makePairedUnpaired.hoc

///////////////////////////////////////////////////////////////////////////////
// makeSynapses.hoc: builds synapses in the model
//
// Note: this must be run *after* the cell geometry has been initialized
///////////////////////////////////////////////////////////////////////////////

//////////////////// declarations /////////////////////////////////////////////
strdef filename
objref runfile

// post-synaptic objects
objref gaba_paired, gaba_unpaired
gaba_paired = new List()
gaba_unpaired = new List()

// pre-synaptic objects
objref pre_paired, pre_unpaired
// pre_paired = new List()
// pre_unpaired = new List()

// connection objects
objref con_paired, con_unpaired
con_paired = new List()
con_unpaired = new List()


// Vectors for recording NetCon events
objref gaba_paired_tvec, gaba_paired_idvec
// gaba_paired_tvec   = new Vector()
gaba_paired_idvec  = new Vector()
objref gaba_unpaired_tvec, gaba_unpaired_idvec
// gaba_unpaired_tvec   = new Vector()
gaba_unpaired_idvec  = new Vector()

objref syn_location
syn_location = new Vector()

objref scts
scts = new Vector()

// write synapses 
strdef syn_file, CA1synapses
objref runfile

objref header
header = new Vector()
objref syn_write_info
syn_write_info = new Vector()
//////////////////// procedure definitions ////////////////////////////////////

//-----------------------------------------------------------------------------
// make_gaba(location_paired, density_paired, location_unpaired, density_unpaired)
//-----------------------------------------------------------------------------
// creates the GABAergic post-synaptic objects, and places them in random 
// positions on specifiec locations at the density indicated
// locations are specified using the following:
// 0 = soma
// 1 = proximal
// 2 = middle
// 3 = distal

proc make_gaba() { local secdis, secarea, numsyn, xpos, x, i, j, k  	localobj posr //declares local variablesa components, and add them to the lists
	syn_location.resize(0)
// create a random number generator
  	posr = new Random(seed_prompt)
  	posr.uniform(0,1)
  
// add synapses in the soma
  	// add the paired synapses
  	if ($1 == 0) { // paired is in the soma
	  	forsec somatic {
			
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$2)
		    print "numsyn is ", numsyn
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn{
		    	xpos = posr.repick()
		    	syn_location.append(xpos)
		    	gaba_paired.append(new GABAa(xpos))
		    	gaba_paired.o(gaba_paired.count()-1).gmax = gmax_paired_soma									
		    }
	  	}
	}
	// add the unpaired synapses
  	if ($3 == 0) { // unpaired is in the soma
	  	forsec somatic {
	
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$4)
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn {
		    	xpos = posr.repick()
		    	gaba_unpaired.append(new GABAa(xpos))
		    	gaba_unpaired.o(gaba_unpaired.count()-1).gmax = gmax_unpaired_soma
		    }
	  	}
	}

// add synapses in the proximal dendrites
	// add the paired synapses
	if ($1 == 1) { // paired is in the proximal dendrites
		j = 0
	  	forsec proximal {
	
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$2)
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn {
		    	xpos = posr.repick()
		    	syn_location.append(xpos)
		    	gaba_paired.append(new GABAa(xpos))
		    	gaba_paired.o(gaba_paired.count()-1).gmax = gmax_paired_prox
		    	gaba_paired_idvec.append(proximal_indices.x(j))
		    }
		    j = j + 1
	  	}
	}

	// add the unpaired synapses
	if ($3 == 1) { // unpaired is in the proximal dendrites
	  	j = 0
	  	forsec proximal {
	
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$4)
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn {
		    	xpos = posr.repick()
		    	gaba_unpaired.append(new GABAa(xpos))
		    	gaba_unpaired.o(gaba_unpaired.count()-1).gmax = gmax_unpaired_prox
		    	gaba_unpaired_idvec.append(proximal_indices.x(j))
		    }
		    j = j + 1
	  	}
	}

// add synapses in the middle dendrites
	// add the paired synapses
	if ($1 == 2) { // paired is in the middle dendrites
		j = 0
	  	forsec middle {
	
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$2)
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn {
		    	xpos = posr.repick()
		    	syn_location.append(xpos)
		    	gaba_paired.append(new GABAa(xpos))
		    	gaba_paired.o(gaba_paired.count()-1).gmax = gmax_paired_mid
		    	gaba_paired_idvec.append(middle_indices.x(j))
		    }
		    j = j + 1 
	  	}
	}
	// add the unpaired synapses
	if ($3 == 2) { // unpaired is in the middle dendrites
	  	j = 0
	  	forsec middle {
	
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$4)
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn {
		    	xpos = posr.repick()
		    	gaba_unpaired.append(new GABAa(xpos))
		    	gaba_unpaired.o(gaba_unpaired.count()-1).gmax = gmax_unpaired_mid
		    	gaba_unpaired_idvec.append(middle_indices.x(j))
		    }
		    j = j + 1
	  	}
	}

// add synapss in the distal dendrites
	// add the paired synapses
	if ($1 == 3) { // paired is in the distal dendrites
		j = 0
	  	forsec distal {
	
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$2)
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn {
		    	xpos = posr.repick()
		    	syn_location.append(xpos)
		    	gaba_paired.append(new GABAa(xpos))
		    	gaba_paired.o(gaba_paired.count()-1).gmax = gmax_paired_dist
		    	gaba_paired_idvec.append(distal_indices.x(j))
		    }
		    j = j + 1
	  	}
	}
	// add the unpaired synapses
	if ($3 == 3) { // unpaired is in the distal dendrites
		j = 0
	  	forsec distal {
	
	  		// determine the distance from the center of the soma to the center of this section
	    	secdis = distance(1)
	   
	    	// calculate the area of this section
		    secarea = 0
		    for (x,0) {
		    	secarea = secarea + area(x)
		    }
		
		    // calculate the number of synapses on this section
		    numsyn = int(secarea*$4)
		
		    // for each synapse, pick a random location,
		    // create gaba components, and add them to the lists
		    for i=1,numsyn {
		    	xpos = posr.repick()
		    	gaba_unpaired.append(new GABAa(xpos))
		    	gaba_unpaired.o(gaba_unpaired.count()-1).gmax = gmax_unpaired_dist
		    	gaba_unpaired_idvec.append(distal_indices.x(j))
		    }
		    j = j + 1
	  	}
	}
print "# of GABA synapses is ", gaba_paired.count()

scts.resize(0)
for i = 0, gaba_paired.count()-1{
	scts.append(999)
}

header.resize(0)
header.append(gaba_paired.count())
syn_write_info.resize(0)
syn_write_info.append(scts)
syn_write_info.append(syn_location)


//runfile = new File()  // ask on forum about this
//sprint(syn_file,"./CA1<INSERTSECTIONNAME>synapses.dat") 
//runfile.wopen(syn_file)  // ask on forum about this
//runfile.seek(0)  
//header.vwrite(runfile)
//syn_write_info.vwrite(runfile)
//print "synapses written to file ", syn_file
//runfile.close()
	
}





//-----------------------------------------------------------------------------
// make_gabapre(interval_paired, number_paired, start_paired, interval_unpaired, 
// 				number_unpaired, start_unpaired)
//-----------------------------------------------------------------------------
// creates the presynaptic objects for the GABAergic synapses
proc make_gabapre() { 

	// create paired objects
	pre_paired = new NetStim()
	pre_paired.interval = $1
	pre_paired.number 	= $2 
	pre_paired.start 	= $3
	pre_paired.noise 	= 0


	// create unpaired objects
	pre_unpaired = new NetStim()
	pre_unpaired.interval 	= $4
	pre_unpaired.number 	= $5 
	pre_unpaired.start 		= $6
	pre_unpaired.noise 		= 0
}

//-----------------------------------------------------------------------------
// make_gabacon()
//-----------------------------------------------------------------------------
// creates all of the connections between pre and post-synaptic objects
// for GABAergic synapses
proc make_gabacon() {
	for i = 0,gaba_paired.count()-1 {
		con_paired.append(new NetCon(pre_paired, gaba_paired.o(i), 0, 0, 1))
	}
	for i = 0,gaba_unpaired.count()-1 {
		con_unpaired.append(new NetCon(pre_unpaired, gaba_unpaired.o(i), 0, 0, 1))
	}
}


//////////////////// procedure calls /////////////////////////////////////
make_gaba(location_paired, density_paired, location_unpaired, density_unpaired)
make_gabapre(interval_paired, number_paired, start_paired, interval_unpaired, number_unpaired, start_unpaired)
make_gabacon()