// written by Gabriela Cirtala
// Heterogenous ion channel conductance density model
// This code corresponds to Branch 8 of the PC (Figure 4A-C in Cirtala2024)
// This code only runs the case of 76PF (i.e. the threshold for br8)
// Shows the dendritic spike propagation (check the shape plot at the PF activation time)
// this code is based on the homogenous model proposed by Zang et al. (Zang 2021).
load_file("nrngui.hoc")
Default_Eleak = -65
membranecap = 0.64 /* specific membrane capacitance in uF cm^-2 */
membraneresist = 120236 /* specific membrane resistance in ohm cm^2 */
axialresist = 120 /* axial resistivity in ohm cm */
xopen("PurkinjeMorphology_allbr.nrn") // Load the morphology file.
forsec "axon" delete_section() // Delete original axon and add a fake AIS
objref g2, b2,c2, distrx, distry, cdistry, p
forall {
insert pas e_pas=Default_Eleak /* Insert Leak everywhere */
insert hpkj // Ih inserted everywhere
insert ds
insert pk
}
AIS { g_pas=1/membraneresist Ra=axialresist cm=membranecap}
forsec spinydend {g_pas=5.3/membraneresist Ra=axialresist cm=5.3*membranecap}
forsec maindend {g_pas=1.2/membraneresist Ra=axialresist cm=1.2*membranecap}
forsec "soma" { g_pas=1/membraneresist Ra=axialresist cm=membranecap}
forsec maindend {insert cdp4N}
forsec alldend {
insert Kv3
gbar_Kv3 = 0.1512
vshift_Kv3 = 4
insert newCaP
pcabar_newCaP = 1.90e-4
vshift_newCaP =-5
insert CaT3_1
pcabar_CaT3_1 = 2.7e-5
insert mslo
gbar_mslo = 0.21504
insert SK2
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
ghbar_hpkj = 0.00036
insert Kv1
gbar_Kv1 = 0.002//*2
insert Kv4
gbar_Kv4 = 0.0252
insert Kv4s
gbar_Kv4s = 0.015
}
forsec spinydend {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch1 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch2 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch3 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch4 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch5 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch6 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch7 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch8 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04*0.9
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch9 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch10 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch11 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch12 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04*0.8
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch13 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch14 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch15 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch16 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch17 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch18 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264*1.0
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch19 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264*1.0
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch20 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264*1.0
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch21 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP =7.6000e-04*0.8
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
forsec branch22 {
insert cdp4Nsp
gkbar_SK2 = 3.6000e-04
scal_SK2 = 1.0
gbar_Kv4 = 0.0264
gbar_Kv4s = 0.015
ghbar_hpkj = 3.2400e-04
vshift_Kv4 = 0
gbar_Kv1 = 0.001
gbar_Kv3 = 0.1512
vshift_Kv3 = 0
pcabar_CaT3_1 = 1.0800e-04
pcabar_newCaP = 7.6000e-04*0.8
vshift_newCaP = -5
scale_cdp4Nsp = 3.5
gbar_mslo = 0.0896
insert abBK
gabkbar_abBK = 0.15
}
access somaA
somaA distance(0,0.5)
forsec "soma" {
// INa & IK's at soma only
//for soma, I make it fire under dissociated condition. The firing properties is comparable with Bean's data
insert naRsg // INa + resurgent
gbar_naRsg = 0.03168
vshifta_naRsg = 0
vshiftk_naRsg = 0
vshifti_naRsg = -5
insert nap
gbar_nap = 1.4000e-04
insert pk
ena = 63
ghbar_hpkj = 1.0800e-04 // Default = 1
insert cdp20N_FD2
insert Kv3
gbar_Kv3 = 1.8
vshift_Kv3 = 4
insert Kv1
gbar_Kv1 = 0
insert newCaP
pcabar_newCaP = 1.9000e-04
kt_newCaP = 1
vshift_newCaP = -5
insert mslo
gbar_mslo = 0.8736
insert abBK
gabkbar_abBK = 0.3
insert SK2
gkbar_SK2 = 0.0075
}
AIS {
insert naRsg // INa + resurgent
gbar_naRsg = 0.56
vshifta_naRsg = 15
vshiftk_naRsg = 5
vshifti_naRsg = -5
insert nap
gbar_nap = 0.0023
insert CaT3_1
pcabar_CaT3_1 = 1.2800e-04
ena = 63
ghbar_hpkj = 1.0800e-04
insert cdpAIS
insert Kv3
gbar_Kv3 = 115.2
vshift_Kv3 = 4
insert Kv1
gbar_Kv1 = 0
insert newCaP
pcabar_newCaP = 0.00228
kt_newCaP = 1
vshift_newCaP = -5
insert mslo
gbar_mslo = 6
insert abBK
gabkbar_abBK = 1.05
insert SK2
gkbar_SK2 = 0.0278
}
objref patch_site
patch_site = new List()
ip = 0
forsec patch_list {
patch_site.append(new SectionRef())
}
celsius = 34
dt = 0.02
steps_per_ms = 1/dt
dtsim = 0.02
objref g2, b2,c2, distrm, distrd
xopen ("electrode.hoc")
xopen("distri.hoc") //voltage spatial distribution
proc clamp_cc() {
somaA {
stim1.del = 0
stim1.dur = 1000000
stim1.amp = $1
}
}
v_init = -70
tstop = 600
objref scalefile
scalefile=new File()
xopen("distri_synapse.hoc")
objref pc
pc = new ParallelContext()
//function farmed out to slave nodes
func distscale() {local key, errval, cu_id, fr_id, dend_id localobj parvec, returnlist
key = $1
cu_id = int($1/100000000)
fr_id = int(($1 - cu_id*100000000)/1000000)
site_id = int(($1 - cu_id*100000000-fr_id*1000000)/10000)
dend_id = int(($1 - cu_id*100000000-fr_id*1000000-site_id*10000)/100)
trial_id = $1 - cu_id*100000000-fr_id*1000000-site_id*10000-dend_id*100
returnlist = new List()
returnlist = calc_EPSP_single(cu_id,fr_id,site_id,dend_id,trial_id)
pc.pack(returnlist.o(0))
pc.pack(returnlist.o(1))
pc.pack(returnlist.o(2))
pc.pack(returnlist.o(3))
pc.pack(returnlist.o(4))
pc.pack(returnlist.o(5))
pc.pack(returnlist.o(6))
pc.pack(returnlist.o(7))
pc.pack(returnlist.o(8))
pc.pack(returnlist.o(9))
pc.pack(returnlist.o(10))
pc.pack(returnlist.o(11))
pc.pack(returnlist.o(12))
pc.pack(returnlist.o(13))
pc.pack(returnlist.o(14))
pc.pack(returnlist.o(15))
pc.pack(returnlist.o(16))
pc.pack(returnlist.o(17))
pc.pack(returnlist.o(18))
pc.pack(returnlist.o(19))
pc.pack(returnlist.o(20))
pc.pack(returnlist.o(20))
pc.post(key)
return key
}
objref aSynapseList[11]
objref recording, baby1, babyend,babybranchlet, temone,terminal
obfunc calc_EPSP_single() {localobj outlist, currecord, integ_soma, br1,tip,onpath,patch,br1_dist,br1_prox,br2_dist,br2_prox,br3_dist,br3_prox,br4_dist,br4_prox,br5_dist,br5_dist2,br5_prox,br5_prox2,br6_dist,br6_prox,br7_dist,br7_prox,br8_dist,br8_prox,br8_mid
//function to calculate the max deflection due to a single synapse
cu_id = $1
fr_id = $2
siteval = $3
synval= $4
tr_id = $5
curr = -0.4+(cu_id-1)*0.2
nlist = fr_id // in fact nlist can be multiple, make synapses firing at bursting
Npf = 2+(synval-1)*2
for i = 1,nlist {aSynapseList[i-1] = new List() } // every time this will be initialized.
randomseed = cu_id*100000000+fr_id*1000000+siteval*10000 +synval*100 + tr_id
br1 = new SectionList()
patch_site.o(siteval-1).sec br1.subtree()
br1.remove(cf)
br1.unique()
if (siteval==12) {
br1 = new SectionList()
forsec "dendA1_001101100*" br1.append()
}
if (i==13) {
br1 = new SectionList()
forsec "dendA1_0011011100*" br1.append()
forsec "dendA1_0011011101*" br1.append()
}
for i = 1,nlist {aSynapseList[i-1] = distSyns(Npf,br1,randomseed)}
for i = 1,nlist {
for ii=1,aSynapseList[i-1].count() {
aSynapseList[i-1].object(ii-1).onset = 410
aSynapseList[i-1].object(ii-1).tau0 = 0.3
aSynapseList[i-1].object(ii-1).tau1 = 3
aSynapseList[i-1].object(ii-1).e = 0
aSynapseList[i-1].object(ii-1).gmax = 0.5e-3//
}
}
forsec br1 {
temone = new SectionRef()
if (temone.nchild == 0) {temone.sec terminal = new SectionRef()}
}
outlist=new List()
integ_soma = new Vector()
integ_soma.record(&somaA.v(0.5))
tip = new Vector()
tip.record(&terminal.sec.v(0.5))
patch = new Vector()
patch.record(&patch_site.o(siteval-1).sec.v(0.5))
br1_dist = new Vector()
br1_dist.record(&dendA1_00001101.v(0.05))
br1_prox = new Vector()
br1_prox.record(&dendA1_000.v(0.05))
br2_dist = new Vector()
br2_dist.record(&dendA1_001000111.v(0.05))
br2_prox = new Vector()
br2_prox.record(&dendA1_00100.v(0.05))
br3_dist = new Vector()
br3_dist.record(&dendA1_0010101100.v(0.05))
br3_prox = new Vector()
br3_prox.record(&dendA1_001010.v(0.05))
br4_dist = new Vector()
br4_dist.record(&dendA1_00101101001111.v(0.05))
br4_prox = new Vector()
br4_prox.record(&dendA1_00101100.v(0.05))
br5_dist = new Vector()
br5_dist.record(&dendA1_00101110101000110.v(0.05))
br5_dist2 = new Vector()
br5_dist2.record(&dendA1_0010111011000.v(0.05))
br5_prox = new Vector()
br5_prox.record(&dendA1_001011101111.v(0.05))
br5_prox2 = new Vector()
br5_prox2.record(&dendA1_0010111010.v(0.05))
br6_dist = new Vector()
br6_dist.record(&dendA1_0010111100111.v(0.05))
br6_prox = new Vector()
br6_prox.record(&dendA1_0010111100.v(0.05))
br7_dist = new Vector()
br7_dist.record(&dendA1_0010111101011001111.v(0.05))
br7_prox = new Vector()
br7_prox.record(&dendA1_00101111010.v(0.05))
br8_dist = new Vector()
br8_dist.record(&dendA1_001011110110010101.v(0.05))
br8_prox = new Vector()
br8_prox.record(&dendA1_001011110110.v(0.05))
br8_mid = new Vector()
br8_mid.record(&dendA1_00101111011001.v(0.05))
clamp_cc(curr)
finitialize(v_init)
continuerun(tstop)
outlist.append(integ_soma)
outlist.append(tip)
outlist.append(patch)
outlist.append(br1_dist)
outlist.append(br1_prox)
outlist.append(br2_dist)
outlist.append(br2_prox)
outlist.append(br3_dist)
outlist.append(br3_prox)
outlist.append(br4_dist)
outlist.append(br4_prox)
outlist.append(br5_dist)
outlist.append(br5_dist2)
outlist.append(br5_prox)
outlist.append(br5_prox2)
outlist.append(br6_dist)
outlist.append(br6_prox)
outlist.append(br7_dist)
outlist.append(br7_prox)
outlist.append(br8_dist)
outlist.append(br8_prox)
outlist.append(br8_mid)
return outlist
}
pc.runworker()
objref somavec, tipvec, patchvec, onpathvec,br1_distvec, br1_proxvec, br2_distvec, br2_proxvec,br3_distvec, br3_proxvec,br4_distvec, br4_proxvec, br4_distvec, br4_proxvec,br5_distvec, br5_distvec2,br5_proxvec,br5_proxvec2,br6_distvec,br6_proxvec,br7_distvec,br7_proxvec,br8_distvec,br8_proxvec,br8_midvec
somavec = new Vector()
tipvec = new Vector()
patchvec = new Vector()
br1_distvec = new Vector()
br1_proxvec = new Vector()
br2_distvec = new Vector()
br2_proxvec = new Vector()
br3_distvec = new Vector()
br3_proxvec = new Vector()
br4_distvec = new Vector()
br4_proxvec = new Vector()
br5_distvec = new Vector()
br5_distvec2 = new Vector()
br5_proxvec = new Vector()
br5_proxvec2 = new Vector()
br6_distvec = new Vector()
br6_proxvec = new Vector()
br7_distvec = new Vector()
br7_proxvec = new Vector()
br8_distvec = new Vector()
br8_proxvec = new Vector()
br8_midvec = new Vector()
strdef tmpstr
strdef outDir
strdef cmd
objref outfile
outfile = new File()
proc calcEPSPs() {
sprint(outDir,"Results")
sprint(cmd, "system(\"mkdir -p %s\")",outDir)
execute(cmd)
somaA distance(0,0.5)
for cu = 3, $1 {
for freq = 1, $2 {
for site = $3, $3 {
for m = $4, $4 {
for nt =$5 ,$5 {
mmtag=cu*100000000 + freq*1000000 + site*10000+m*100 + nt
pc.submit("distscale",mmtag) //send out the error calculations
}
}
}
}
}
//collect error values
while (pc.working()) {
key = pc.retval() //retrieve the tag
pc.look_take(key) //remove the tag/job from the bulletin
somavec = pc.upkvec() //unpack the error value associated with the tag
tipvec = pc.upkvec()
patchvec = pc.upkvec()
br1_distvec = pc.upkvec()
br1_proxvec = pc.upkvec()
br2_distvec = pc.upkvec()
br2_proxvec = pc.upkvec()
br3_distvec = pc.upkvec()
br3_proxvec = pc.upkvec()
br4_distvec = pc.upkvec()
br4_proxvec = pc.upkvec()
br5_distvec = pc.upkvec()
br5_distvec2 = pc.upkvec()
br5_proxvec = pc.upkvec()
br5_proxvec2 = pc.upkvec()
br6_distvec = pc.upkvec()
br6_proxvec = pc.upkvec()
br7_distvec = pc.upkvec()
br7_proxvec = pc.upkvec()
br8_distvec = pc.upkvec()
br8_proxvec = pc.upkvec()
br8_midvec = pc.upkvec()
print "received key ",key
cuno = int(key/100000000)
frno = int((key- cuno*100000000)/1000000)
siteno = int((key - cuno*100000000 - frno*1000000)/10000)
synno= int((key - cuno*100000000 - frno*1000000 - siteno*10000)/100)
trno = key - cuno*100000000-frno*1000000-siteno*10000-synno*100
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vsoma.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
somavec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vtip.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
tipvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vpatch.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
patchvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr1_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br1_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr1_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br1_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr2_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br2_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr2_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br2_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr3_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br3_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr3_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br3_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr4_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br4_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr4_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br4_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr5_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br5_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr5_dist2.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br5_distvec2.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr5_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br5_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr5_prox2.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br5_proxvec2.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr6_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br6_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr6_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br6_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr7_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br7_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr7_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br7_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr8_dist.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br8_distvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr8_prox.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br8_proxvec.printf(outfile)
outfile.close()
sprint(tmpstr,"%s/%03d_%03d_%03d_%03d_%03d_vbr8_mid.dat",outDir,cuno,frno,siteno,synno,trno)
outfile.wopen(tmpstr)
br8_midvec.printf(outfile)
outfile.close()
}
}
calcEPSPs(3,1,8,38,1)
// This codes reproduces Figure 4A-C from Cirtala2024
// Therefore only the case corresponding to br8 - for 76PF (branch 8 PF threshold value)
// If you wish to run it for the entire range of PF please change the following line inside of the proc calcESP:
// for m = $4, $4 ---> for m = 1, $4
// and instead of 35 in calcEPSPs, please put the maximum number of PF you want (e.g. 75 corresponds to 150PF)