i think i did not explain my query clearly.
i again tried to solve the problem but remain unsucessful.
Here i explain it in more detail.
Here is my session file. (i develop it using gui)
Code: Select all
{load_file("nrngui.hoc")}
objectvar save_window_, rvp_
objectvar scene_vector_[5]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List() scene_list_ = new List()}
{pwman_place(0,0,0)}
//Begin CellBuild[0]
{
load_file("celbild.hoc", "CellBuild")
}
{ocbox_ = new CellBuild(1)}
{object_push(ocbox_)}
{
version(5.7)
continuous = 1
}
{object_push(topol)}
{
first = 0
slist.remove_all()
sname = "axon"
objref tobj
}
{
tobj = new CellBuildSection("soma",0, 0, tobj, 0) slist.append(tobj)
tobj.position(0,0,15,0) tobj.lx=7.69231 tobj.ly=-15.2767 tobj.i3d=0
tobj = new CellBuildSection("apical",0, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(0)
tobj.position(15,0,105,0) tobj.lx=85.4251 tobj.ly=-14.0621 tobj.i3d=0
tobj = new CellBuildSection("axon",0, 0, tobj, 0) slist.append(tobj)
tobj.parent=slist.object(0)
tobj.position(0,0,-150,0) tobj.lx=-82.1862 tobj.ly=-11.6329 tobj.i3d=0
tobj = new CellBuildSection("basilar",0, 0, tobj, 0) slist.append(tobj)
tobj.parent=slist.object(0)
tobj.position(0,0,-105,60) tobj.lx=-37.247 tobj.ly=46.6667 tobj.i3d=0
all_init()
}
for i=0, slist.count-1 {slist.object(i).rdses()}
{object_pop()}
{
}
{object_push(subsets)}
{first = 0}
{ tobj = snlist.object(0)}
{tobj = new SNList("has_HH") snlist.append(tobj)}
for i=0,1 tobj.add(bild.topol.slist.object(fscan()))
0
2
{tobj = new SNList("no_HH") snlist.append(tobj)}
for i=0,1 tobj.add(bild.topol.slist.object(fscan()))
1
3
{consist()}
{object_pop()}
{
}
{object_push(geom)}
{
first = 0
tobj = new GeoSpec(7)
tobj.value = 0.1
bild.subsets.snlist.object(0).geo.append(tobj)
tobj = new GeoSpec(2)
tobj.value = 30
bild.topol.slist.object(0).geo.append(tobj)
tobj = new GeoSpec(3)
tobj.value = 30
bild.topol.slist.object(0).geo.append(tobj)
tobj = new GeoSpec(2)
tobj.value = 1000
bild.topol.slist.object(1).geo.append(tobj)
tobj = new GeoSpec(3)
tobj.value = 1
bild.topol.slist.object(1).geo.append(tobj)
tobj = new GeoSpec(2)
tobj.value = 1000
bild.topol.slist.object(2).geo.append(tobj)
tobj = new GeoSpec(3)
tobj.value = 1
bild.topol.slist.object(2).geo.append(tobj)
tobj = new GeoSpec(2)
tobj.value = 1000
bild.topol.slist.object(3).geo.append(tobj)
tobj = new GeoSpec(3)
tobj.value = 2
bild.topol.slist.object(3).geo.append(tobj)
set_default()
}
{object_pop()}
{
}
{object_push(memb)}
{first=0}
{
tobj = new FakeMechStan(1)
tobj.value = 1
tobj.set_default()
tobj = new MStanWrap(tobj, 0)
bild.subsets.snlist.object(0).ml.append(tobj)
}
{
tobj = new FakeMechStan(0)
tobj.value = 100
tobj.set_default()
tobj = new MStanWrap(tobj, 0)
bild.subsets.snlist.object(0).ml.append(tobj)
}
{
tobj = new MechanismStandard("hh")
tobj.set("gnabar_hh", 0.12, 0)
tobj.set("gkbar_hh", 0.036, 0)
tobj.set("gl_hh", 0.0003, 0)
tobj.set("el_hh", -54.3, 0)
tobj = new MStanWrap(tobj, 1)
bild.subsets.snlist.object(1).ml.append(tobj)
}
{
tobj = new MechanismStandard("pas")
tobj.set("g_pas", 0.0002, 0)
tobj.set("e_pas", -65, 0)
tobj = new MStanWrap(tobj, 1)
bild.subsets.snlist.object(2).ml.append(tobj)
}
{object_pop()}
{
}
{object_push(manage)}
{
first = 0
classname = "Cell"
etop=1 esub=1 egeom=1 emem=1
itop=1 isub=0 igeom=0 imem=0
bild.topol.names_off = 0
bild.topol.circles_off = 0
output_index = 0 output_x = 1
thresh = 10
}
{object_pop()}
{
cexport()
}
{object_pop()}
{
save_window_=ocbox_.gtopol
save_window_.size(-200,200,-150,150)
scene_vector_[2] = save_window_
ocbox_.gtopol = save_window_
save_window_.save_name("ocbox_.gtopol")
}
{
ocbox_.map("CellBuild[0]", 978, 42, 774, 755.1)
}
objref ocbox_
//End CellBuild[0]
//Begin PointProcessManager
{
load_file("pointman.hoc")
}
{
basilar ocbox_ = new PointProcessManager(0)
}
{object_push(ocbox_)}
{
mt.select("IClamp") i = mt.selected()
ms[i] = new MechanismStandard("IClamp")
ms[i].set("del", 5, 0)
ms[i].set("dur", 50, 0)
ms[i].set("amp", 1, 0)
mt.select("AlphaSynapse") i = mt.selected()
ms[i] = new MechanismStandard("AlphaSynapse")
ms[i].set("onset", 0.5, 0)
ms[i].set("tau", 0.1, 0)
ms[i].set("gmax", 0.05, 0)
ms[i].set("e", 0, 0)
mt.select("SEClamp") i = mt.selected()
ms[i] = new MechanismStandard("SEClamp")
ms[i].set("rs", 1, 0)
ms[i].set("dur1", 100, 0)
ms[i].set("amp1", 10, 0)
ms[i].set("dur2", 0, 0)
ms[i].set("amp2", 0, 0)
ms[i].set("dur3", 0, 0)
ms[i].set("amp3", 0, 0)
mt.select("IClamp") i = mt.selected() maction(i)
hoc_ac_ = 0.22
sec.sec move() d1.flip_to(0)
}
{object_pop() doNotify()}
{
ocbox_ = ocbox_.v1
ocbox_.map("PointProcessManager", 1224, 564, 279.9, 594)
}
objref ocbox_
//End PointProcessManager
{
xpanel("RunControl", 0)
v_init = -65
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 = 50
xvalue("t","t", 2 )
tstop = 50
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 = 0.05
xvalue("Scrn update invl","screen_update_invl", 1,"", 0, 1 )
realtime = 0.05
xvalue("Real Time","realtime", 0,"", 0, 1 )
xpanel(733,582)
}
{
save_window_ = new Graph(0)
save_window_.size(0,50,-80,40)
scene_vector_[4] = save_window_
{save_window_.view(0, -80, 50, 120, 1260, 151, 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)
}
objectvar scene_vector_[1]
{doNotify()}
when i run it, it gives a graph of soma voltage vs time.
there are 4 spikes/peaks in this graph.
Now if we increase the Iclamp amplitude to 2nA, there will be 5 spikes.
similarly for 4nA there will be 6 spikes/peaks.
increase in current amplitude.
Y-axis spike frequency corresponding to that current.
for this, first we have to find the spike frequency for a particular current.
when i put these line in the .ses file. (with in the Runcontrol braces)
it gives error.