// Author: Ronald van Elburg (RonaldAJ at vanElburg eu)
//
// NEURON script for the paper:
//
// Ronald A.J. van Elburg and Arjen van Ooyen (2010) `Impact of dendritic size and
// dendritic topology on burst firing in pyramidal cells',
// PLoS Comput Biol 6(5): e1000781. doi:10.1371/journal.pcbi.1000781.
//
// Please consult readme.txt or instructions on the usage of this file.
//
// This software is released under the GNU GPL version 3:
// http://www.gnu.org/copyleft/gpl.html
objectvar save_window_, rvp_
objectvar scene_vector_[4]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
load_file("../modelSimplifiedCells.hoc")
tstop = 5000 //tstop = 10000 used in paper
//Transform MRC_Slice(No) number to multidimensional quantity
double MRC_SliceIndex[3]
NaSliceNo=int(MRC_Slice/4) // Combined 2D Km-KCa ranges contains four points
KmSliceNo=int((MRC_Slice-4*NaSliceNo)/2) // KCa ranges contains two points
KCaSliceNo=MRC_Slice-4*NaSliceNo-2*KmSliceNo
MRC_SliceIndex[0]=NaSliceNo
MRC_SliceIndex[1]=KmSliceNo
MRC_SliceIndex[2]=KCaSliceNo
proc customModifications(){
setNa("dend")
setKm("dend")
setKCa("dend")
}
proc setNa(){local sectionLength localobj allSections
allSections=new SectionList()
forsec $s1 {
allSections.append()
}
forsec allSections {
if(bActiveDendrites==1){
gbar_na = 15*NaFactor // fast Na+
}
}
}
proc setKm(){local sectionLength localobj allSections
allSections=new SectionList()
forsec $s1 {
allSections.append()
}
forsec allSections {
if(bActiveDendrites==1){
gbar_km = 0.1*KmFactor // slow voltage dependent non-inactivating K+
}
}
}
proc setKCa(){local sectionLength localobj allSections
allSections=new SectionList()
forsec $s1 {
allSections.append()
}
forsec allSections {
if(bActiveDendrites==1){
gbar_kca = 3*KCaFactor // slow Ca++ activated K+
}
}
}
{ocbox_list_ = new List() scene_list_ = new List()}
{
xpanel("RunControl", 0)
v_init = -70
xvalue("Init","v_init", 1,"stdinit()", 1, 1 )
xbutton("Init & Run","run()")
xbutton("Stop","stoprun=1")
runStopAt = 5
xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 )
runStopIn = 1
xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 )
xbutton("Single Step","steprun()")
t = 0
xvalue("t","t", 2 )
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
dt = 0.025
xvalue("dt","dt", 1,"setdt()", 0, 1 )
steps_per_ms = 40
xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 )
screen_update_invl = 1
xvalue("Scrn update invl","screen_update_invl", 1,"", 0, 1 )
realtime = 0
xvalue("Real Time","realtime", 0,"", 0, 1 )
xpanel(-1,1500)
}
{
save_window_ = new Graph(0)
save_window_.size(0,1500,-80,40)
scene_vector_[3] = save_window_
{save_window_.view(0, -80, 1500, 120, 295, 661, 300.6, 200.8)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addexpr("v(.5)", 1, 1, 0.8, 0.9, 2)
}
{
save_window_ = new PlotShape(0)
save_window_.size(-346.486,1827.84,-58.5592,2115.77)
save_window_.variable("v")
scene_vector_[2] = save_window_
{save_window_.view(-346.486, -58.5592, 2174.33, 2174.33, 714, 661, 200.7, 200.8)}
fast_flush_list.append(save_window_)
save_window_.save_name("fast_flush_list.")
}
//Begin MultipleRunControlGUI[0]
{
load_file("../hoc/mrc/MultipleRunControl.hoc","MultipleRunControlGUI")
}
{
ocbox_ = new MultipleRunControlGUI(1)
}
{object_push(ocbox_)}
{
file_name="SimplifiedTopologiesGKCaGActScan/Results/Sim"
file_index_start=0
}
{tobj=new MRC_Protocol()}
{object_push(tobj)}
{
output_matlab_mfile=0
output_neuronbinary=1
output_axontextfile=0
}
{object_pop()}
{protocol=tobj}
{tobj=new MRC_LoopParameter()}
{object_push(tobj)}
{
name="NaFactor"
lower_limit=0.9
upper_limit=1.1
stepsize=0.2
restart=2
restart_at=lower_limit+ MRC_SliceIndex[0]*stepsize
end_before=lower_limit+( MRC_SliceIndex[0]+1)*stepsize
use=1
setdisplaytext()
}
{object_pop()}
{looppars.append(tobj)}
{tobj=new MRC_LoopParameter()}
{object_push(tobj)}
{
name="KmFactor"
lower_limit=0.7
upper_limit=1.3
stepsize=0.6 //stepsize=0.2 used in paper
restart=2
restart_at=lower_limit+MRC_SliceIndex[1]*stepsize
end_before=lower_limit+(MRC_SliceIndex[1]+1)*stepsize
use=1
setdisplaytext()
}
{object_pop()}
{looppars.append(tobj)}
{tobj=new MRC_LoopParameter()}
{object_push(tobj)}
{
name="KCaFactor"
lower_limit=0.7
upper_limit=1.3
stepsize=0.6 //stepsize=0.2 used in paper
restart=2
restart_at=lower_limit+MRC_SliceIndex[2]*stepsize
end_before=lower_limit+(MRC_SliceIndex[2]+1)*stepsize
use=1
setdisplaytext()
}
{object_pop()}
{looppars.append(tobj)}
{tobj=new MRC_LoopParameter()}
{object_push(tobj)}
{
name="currentTopologyNo"
lower_limit=1
upper_limit=23
stepsize=11 // stepsize=1 used in paper
use=1
setdisplaytext()
}
{object_pop()}
{looppars.append(tobj)}
{tobj=new MRC_LoopParameter()}
{object_push(tobj)}
{
name="bStimSoma"
lower_limit=0 // lower_limit=0 used in paper
upper_limit=1
stepsize=1
use=1
setdisplaytext()
}
{object_pop()}
{looppars.append(tobj)}
{tobj=new MRC_LoopParameter()}
{object_push(tobj)}
{
name="totalDendriticLength"
lower_limit=1000
upper_limit=3500
stepsize=500 // stepsize=25 used in paper
use=1
setdisplaytext()
}
{object_pop()}
{looppars.append(tobj)}
{tobj1=types_outpar.gettypefromindex(2)}
{tobj=new MRC_OutputVariable("spikes",tobj1,protocol)}
{object_push(tobj)}
{
use=1
setdisplaytext()
}
{object_pop()}
{tobj1=tobj.gethandler()}
{object_push(tobj1)}
{
record_start=0
record_stop=9000
threshold=0
listname="soma"
sectionname=""
membername="v(0.5)"
listtype=2
useindexing=0
isart=0
shortname="spikes"
}
{object_pop()}
{outpars.append(tobj)}
{tobj1=types_outpar.gettypefromindex(1)}
{tobj=new MRC_OutputVariable("vtrace_soma",tobj1,protocol)}
{object_push(tobj)}
{
use=0
setdisplaytext()
}
{object_pop()}
{tobj1=tobj.gethandler()}
{object_push(tobj1)}
{
record_start=0
record_stop=9000
sectionname="soma"
membername="v(0.5)"
useindexing=0
isart=0
shortname="vtrace_soma"
}
{object_pop()}
{outpars.append(tobj)}
{object_pop()}
{
ocbox_.map("MultipleRunControlGUI[0]", 931, 134, 399.6, 385.2)
}
objref ocbox_
//End MultipleRunControlGUI[0]
objectvar scene_vector_[1]
{doNotify()}
if(name_declared("MRC_Slice")==5){
execute("looprun()",MultipleRunControlGUI[0])
}