mosinit_PC_SC_SplusCNO.hoc

//Developer Fabio Simoes de Souza, 2020 
//University of Colorado Anschutz Medical Campus
//University Federal of ABC

load_file("nrngui.hoc")
load_file("2_compartment_template.hoc")  //PC
load_file("PF_template.hoc")  //PF
load_file("SC_template.hoc")  //SC

totalruntime = startsw() - totalruntime
print "total run time ", totalruntime

//Setting the random seed 
objref semente
semente = new Random(RANDOM_SEED)
semente.uniform(0,1000000000)
semente_pick=(semente.repick())
semente_randomica = semente_pick

print semente_randomica


//PARAMETERS

// Fiber frequencies
PFfreq=50 //Hz
CFfreq=300  // Hz Mathy et al., Neuron 62: 388-399, 2009
BGfreq=10   //Hz background for two SCs
SCfreq= 20 // Stellate cell freq Hausser and Clark 1997

//number of fibers
NSC=40 //number of BG stellate cells to inhibity PCs
NBGPF=5 //number of background PF inputs to drive real SCs
NCF=1 //number of CF inputs
NPF= 10 //number of PF inputs

//Synaptic conductances
//PC AMPAR
Gmax_PF_PC_AMPAR = 0.2857e-3  //uS (Hausser and Roth, 1997)

//PC GABAaR
Gmax_SC_PC_GABAaR_dist = 0.5*15e-3  //uS (Houston et al., 2009)
Gmax_SC_PC_GABAaR_prox = 0.5*15e-3  //uS (Houston et al., 2009)
Gmax_SC_PC_GABAaR_BG = 15e-3  //uS (Houston et al., 2009)

//SC AMPAR
Gmax_PF_SC0_AMPAR = 0.5*1.3774e-3  //uS (Chu et al., 2012)
Gmax_PF_SC1_AMPAR = 0.5*1.3774e-3  //uS (Chu et al., 2012)

//SC GABAaR
Gmax_SC_SC_GABAaR = 1.0786e-3  //uS (Kondo and Marty, 1998)

// CF and PF timing
PF_onset = 2000 
CF_onset = 4000 // S+

duration= 10e-3 // s

tsim = 5000
tstop=5000 //20e3

//////////
//PC
/////////

objref PC[1]
PC[0]=new Purkinje_simple(0,0,0)
PC[0].position(-100,100,0)


//AMPAR
PC[0].Esynapse.tau1=0.28 //ms rise time (Hausser and Roth, 1997)
PC[0].Esynapse.tau2=1.23  //ms decay time (Hausser and Roth, 1997)
PC[0].Esynapse.e=0       //mV reversal potential


//GABAaR 
PC[0].Isynapse_dist.tau1= 1.8 //ms rise time 
PC[0].Isynapse_dist.tau2= 8.5  //ms decay time 
PC[0].Isynapse_dist.e=-85       //mV reversal potential (Houston et al., 2009) //J neurosci. 29: 10416, 2009

PC[0].Isynapse_prox.tau1= 1.8 //ms rise time 
PC[0].Isynapse_prox.tau2= 8.5  //ms decay time 
PC[0].Isynapse_prox.e=-85       //mV reversal potential (Houston et al., 2009) //J neurosci. 29: 10416, 2009

PC[0].Isynapse_BG.tau1= 1.8 //ms rise time 
PC[0].Isynapse_BG.tau2= 8.5  //ms decay time 
PC[0].Isynapse_BG.e=-85       //mV reversal potential (Houston et al., 2009) //J neurosci. 29: 10416, 2009


//////////
//SC
/////////

//creating cells
objref SC[2]
SC[0]=new StellateCell(0,0,0)
SC[1]=new StellateCell(0,0,0)

SC[0].position(150,0,0)
SC[1].position(400,0,0)



//creating synaptic receptors
//AMPAR
SC[0].Esynapse.tau1=3.45 //ms rise time (Chu et al., 2012)
SC[0].Esynapse.tau2=3.17  //ms decay time (Chu et al., 2012)
SC[0].Esynapse.e=0       //mV reversal potential

SC[1].Esynapse.tau1=3.45 //ms rise time (Chu et al., 2012)
SC[1].Esynapse.tau2=3.17  //ms decay time (Chu et al., 2012)
SC[1].Esynapse.e=0       //mV reversal potential


//GABAaR 
SC[0].Isynapse.tau1= 0.6 //ms rise time (Kondo and Marty, 1998) 
SC[0].Isynapse.tau2= 5.9  //ms decay time (Kondo and Marty, 1998) 
//SC[0].Isynapse.e=-85       //mV reversal potential (Kondo and Marty, 1998) 
SC[0].Isynapse.e=-60       //mV reversal potential (Chavas and Marty, 2003) 

SC[1].Isynapse.tau1= 0.6 //ms rise time (Kondo and Marty, 1998) 
SC[1].Isynapse.tau2= 5.9  //ms decay time (Kondo and Marty, 1998) 
//SC[1].Isynapse.e=-85       //mV reversal potential (Kondo and Marty, 1998) 
SC[1].Isynapse.e=-60       //mV reversal potential (Chavas and Marty, 2003) 

//Chavas, J. & Marty, A. (2003). Coexistence of excitatory and //inhibitory GABA synapses in the cerebellar interneuron network. //J. Neurosci. 23, 2019-2031.    


// Creating the Input Fibers 

XORIGIN0 = 0
YORIGIN0 = 0
ZORIGIN0 = 0

XORIGIN1 = 0
YORIGIN1 = -200
ZORIGIN1 = 0

//Creating PF inputs
objref fiber[NPF]	//define objects for cells
for i=0,NPF-1 {

//pick a new seed for each fiber
semente_pick=(semente.repick())
semente_randomica = semente_pick

fiber[i]=new fibre(-10,0,0,semente_randomica) 



//Move cell location
fiber[i].position(XORIGIN0+10*i,YORIGIN0,ZORIGIN0)

fiber[i].Presynapse fiber[i].nclist.append(new NetCon(fiber[i].StimTrigger,fiber[i].syn,0.5,0,0.01)) 
}



//setting up PF stimulus
NETIN_SP_START= PF_onset // start time
NETIN_SP_NUMBER= PFfreq*2000*1e-3 - 5 //PFfreq*duration //total number of spikes
SEED=1
NETIN_SP_INTERVAL=1000/PFfreq 
NETIN_SP_NOISE=1  // 1=randomized spikes

for i = 0, NPF-1 {
   fiber[i].StimTrigger.start=NETIN_SP_START
   fiber[i].StimTrigger.interval=NETIN_SP_INTERVAL
   fiber[i].StimTrigger.number=NETIN_SP_NUMBER
   fiber[i].StimTrigger.noise=NETIN_SP_NOISE
   //fiber[i].StimTrigger.seed(i)
}

XORIGIN0 = 0
YORIGIN0 = 0
ZORIGIN0 = 0

XORIGIN1 = 0
YORIGIN1 = -300
ZORIGIN1 = 0

//Creating CF inputs
objref fiber2[NCF]	//define objects for cells
for i=0,NCF-1 {

//pick a new seed for each fiber
semente_pick=int(semente.repick())
semente_randomica = semente_pick
fiber2[i]=new fibre(-10,0,0,semente_randomica) 

//Move cell location
fiber2[i].position(XORIGIN0+10*i,YORIGIN0,ZORIGIN0)


fiber2[i].Presynapse fiber2[i].nclist.append(new NetCon(fiber2[i].StimTrigger,fiber2[i].syn,0.5,0,0.01)) 
}

//setting up CF stimulus
NETIN_SP_START= CF_onset //5000 // start time
NETIN_SP_NUMBER= 2 //CFfreq*duration //total number of spikes (Mathy et al., Neuron 62: 388-399, 2009)
SEED=1
NETIN_SP_INTERVAL=1000/CFfreq 
NETIN_SP_NOISE=0  // 1=randomized spikes

for i = 0, NCF-1 {
   fiber2[i].StimTrigger.start=NETIN_SP_START
   fiber2[i].StimTrigger.interval=NETIN_SP_INTERVAL
   fiber2[i].StimTrigger.number=NETIN_SP_NUMBER
   fiber2[i].StimTrigger.noise=NETIN_SP_NOISE
   //fiber2[i].StimTrigger.seed(i)
}

XORIGIN0 = 0
YORIGIN0 = 0
ZORIGIN0 = 0

XORIGIN1 = 0
YORIGIN1 = -400
ZORIGIN1 = 0


//Background GABAR inhibitory inputs to PC
objref fiber3[NSC]	//define objects for cells
for i=0,NSC-1 {

//pick a new seed for each fiber
semente_pick=int(semente.repick())
semente_randomica = semente_pick
fiber3[i]=new fibre(-10,0,0,semente_randomica) 

//Move cell location
fiber3[i].position(XORIGIN0+10*i,YORIGIN0,ZORIGIN0)

fiber3[i].Presynapse fiber3[i].nclist.append(new NetCon(fiber3[i].StimTrigger,fiber3[i].syn,0.5,0,0.01)) 
}

//setting up SC stimulus
NETIN_SP_START=0 // start time
NETIN_SP_NUMBER= SCfreq*tsim*1e-3 //total number of spikes
SEED=1
NETIN_SP_INTERVAL=1000/SCfreq 
NETIN_SP_NOISE=1  // 1=randomized spikes

for i = 0, NSC-1 {
   fiber3[i].StimTrigger.start=NETIN_SP_START
   fiber3[i].StimTrigger.interval=NETIN_SP_INTERVAL
   fiber3[i].StimTrigger.number=NETIN_SP_NUMBER
   fiber3[i].StimTrigger.noise=NETIN_SP_NOISE
   //fiber3[i].StimTrigger.seed(i)
}


XORIGIN0 = 0
YORIGIN0 = 0
ZORIGIN0 = 0

XORIGIN1 = 0
YORIGIN1 = -500
ZORIGIN1 = 0

//Background PF inputs to PC
objref fiber4[NBGPF]	//define objects for cells
for i=0,NBGPF-1 {

//pick a new seed for each fiber
semente_pick=int(semente.repick())
semente_randomica = semente_pick
fiber4[i]=new fibre(-10,0,0,semente_randomica) 

//Move cell location
fiber4[i].position(XORIGIN0+10*i,YORIGIN0,ZORIGIN0)


fiber4[i].Presynapse fiber3[i].nclist.append(new NetCon(fiber4[i].StimTrigger,fiber4[i].syn,0.5,0,0.01)) 
}

//setting up PF background stimulus
NETIN_SP_START=0 // start time
NETIN_SP_NUMBER=SCfreq*tsim*1e-3 //total number of spikes
SEED=1
NETIN_SP_INTERVAL=1000/SCfreq 
NETIN_SP_NOISE=1  // 1=randomized spikes

for i = 0, NBGPF-1 {
   fiber4[i].StimTrigger.start=NETIN_SP_START
   fiber4[i].StimTrigger.interval=NETIN_SP_INTERVAL
   fiber4[i].StimTrigger.number=NETIN_SP_NUMBER
   fiber4[i].StimTrigger.noise=NETIN_SP_NOISE
   //fiber4[i].StimTrigger.seed(i)
}


//Creating Synaptic Connections

//PF -> PC

//PF parameters
CONNECTION_THRESHOLD_PFPC = -10
CONNECTION_DELAY_PFPC = 0.0 
CONNECTION_WEIGHT_PFPC = Gmax_PF_PC_AMPAR 
min=0 // 0 ms delay
max=10 // 10 ms delay

objref prob
prob=new Random()

//Connecting PF -> PC
for i=0,NPF-1 {

dprob=prob.uniform(min,max) //normal distribution delays

fiber[i].Presynapse PC[0].nclist.append(new NetCon(&fiber[i].Presynapse.v(0.5),PC[0].Esynapse, CONNECTION_THRESHOLD_PFPC,CONNECTION_DELAY_PFPC+dprob,CONNECTION_WEIGHT_PFPC))
}


//CF -> PC

//Increase those factor to create a CF-like effect
CF_weightfactor = 100

//CF parameters
CONNECTION_THRESHOLD_CFPC = -10
CONNECTION_DELAY_CFPC = 0.0
CONNECTION_WEIGHT_CFPC = Gmax_PF_PC_AMPAR * CF_weightfactor 
min=0 // 0 ms delay
max=10 // 100 ms delay

objref prob
prob=new Random()

//Connecting CF -> PC
for i=0,NCF-1 {

dprob=prob.uniform(min,max) //normal distribution delays

fiber2[i].Presynapse PC[0].nclist.append(new NetCon(&fiber2[i].Presynapse.v(0.5),PC[0].Esynapse, CONNECTION_THRESHOLD_CFPC,CONNECTION_DELAY_CFPC+dprob,CONNECTION_WEIGHT_CFPC))
}


//Spontaneous PF -> SC

//PF parameters
CONNECTION_THRESHOLD_PFSC = -10
CONNECTION_DELAY_PFSC = 0.0
CONNECTION_WEIGHT_PFSC0 = Gmax_PF_SC0_AMPAR
CONNECTION_WEIGHT_PFSC1 = Gmax_PF_SC1_AMPAR
min=0 // 0 ms delay
max=10 // 10 ms delay

objref prob
prob=new Random()

//Connecting PF -> SC 0
i=0
dprob=prob.uniform(min,max) //normal distribution delays

fiber4[i].Presynapse SC[0].nclist.append(new NetCon(&fiber4[i].Presynapse.v(0.5),SC[0].Esynapse, CONNECTION_THRESHOLD_PFSC,CONNECTION_DELAY_PFSC+dprob,CONNECTION_WEIGHT_PFSC0))

//Connecting PF -> SC 1
i=1
dprob=prob.uniform(min,max) //normal distribution delays

fiber4[i].Presynapse SC[1].nclist.append(new NetCon(&fiber4[i].Presynapse.v(0.5),SC[1].Esynapse, CONNECTION_THRESHOLD_PFSC,CONNECTION_DELAY_PFSC+dprob,CONNECTION_WEIGHT_PFSC1))



//PF -> SC

//PF parameters
CONNECTION_THRESHOLD_PFSC = -10
CONNECTION_DELAY_PFSC = 0.0
CONNECTION_WEIGHT_PFSC0 = Gmax_PF_SC0_AMPAR
CONNECTION_WEIGHT_PFSC1 = Gmax_PF_SC1_AMPAR
min=0 // 0 ms delay
max=10 // 10 ms delay

objref prob
prob=new Random()

//Connecting PF -> SC 0
for i=0,NPF-1 {

dprob=prob.uniform(min,max) //normal distribution delays

fiber[i].Presynapse SC[0].nclist.append(new NetCon(&fiber[i].Presynapse.v(0.5),SC[0].Esynapse, CONNECTION_THRESHOLD_PFSC,CONNECTION_DELAY_PFSC+dprob,CONNECTION_WEIGHT_PFSC0))
}

//Connecting PF -> SC 1
for i=0,NPF-1 {

dprob=prob.uniform(min,max) //normal distribution delays

fiber[i].Presynapse SC[1].nclist.append(new NetCon(&fiber[i].Presynapse.v(0.5),SC[1].Esynapse, CONNECTION_THRESHOLD_PFSC,CONNECTION_DELAY_PFSC+dprob,CONNECTION_WEIGHT_PFSC1))
}



//CF -> SC

//Increase those factor to create a CF-like effect
CF_weightfactor = 100

//CF parameters
CONNECTION_THRESHOLD_CFSC = -10
CONNECTION_DELAY_CFSC = 10 //assumed a 10ms for glu spillover
//Based on the olfactory glomerulus
//Christie and Westbrook, J Neurosci. 26: 2269-2277, 2006


CONNECTION_WEIGHT_CFSC0 = Gmax_PF_SC0_AMPAR * CF_weightfactor 
CONNECTION_WEIGHT_CFSC1 = Gmax_PF_SC1_AMPAR * CF_weightfactor 

min=0 // 0 ms delay
max=10 // 10 ms delay

objref prob
prob=new Random()


//Connecting CF -> SC 0
for i=0,NCF-1 {

dprob=prob.uniform(min,max) //normal distribution delays

fiber2[i].Presynapse SC[0].nclist.append(new NetCon(&fiber2[i].Presynapse.v(0.5),SC[0].Esynapse, CONNECTION_THRESHOLD_CFSC,CONNECTION_DELAY_CFSC+dprob,CONNECTION_WEIGHT_CFSC0))
}

//Connecting CF -> SC 1
for i=0,NCF-1 {

dprob=prob.uniform(min,max) //normal distribution delays

fiber2[i].Presynapse SC[1].nclist.append(new NetCon(&fiber2[i].Presynapse.v(0.5),SC[1].Esynapse, CONNECTION_THRESHOLD_CFSC,CONNECTION_DELAY_CFSC+dprob,CONNECTION_WEIGHT_CFSC1))
}



//SC -> PC

//SC-PC parameters
CONNECTION_THRESHOLD_SCPC = -10
CONNECTION_DELAY_SCPC = 5 // Assuming a 5ms delay for spike to reach PC 
CONNECTION_WEIGHT_SCPC_dist = Gmax_SC_PC_GABAaR_dist 
CONNECTION_WEIGHT_SCPC_prox = Gmax_SC_PC_GABAaR_prox 

//Connecting SC[0] -> PC
SC[0].soma PC[0].nclist.append(new NetCon(&SC[0].soma.v(0.5),PC[0].Isynapse_dist, CONNECTION_THRESHOLD_SCPC,CONNECTION_DELAY_SCPC,CONNECTION_WEIGHT_SCPC_dist))

//Connecting SC[1] -> PC
SC[1].soma PC[0].nclist.append(new NetCon(&SC[1].soma.v(0.5),PC[0].Isynapse_prox, CONNECTION_THRESHOLD_SCPC,CONNECTION_DELAY_SCPC,CONNECTION_WEIGHT_SCPC_prox))


//SC -> SC 

//SC-SC parameters
CONNECTION_THRESHOLD_SCSC = -10
CONNECTION_DELAY_SCSC = 2.0 // 2ms delay (Kondo and Marty, 1998) 
CONNECTION_WEIGHT_SCSC = Gmax_SC_SC_GABAaR 

//Connecting SC[0] -> SC[1] 
SC[0].soma SC[1].nclist.append(new NetCon(&SC[0].soma.v(0.5),SC[1].Isynapse, CONNECTION_THRESHOLD_SCSC,CONNECTION_DELAY_SCSC,CONNECTION_WEIGHT_SCSC))


// Background (BG) inhibitory inputs -> PC

CONNECTION_THRESHOLD_BGPC = -10
CONNECTION_DELAY_BGPC = 0.0
CONNECTION_WEIGHT_BGPC = Gmax_SC_PC_GABAaR_BG 
min=0 // 0 ms delay
max=10 // 10 ms delay

objref prob
prob=new Random()

//Connecting BG -> PC
for i=0,NSC-1 {

dprob=prob.uniform(min,max) //normal distribution delays

fiber3[i].Presynapse PC[0].nclist.append(new NetCon(&fiber3[i].Presynapse.v(0.5),PC[0].Isynapse_BG, CONNECTION_THRESHOLD_BGPC,CONNECTION_DELAY_BGPC+dprob,CONNECTION_WEIGHT_BGPC))
}

// Plotting the figures


objref grafico[6]
grafico[0]=new Graph()
grafico[0].size(0,tstop, -100, 50)
grafico[0].beginline()
grafico[0].addvar("Soma PC", &PC[0].soma.v(0.5),2,1)
grafico[0].flush()

grafico[1]=new Graph()
grafico[1].size(0,tstop, -100, 50)
grafico[1].beginline()
grafico[1].addvar("Soma SC[0]", &SC[0].soma.v(0.5),3,1)
grafico[1].flush()


grafico[2]=new Graph()
grafico[2].size(0,tstop, -100, 50)
grafico[2].beginline()
grafico[2].addvar("Soma SC[1]", &SC[1].soma.v(0.5),4,1)
grafico[2].flush()


graphList[0].append(grafico[0])
graphList[0].append(grafico[1])
graphList[0].append(grafico[2])


objref ps
ps = new PlotShape(1)
ps.variable("v")                                               
ps.exec_menu("Show Diam")
ps.exec_menu("Shape Plot")
fast_flush_list.append(ps)


//Recording data

objref PC_spiketimes, PC_nc, PC_nil
PC_spiketimes = new Vector()
PC[0].soma PC_nc=new NetCon(&PC[0].soma.v(0.5),PC_nil)
PC_nc.record(PC_spiketimes)

objref SC0_spiketimes, SC0_nc, SC0_nil
SC0_spiketimes = new Vector()
SC[0].soma SC0_nc=new NetCon(&SC[0].soma.v(0.5),SC0_nil)
SC0_nc.record(SC0_spiketimes)

objref SC1_spiketimes, SC1_nc, SC1_nil
SC1_spiketimes = new Vector()
SC[1].soma SC1_nc=new NetCon(&SC[1].soma.v(0.5),SC1_nil)
SC1_nc.record(SC1_spiketimes)


//begining
init()
run()



//save spike times

objref savdataspkt0
savdataspkt0=new File()
savdataspkt0.wopen("data_spkt_PC_soma.dat")
PC_spiketimes.printf(savdataspkt0)
savdataspkt0.close()

objref savdataspkt1
savdataspkt1=new File()
savdataspkt1.wopen("data_spkt_SC0_soma.dat")
SC0_spiketimes.printf(savdataspkt1)
savdataspkt1.close()

objref savdataspkt2
savdataspkt2=new File()
savdataspkt2.wopen("data_spkt_SC1_soma.dat")
SC1_spiketimes.printf(savdataspkt2)
savdataspkt2.close()