I try to delete dendrites in my code. The aim is to investigate firing patterns, and as when active dendrites are present, dendritic topology may influence firing behaviour, I want to delete dendrites, or their ion channels. I tried both, but this did not succeed.
The whole model is this:
http://senselab.med.yale.edu/ModelDB/Sh ... ell1zr.hoc
The main hoc file (ca3b-cell1zr.hoc) contains this code, which is related to the dendrites:
Code: Select all
numaxon=1
numsoma=1
[u]numbasal=52
numapical=81[/u]
...
xopen("geo-cell1zr.hoc")
xopen("fixnseg.hoc")
...
}
forall {insert pas area(.5)}
[i]forsec "dendrite" {
insert ds
insert hd
insert na3
insert kdr
insert kap
insert cacum depth_cacum=diam/2
insert cal
insert can
insert cat
insert cagk
insert KahpM95
}[/i]
forsec "soma" {
insert ds
insert hd
insert na3
insert kdr
insert kap
insert km
insert kd
insert cacum depth_cacum=diam/2
insert cal
insert can
insert cat
insert cagk
insert KahpM95
}
forsec "axon" {
insert na3
insert kdr
insert kap
}
proc init() {
access soma
forall {
v=Vrest e_pas=Vrest
if (ismembrane("cal")) {
gcalbar_cal=gc
gcanbar_can=gc
gcatbar_cat=gc
gbar_cagk= gKc
gbar_KahpM95 = gahp
}
}
forsec "axon" {
gbar_na3=gna*AXONM
gkdrbar_kdr=gkdr
gkabar_kap = KMULTP sh_kap=0
}
forsec "soma" {
ghdbar_hd=ghd
gbar_na3=gna
gkdrbar_kdr=gkdr
gkabar_kap = KMULTP
gbar_km= gkm
gkdbar_kd = gkd
}
for i=0, numbasal-1 dendrite[i] {
ghdbar_hd=ghd
gbar_na3=gna
gkdrbar_kdr=gkdr
gkabar_kap=KMULTP
}
[i]forsec "apical_dendrite" {
ghdbar_hd=ghd
gbar_na3=gna
gkdrbar_kdr=gkdr
gkabar_kap=KMULTP
}[/i]
The second option for me was to delete all dendrites. Therefore, in the hoc file I deleted the above italic code, and the underscore code, plus all geometry in the geo-cell1zr.hoc file which was related to dendrites, till only the code below was left:
Code: Select all
//changed axon and soma
{create soma[1.]}
{create axon[1]}
{access soma[0.]}
{pt3dclear()}
{pt3dadd(-1.135,21.,1.702,13.21)}
{pt3dadd(-1.135,21.,12.92,13.21)}
{soma[0] connect axon[0](0), 1}
{access axon[0]}
{pt3dclear()}
{pt3dadd(-0.568,-1,-0.023,1.5)}
{pt3dadd(3.5,7,7,1)}
{pt3dadd(5.5,14,7,1)}
{pt3dadd(6.5,22.5,6,1)}
{pt3dadd(6,29.5,7,1)}
{pt3dadd(1.5,36,12,1)}
{pt3dadd(-2.5,41,14,1)}
{pt3dadd(-7.5,45,15.5,1)}
{pt3dadd(-9,45,19.5,1)}
{pt3dadd(-13.5,45.5,22.5,1)}
{pt3dadd(-16.5,47,25.5,1)}
{pt3dadd(-11.5,51.5,30,1)}
{pt3dadd(-11.5,54.5,36.5,1)}
{pt3dadd(-11,57.5,40.5,1)}
{pt3dadd(-8.5,60.5,44.5,1)}
Thank you in advance.