{load_file("nrngui.hoc")} // load the GUI and standard run libraries //////////Parameters////////////////////////// connect_random_low_start_ = 1 NCELL = 1 n_simul=1 // number of simulations, load_file("ranstream.hoc") load_file("pyramidal_cell4b.hoc") load_file("stim_cell.hoc") cvode_active(1) tstopI=200 tstop =tstopI+200 strdef str, flagname str="HH" celsius=34 flagname="Control" redsAHP=1 redmAHP=1 tauca=3.6 thna3=-28 thna3dend=-28 somakap =0.007 somakad =0.007 somacaL=0.006// AD case 0.01 ctrl 0.006 ghsoma = 0.00004 somacaT= 0.0007// 0.0004 shift=0 shiftkap=shift shiftkad=shift shifth=shift shifth=shift //******************************************** //////////////////// v_init=-65 // resting potential /////////////////////// objref cells,ncstim[40],ranlist3,ranlist4,rs1,rs2,rs3,rs4,ncslist, nclist,ncc[40],ncslist2, nclist2,ncc2[100],ncstim2[100],rs,rs2 proc mkcells() {local i localobj cell cells = new List() for i=0, $1-1 { cell = new PyramidalCell(redsAHP,redmAHP,v_init,tauca,thna3,thna3dend,somakap,somakad,ghsoma,somacaT,somacaL,shift) cells.append(cell) } } proc input(){ mcell_ran4_init(1) Nstim=20 Nstim2=20 rs = new RandomStream ($1*2+1) for i=0, Nstim-1 { ncstim[i] = new StimCell() ncc[i]= ncstim[i].stim //EC ncc[i].number = 100000 ncc[i].start = 100 ncc[i].interval = 25 ncc[i].noise = 0.2 ncc[i].noiseFromRandom(rs.r) rs.r.normal(0,1) rs.start() } rs2 = new RandomStream ($1*2) for i=0, Nstim2-1 { ncstim2[i] = new StimCell() // CA3 //ncstim2[i] = new NetStim(.5) ncc2[i]= ncstim2[i].stim //ncc2[i]=ncstim2[i] ncc2[i].number = 100000 ncc2[i].start = 100+9 ncc2[i].interval = 25 ncc2[i].noise = 0.2 ncc2[i].noiseFromRandom(rs2.r) rs2.r.normal(0,1) rs2.start() } } ECW=0.001 proc connectcells() {local i,k,s,j localobj synE2,src,nc,ncs,synE ncslist = new List() nclist = new List() for i=0, cells.count-1 { // iterating over sources for k=0, Nstim-1{ src = ncstim[k].stim //src = ncstim[i] synE = cells.object(i).pre_list.object(0) nc = new NetCon(src, synE) nclist.append(nc) nc.delay = 1 nc.weight =ECW synE2 = cells.object(i).pre_list.object(1) ncs = new NetCon(src, synE2) ncslist.append(ncs) ncs.delay = 1 ncs.weight =ECW } } } proc concells2() {local i,k,s,j localobj synE2,src2,nc2,ncs2,synE ncslist2 = new List() nclist2 = new List() for i=0, cells.count-1 { // iterating over sources for k=0, Nstim2-1{ src2 = ncstim2[k].stim //src2 = ncstim2[k] synE = cells.object(i).pre_list.object(23) synE.d=0*8/2 synE.p=0*(1.2)/2 nc2 = new NetCon(src2, synE) nclist2.append(nc2) nc2.delay = 1 nc2.weight =$1 synE2 = cells.object(i).pre_list.object(3) ncs2 = new NetCon(src2, synE2) ncslist2.append(ncs2) ncs2.delay = 1 ncs2.weight =$2 } } } //// Instrumentation, i.e. stimulation and recording//// objref apc, v1 proc insert_APC() { apc = new APCount(0.5) apc.thresh = -20 v1 = new Vector() apc.record(v1) } objref clamp2 proc insert_IClamp2() { clamp2 = new IClamp(0.5) clamp2.del = 100 clamp2.dur = tstopI clamp2.amp = $1 } /////////////////////////////////////////////// objref tvec, idvec // will be Vectors that record all spike times (tvec) proc spikerecord() {local i localobj nc, nil // if ($1==0){ tvec = new Vector() idvec = new Vector() // } for i=0, NCELL-1 { cells.object(i).soma nc=new NetCon(&v(1),nil,10,1,0.01) nc.record(tvec, idvec, i) // the Vector will continue to record spike times // even after the NetCon has been destroyed } } ///////////////// currents ///// proc caT_insert() { for (x) if (x>0 && x<1) { xdist = distance(x) insert cat if (xdist < 300) { gcatbar_cat(x) = $1*(1+xdist/60) } else { gcatbar_cat(x) = $1*6 } } } proc caL_insert() { cal_distance=200 for (x) if (x>0 && x<1) { xdist = distance(x) insert calH mytau_calH=$2 if (xdist < cal_distance) { gcalbar_calH(x) = $1 *(1-xdist/cal_distance) } else { gcalbar_calH(x) = 0 } } } proc A_h_insert(){ ghend=$1*7 dhalf=280 steep=50 KMA=3 insert h ghdbar_h=0 insert kap gkabar_kap = 0 insert kad gkabar_kad = 0 for (x) if (x>0 && x<1) { xdist=distance(x) ghdbar_h(x)= $1 + (ghend - $1)/(1.0 + exp((dhalf-xdist)/steep)) if (xdist < 100){ gkabar_kap(x) = $2*(1+KMA*xdist/100) vhalfl_h=-73 }else{ vhalfl_h=-81 gkabar_kad(x) = $3*(1+KMA*xdist/100) // print secname(), " ",xdist, gkabar_kad(x) } } } proc acc_dist(){local i for i=0, cells.count-1 { access cells.object(i).soma distance(0,x) access cells.object(i).radTprox A_h_insert(ghsoma,somakap,somakad) caT_insert(somacaT) caL_insert(somacaL,tauca) access cells.object(i).radTmed A_h_insert(ghsoma,somakap,somakad) caT_insert(somacaT) caL_insert(somacaL,tauca) access cells.object(i).radTdist A_h_insert(ghsoma,somakap,somakad) caT_insert(somacaT) caL_insert(somacaL,tauca) access cells.object(i).lm_thick1 A_h_insert(ghsoma,somakap,somakad) access cells.object(i).lm_medium1 A_h_insert(ghsoma,somakap,somakad) access cells.object(i).lm_thin1 A_h_insert(ghsoma,somakap,somakad) access cells.object(i).lm_thick2 A_h_insert(ghsoma,somakap,somakad) access cells.object(i).lm_medium2 A_h_insert(ghsoma,somakap,somakad) access cells.object(i).lm_thin2 A_h_insert(ghsoma,somakap,somakad) } } /// Report simulation results-save potential and time//////////////////////// proc spikeout() { local i printf("\ntime\t cell\n") for i=0, tvec.size-1 { printf("%g\t %d\n", tvec.x[i], idvec.x[i]) } } objref rect, recv, listrecv proc potential_record() {local i rect = new Vector() listrecv = new List() rect.record(&t) for i=0, cells.count-1 { recv = new Vector() recv.record(&cells.object(i).soma.v(0.5)) listrecv.append(recv) } } /////////Main//////////////// mkcells(NCELL) objref vec,vec_2,savdata3 strdef name3 proc batchrun() { local i,k sum=0 sum_2=0 mean=0 mean_2=0 SD=0 vec=new Vector(n_simul) vec_2=new Vector(n_simul) for i=1,$1 { printf("\nRun %d\n", i) run() printf("//////Simulation: %d ////// \n", i) printf("g: %f| # Spike: %d\n", $2, apc.n) //calculates mean and standard deviation vec.x[i-1]=apc.n vec_2.x[i-1]=(apc.n)^2 temp=sum + vec.x[i-1] temp_2=sum_2 + vec_2.x[i-1] sum=temp sum_2=temp_2 } // end for i //////Mean and SD///////// mean = sum/n_simul mean_2 = sum_2/n_simul SD=sqrt(mean_2-mean^2) printf("___________________\n") printf("Mean: %lf\n", mean) printf("Std. Dev.: %lf\n", SD) printf("___________________\n") if ($1==1) { savdata3.printf("%f \t %d\n",$2, apc.n) }else{ savdata3.printf("%.2f \t %.2f \t %.2f\n",$2*1000,mean,SD) } } acc_dist() inizio=6 for j=inizio,6{ current=j*0.05 access cells.object(0).soma insert_IClamp2(current) insert_APC() cells.object(0).current_balance(v_init) CWT=0.0004+j*0.00005 CNWT=0.00045 if (j==inizio){ savdata3 = new File() sprint(name3,"Simulation_%s.dat",str) savdata3.wopen(name3) savdata3.printf("Current \t # Spikes\n") //savdata3.printf("g \t # Spikes \t SD\n") } load_file("ses.ses") batchrun(n_simul,current,CWT,CNWT) } // for savdata3.close() //quit()
