//moddir mod_files
load_file("nrngui.hoc")
print "This copy of Batch.hoc allows the model to be auto-launched"
print "from ModelDB. This version however stops after one time step"
print "and allows the exploration of the model through the NEURON"
print "gui interface. For example see Tools -> Model View, or use"
print "Tools -> RunControl to further run the model."
begintime = startsw()
// 2D init file
X_DIM = 10 // number of Pyramidal cells along the X dimension
Y_DIM = 10 // number of Pyramidal cells along the Y dimension
N_TYPE = 4 // number of cell types
{load_file("parlib.hoc")} // create pc and all the parallel specific functions, etc.
declare_gids()
stim_delay_offset = 1
Tfactor=0.0002
Ttau=0.0
Hfactor=0.000001
Htau=0.003
FSx=4 // Coordinates for *all* feeds
FSy=4
{load_file("sj10-cortex.hoc")}
{load_file("wiring_proc_2Dv2.hoc")}
/*
load_file("noise2D_V2.hoc")
UnoiseV(-0.3,0.3)
UnoiseII(-0.3,0.3)
UnoiseIPL5(-0.3,0.3)
UnoiseIPL2(-0.3,0.3)
*/
// Intra-cortical wiring
{load_file("wiring-SmlFeed-3_7.hoc")}
//----------------------------------------
// Mu timing
{load_file("MuBurst_10.hoc")}
//----------------------------------------
// Mu weights
{load_file("E-FFFBx_fixed_10.hoc")}
//----------------------------------------
// Evoked signal below
// Redefinition of init()
// Read files containing segment rest voltages and state variables
// at steady-state. **PL2 not comprhensive**
objref f1,f2,f3,f4,f5,f6,f7,f8,f9,f10,f11,f12,f13,f14,f15,f16
objref PL5rest,PL2rest,MAR,HCAT,MCAT,HCA,MCA,PL5CAI
objref HHH,MHH,NHH,NKCA,NKM,PL5_DPL,PL2_DPL,PL5_Q
{
f1 = new File()
{f1.ropen("./STATES/PL5_Rest.dat")}
PL5rest = new Vector()
NumF1=PL5rest.scanf(f1,1,1)
f1.close()
f2 = new File()
{f2.ropen("./STATES/PL2_Rest.dat")}
PL2rest = new Vector()
NumF2=PL2rest.scanf(f2,1,1)
f2.close()
f3 = new File()
{f3.ropen("./STATES/M_AR.dat")}
MAR = new Vector()
NumF3=MAR.scanf(f3,1,1)
f3.close()
f4 = new File()
{f4.ropen("./STATES/H_CAT.dat")}
HCAT = new Vector()
NumF4=HCAT.scanf(f4,1,1)
f4.close()
f5 = new File()
{f5.ropen("./STATES/M_CAT.dat")}
MCAT = new Vector()
NumF5=MCAT.scanf(f5,1,1)
f5.close()
f6 = new File()
{f6.ropen("./STATES/H_CA.dat")}
HCA = new Vector()
NumF6=HCA.scanf(f6,1,1)
f6.close()
f7 = new File()
{f7.ropen("./STATES/M_CA.dat")}
MCA = new Vector()
NumF7=MCA.scanf(f7,1,1)
f7.close()
f8 = new File()
{f8.ropen("./STATES/H_HH.dat")}
HHH = new Vector()
NumF8=HHH.scanf(f8,1,1)
f8.close()
f9 = new File()
{f9.ropen("./STATES/M_HH.dat")}
MHH = new Vector()
NumF9=MHH.scanf(f9,1,1)
f9.close()
f10 = new File()
{f10.ropen("./STATES/N_HH.dat")}
NHH = new Vector()
NumF10=NHH.scanf(f10,1,1)
f10.close()
f11 = new File()
{f11.ropen("./STATES/N_KCA.dat")}
NKCA = new Vector()
NumF11=NKCA.scanf(f11,1,1)
f11.close()
f12 = new File()
{f12.ropen("./STATES/N_KM.dat")}
NKM = new Vector()
NumF12=NKM.scanf(f12,1,1)
f12.close()
f13 = new File()
{f13.ropen("./STATES/PL5_Dipole.dat")}
PL5_DPL = new Vector()
NumF13=PL5_DPL.scanf(f13,1,1)
f13.close()
f14 = new File()
{f14.ropen("./STATES/PL5_CAI.dat")}
PL5CAI = new Vector()
NumF14=PL5CAI.scanf(f14,1,1)
f14.close()
f15 = new File()
{f15.ropen("./STATES/PL2_Dipole.dat")}
PL2_DPL = new Vector()
NumF15=PL2_DPL.scanf(f15,1,1)
f15.close()
//
f16 = new File()
{f16.ropen("./STATES/PL5_Q.dat")}
PL5_Q = new Vector()
NumF16=PL5_Q.scanf(f16,1,1)
f16.close()
}
// Redefine init() to use those voltages & state variables
proc init(){ local i,j,Vnum,v2num,DPnum
finitialize(-64.9737) // initialize all cells to Inhibitory rest potential
//
// Initialize Layer V Pyramidal voltage and states
for i=0,XD{
for j=0,YD{
v2num=0 Vnum=0
if (cell_exist(PL5_type, i, j)) {
PL5[i][j].soma {v=-70.197014 m_ar=0.29453859 h_cat=0.079413855 m_cat=0.091981604\
h_hh=0.75925494 m_hh=0.028240063 n_hh=0.24191157 n_km=0.011362846 h_ca=0.63961253\
m_ca=3.8876755e-05 n_kca=4.9998916e-05 cai=0.00010000285}
PL5[i][j].soma distance()
forsec PL5[i][j].dendritic for(x,0){v=PL5rest.x(Vnum) m_ar=MAR.x(Vnum)\
h_cat=HCAT.x(Vnum) m_cat=MCAT.x(Vnum) h_ca=HCA.x(Vnum) m_ca=MCA.x(Vnum)\
h_hh=HHH.x(Vnum) m_hh=MHH.x(Vnum) n_hh=NHH.x(Vnum) n_kca=NKCA.x(Vnum)\
n_km=NKM.x(Vnum) Qsum_dipole=PL5_DPL.x(Vnum) Q_dipole=PL5_Q.x(Vnum) cai=PL5CAI.x(Vnum)
Vnum=Vnum+1}
//
// dend[5] not properly set by above ???
PL5[i][j].dend[5].v = -70.22481
}
//
// Initialize Layer II Pyramidal
if (cell_exist(PL2_type, i, j)) {
PL2[i][j].soma {v=-71.462514 n_km=0.0098896622}
PL2[i][j].soma distance()
forsec PL2[i][j].dendritic for(x,0){v=PL2rest.x(v2num) Qsum_dipole=PL2_DPL.x(v2num)
v2num=v2num+1}
}
} }
// if (cvode.active()) {cvode.re_init() }else {fcurrent()}
fcurrent()
frecord_init()
}
/////////////////////////////////////////////////////////////
// Define the evoked signal with initial start times
FFgid = 1+gidAlphaend
FBgid = 2+gidAlphaend
FF2gid = 3+gidAlphaend
objref FF, FB, FF2
if (pc.id == 0) {
FF = new FeedX() // Thalamic input (Feed-forward)
FF.pp.number=1
FF.pp.start=454 - stim_delay_offset
FB = new FeedX() // Feed-Back (eg. Pre-frontal input)
FB.pp.number=1
FB.pp.start=499 - stim_delay_offset
FF2 = new FeedX() // Thalamic input (Feed-forward)
FF2.pp.number=1
FF2.pp.start=564 - stim_delay_offset
pc.set_gid2node(FFgid, pc.id)
pc.set_gid2node(FBgid, pc.id)
pc.set_gid2node(FF2gid, pc.id)
pc.cell(FFgid, new NetCon(FF.pp, nil))
pc.cell(FBgid, new NetCon(FB.pp, nil))
pc.cell(FF2gid, new NetCon(FF2.pp, nil))
}
// and connect it
{load_file("scale_ep_thresh.hoc")}
///////////////////////////////////////////////////////////////
//Total time for one run
tstop=0.05 // 1500
// time increment
dt=0.05
// Number of runs
NRUN = 1 // orig 26
proc runonce(){local runtime
//
runtime = startsw()
if (0) {
init()
while (t<tstop){
fadvance()
// below put a '%f' for every data type defined
fprint( "%f %f \n", \
t, \
L2_dipole() + L5_dipole() ) // end print statement
}
}else{
psolve(tstop)
// end of run print the total dipole
calc_total_dipole()
if (pc.id == 0) {
print_total_dipole()
}
}
if (pc.id == 0) printf("runtime = %g\n", startsw() - runtime)
} //end runonce()
make_MuBursts(400)
e_fffbx(0.00004,0.00004,5,1)
proc runit(){ local i
if (pc.id == 0) wopen("Mu_output.dat")
for i=0, NRUN-1{ runonce() //increments the evoked response starttime each run
if (pc.id == 0) {
FF.pp.start = FF.pp.start + 3.85
FB.pp.start = FB.pp.start + 3.85
FF2.pp.start = FF2.pp.start + 3.85
}
if (pc.id == 0) print(i)}
if (pc.id == 0) wopen()
}
setuptime = startsw() - begintime
if (pc.id == 0) printf("setuptime = %g\n", setuptime)
//
want_all_spikes()
runit()
spikeout()
finishtime = startsw() - begintime
if (pc.id == 0) printf("finishtime = %g\n", finishtime)
if (pc.nhost > 1) {
pc.runworker()
pc.done()
quit()
}