > 0) {
	//nodes consume setup message
	while (pnm.pc.look("setupIds") != 1) {
	}

	vmRecIds = pnm.pc.upkvec()	//unpack vector of ids to record
}

for i=0,vmRecIds.size-1 {
	if (pnm.pc.gid_exists(vmRecIds.x(i))) {
		//vm goes out of context, but pointer in vmL should remain to hold object
		vm = new Vector()	
		vm.record(&pnm.pc.gid2obj(vmRecIds.x(i)).soma.v)
		vmL.append(vm)
		vmI.append(vmRecIds.x(i))
	}
}

if (pnm.pc.id > 0) {
	pnm.pc.post("setupvm")	//nodes tell master they're done
}

}


proc postVms() {local i
////////////////
pnm.pc.pack(vmI)	//send back vector of ids recorded by this node
for i=0,vmI.size-1 {	//... as well as the recorded data
	pnm.pc.pack(vmL.o(i))
}

pnm.pc.post("postvm")	//tell master this node is done

}


proc recGidVm() { local i,j localobj v1,v2	//($1:mode(0=setup, 1=get values))
////////////////

if (pnm.pc.nhost > 1 && pnm.pc.id == 0) {	

	//all this work required only by master node if running parallel with >1 host

	if ($1==0) {
		pnm.pc.pack(vmRecIds)
		pnm.pc.post("setupIds")
		pnm.pc.context("setupVms()\n")	//tell each node to run setupVms
		for i=0, pnm.pc.nhost-2 {
			pnm.pc.take("setupvm")	//wait until all responses are consumed
		}

		setupVms()			//call setup for ids owned by master itself

		pnm.pc.take("setupIds")		//clear the setup message

	} else {
		pnm.pc.context("postVms()\n")	//tell each node to run postVms
		for i=0, pnm.pc.nhost-2 {
			pnm.pc.take("postvm")	//consume message once for each node (not master)

			v1 = pnm.pc.upkvec()	//deal with data sent back from nodes
			vmI.append(v1)		//... appending to data already on master
			for j=0,v1.size-1 {
				v2 = pnm.pc.upkvec()
				vmL.append(v2)
			}
		}
	}

}


}



////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
proc poststims() {
////////////////
	for i=0, numGPi-1 {
		//send back vector of GPI stim times for ids on this node
		pnm.pc.pack(timesDBSGPi[i])
	}
	pnm.pc.post("poststim")	//tell master this node is done
	
}

proc gatherstims() {local i,j  localobj s
////////////////
	if (pnm.pc.nhost > 1) {
		s = new Vector()
		pnm.pc.context("poststims()\n")	//tell each node to run poststims
		for i=0, pnm.pc.nhost-2 {
			pnm.pc.take("poststim") //consume message once for each node (not master)
                  for j=0,numGPi-1 {
				s = pnm.pc.upkvec()	//deal with data sent back from nodes
				timesDBSGPi[j].append(s)//... appending to data already on master
			}
		}
	}
}


proc saveStims() { local i localobj f	//($s1:filename)
////////////////

gatherstims() //  need this for parallel to pull stim times on nodes other than master

f =  new File()
f.wopen($s1)
for i=0,numGPi-1 {
	for j=0,timesDBSGPi[i].size-1 {
		f.printf("%f\t%f\n", timesDBSGPi[i].x(j), cellID(ID_GPi,i))
	}
}
f.close()

}




////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
objref st[ncell], isi[ncell], bur[ncell]
for i=0,ncell-1 {
	st[i] = new Vector()
	isi[i] = new Vector()
        bur[i] = new Matrix()
}


proc netStats() {local i,j localobj res,spkRate, burRate			//$o1:res
//////////////////

//pnm.gatherspikes()	should be called right after prun, calling twice produces error?

res = $o1

spkRate = new Vector(ncell)
burRate = new Vector(ncell)

for i=0,ncell-1 {
	st[i].resize(0)
	isi[i].resize(0)
        bur[i].resize(1,1)
}

// get spike times for each cell
for i=0,pnm.idvec.size-1 {
	st[pnm.idvec.x(i)].append(pnm.spikevec.x(i))
}

// process each cell
for i=0,ncell-1 {

	if (st[i].size > 2) {

		// calculate interspike intervals
		for j=0,st[i].size-2 {
			isi[i].append(st[i].x(j+1) - st[i].x(j))
		}

		// get burst times

		burstSearch(st[i], isi[i], bur[i])

		// calculate average spike and burst rates
		spkRate.x(i) = 1000*(st[i].size - 1)/st[i].x(st[i].size-1)	      //using total time is time of last spike
		if (bur[i].ncol == 1) {
			burRate.x(i) = 0
		} else {
		      burRate.x(i) = 1000*bur[i].nrow/st[i].x(st[i].size-1)		//using total time is t at end???
		}

	} else {
		spkRate.x(i) = 0
		burRate.x(i) = 0
	}
}



f_stn = spkRate.mean(cellID(ID_STN, 0), cellID(ID_STN, numSTN-1))
std_stn = spkRate.stdev(cellID(ID_STN, 0), cellID(ID_STN, numSTN-1))
//print "STN ", f_stn, std_stn

f_gpe = spkRate.mean(cellID(ID_GPe, 0), cellID(ID_GPe, numGPe-1))
std_gpe = spkRate.stdev(cellID(ID_GPe, 0), cellID(ID_GPe, numGPe-1))
//print "GPe ", f_gpe, std_gpe

f_gpi = spkRate.mean(cellID(ID_GPi, 0), cellID(ID_GPi, numGPi-1))
std_gpi = spkRate.stdev(cellID(ID_GPi, 0), cellID(ID_GPi, numGPi-1))
//print "GPi ", f_gpi, std_gpi



br_stn = 60*burRate.mean(cellID(ID_STN, 0), cellID(ID_STN, numSTN-1))
brstd_stn = 60*burRate.stdev(cellID(ID_STN, 0), cellID(ID_STN, numSTN-1))
//print "STN(br) ", br_stn, brstd_stn

br_gpe = 60*burRate.mean(cellID(ID_GPe, 0), cellID(ID_GPe, numGPe-1))
brstd_gpe = 60*burRate.stdev(cellID(ID_GPe, 0), cellID(ID_GPe, numGPe-1))
//print "GPe(br) ", br_gpe, brstd_gpe

br_gpi = 60*burRate.mean(cellID(ID_GPi, 0), cellID(ID_GPi, numGPi-1))
brstd_gpi = 60*burRate.stdev(cellID(ID_GPi, 0), cellID(ID_GPi, numGPi-1))
//print "GPi(br) ", br_gpi, brstd_gpi



res.resize(6)
res.x(0) = f_stn
res.x(1) = f_gpe
res.x(2) = f_gpi
res.x(3) = br_stn
res.x(4) = br_gpe
res.x(5) = br_gpi


}



////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
proc updateAll() { 
//////////////////
//Distribute any global parameter changes to cells

readParms($s1)
BIAupdateWeights()
CONupdateWeights()
INPupdateWeights()

}



////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
proc saveCON() { local i localobj f
////////////////

f = new File()

f.wopen("pBG_CON.txt")

for i=0,pnm.nclist.count-1 {
	f.printf("Cell %s -> cell %s\n", pnm.nclist.o(i).precell, pnm.nclist.o(i).postcell)
}

f.close()

}


////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

strdef junkStr
//-----------------------------------------------------------------------------------------------------
proc getOutput() {local i,numFields,tmp localobj f 	//(filename, skipLines, readInputs)
//---------------

numTargets = 6

f = new File()

f.ropen($s1)

for i=0,$2-1 {
	f.gets(junkStr)
}


for i=0,3+numTargets-1 {
	tmp = f.scanvar()
}


gmaxSTNGPi = f.scanvar()
gmaxGPeGPi = f.scanvar()
gmaxSTNGPe = f.scanvar()
gmaxGPeGPe = f.scanvar()
gmaxGPeSTN = f.scanvar()
gDA_STNGPi = f.scanvar()
gDA_GPeGPi = f.scanvar()
gDA_STNGPe = f.scanvar()
gDA_GPeGPe = f.scanvar()
gDA_GPeSTN = f.scanvar()
iBiasSTN = f.scanvar()
iBiasGPe = f.scanvar()
iBiasGPi = f.scanvar()


if ($3) {
	// read in input parameters (assumes format is same as listed here)

	gmaxCtxSTN = f.scanvar()	
	gmaxStrGPe = f.scanvar()	
	gmaxStrGPi = f.scanvar()

/* ... removed in distribution ... */

}


f.close()

BIAupdateWeights()
CONupdateWeights()
INPupdateWeights()

}