Spatial gridding and temporal accuracy in NEURON (Hines and Carnevale 2001)

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Accession:53451
A heuristic for compartmentalization based on the space constant at 100 Hz is proposed. The paper also discusses spatio/temporal accuracy and the use of CVODE.
Reference:
1 . Hines ML, Carnevale NT (2001) NEURON: a tool for neuroscientists. Neuroscientist 7:123-35 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Tutorial/Teaching; Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
{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 = "dend"
objref tobj
}
{
tobj = new CellBuildSection("soma",0, 0, tobj, 0) slist.append(tobj)
  tobj.position(0.203,-0.587,0.203,-0.587) tobj.lx=0.203 tobj.ly=-0.587 tobj.i3d=2
tobj = new CellBuildSection("dend",0, 0, tobj, 0.5) slist.append(tobj)
tobj.parent=slist.object(0)
  tobj.position(0.203,-0.587,1.197,5.118) tobj.lx=0.7 tobj.ly=2.2655 tobj.i3d=7
tobj = new CellBuildSection("dend",1, 0, tobj, 0.5) slist.append(tobj)
tobj.parent=slist.object(0)
  tobj.position(0.203,-0.587,-1.988,-10.429) tobj.lx=-0.8925 tobj.ly=-5.508 tobj.i3d=13
tobj = new CellBuildSection("dend",2, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(1)
  tobj.position(1.197,5.118,-5.977,12.78) tobj.lx=-2.39 tobj.ly=8.949 tobj.i3d=8
tobj = new CellBuildSection("dend",3, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(1)
  tobj.position(1.197,5.118,24.735,36.386) tobj.lx=12.966 tobj.ly=20.752 tobj.i3d=16
tobj = new CellBuildSection("dend",4, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(1)
  tobj.position(1.197,5.118,0.395,9.83) tobj.lx=0.796 tobj.ly=7.474 tobj.i3d=7
tobj = new CellBuildSection("dend",5, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(3)
  tobj.position(-5.977,12.78,-81.574,342.446) tobj.lx=-43.7755 tobj.ly=177.613 tobj.i3d=46
tobj = new CellBuildSection("dend",6, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(3)
  tobj.position(-5.977,12.78,-16.554,265.742) tobj.lx=-11.2655 tobj.ly=139.261 tobj.i3d=72
tobj = new CellBuildSection("dend",7, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(4)
  tobj.position(24.735,36.386,67.008,111.723) tobj.lx=45.8715 tobj.ly=74.0545 tobj.i3d=15
tobj = new CellBuildSection("dend",8, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(4)
  tobj.position(24.735,36.386,100.117,241.345) tobj.lx=62.426 tobj.ly=138.866 tobj.i3d=34
tobj = new CellBuildSection("dend",9, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(5)
  tobj.position(0.395,9.83,13.593,94.987) tobj.lx=6.994 tobj.ly=52.4085 tobj.i3d=18
tobj = new CellBuildSection("dend",10, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(5)
  tobj.position(0.395,9.83,-0.598,11.797) tobj.lx=-0.1015 tobj.ly=10.8135 tobj.i3d=3
tobj = new CellBuildSection("dend",11, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(8)
  tobj.position(67.008,111.723,166.686,376.436) tobj.lx=116.847 tobj.ly=244.08 tobj.i3d=48
tobj = new CellBuildSection("dend",12, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(8)
  tobj.position(67.008,111.723,172.313,271.832) tobj.lx=119.661 tobj.ly=191.778 tobj.i3d=37
tobj = new CellBuildSection("dend",13, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(9)
  tobj.position(100.117,241.345,110.491,259.843) tobj.lx=105.304 tobj.ly=250.594 tobj.i3d=10
tobj = new CellBuildSection("dend",14, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(9)
  tobj.position(100.117,241.345,85.563,320.422) tobj.lx=92.84 tobj.ly=280.883 tobj.i3d=22
tobj = new CellBuildSection("dend",15, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(10)
  tobj.position(13.593,94.987,27.956,177.41) tobj.lx=20.7745 tobj.ly=136.199 tobj.i3d=17
tobj = new CellBuildSection("dend",16, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(10)
  tobj.position(13.593,94.987,-66.986,304.67) tobj.lx=-26.6965 tobj.ly=199.829 tobj.i3d=33
tobj = new CellBuildSection("dend",17, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(11)
  tobj.position(-0.598,11.797,-15.56,125.689) tobj.lx=-8.079 tobj.ly=68.743 tobj.i3d=22
tobj = new CellBuildSection("dend",18, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(11)
  tobj.position(-0.598,11.797,-115.87,243.311) tobj.lx=-58.234 tobj.ly=127.554 tobj.i3d=57
tobj = new CellBuildSection("dend",19, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(16)
  tobj.position(27.956,177.41,89.179,360.334) tobj.lx=58.5675 tobj.ly=268.872 tobj.i3d=22
tobj = new CellBuildSection("dend",20, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(16)
  tobj.position(27.956,177.41,30.747,187.24) tobj.lx=29.3515 tobj.ly=182.325 tobj.i3d=7
tobj = new CellBuildSection("dend",21, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(17)
  tobj.position(-66.986,304.67,-77.156,328.084) tobj.lx=-72.071 tobj.ly=316.377 tobj.i3d=8
tobj = new CellBuildSection("dend",22, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(17)
  tobj.position(-66.986,304.67,-96.694,377.849) tobj.lx=-81.84 tobj.ly=341.26 tobj.i3d=12
tobj = new CellBuildSection("dend",23, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(18)
  tobj.position(-15.56,125.689,-2.587,316.682) tobj.lx=-9.0735 tobj.ly=221.186 tobj.i3d=38
}
{
tobj = new CellBuildSection("dend",24, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(18)
  tobj.position(-15.56,125.689,-66.195,327.666) tobj.lx=-40.8775 tobj.ly=226.677 tobj.i3d=36
tobj = new CellBuildSection("dend",25, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(19)
  tobj.position(-115.87,243.311,-174.709,322.581) tobj.lx=-145.29 tobj.ly=282.946 tobj.i3d=23
tobj = new CellBuildSection("dend",26, 0, tobj, 1) slist.append(tobj)
tobj.parent=slist.object(19)
  tobj.position(-115.87,243.311,-132.424,325.925) tobj.lx=-124.147 tobj.ly=284.618 tobj.i3d=25
all_init()
}
for i=0, slist.count-1 {slist.object(i).rdses()}
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84.761 309.213 6.325 0.54
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13.593 94.987 -17.595 0.88
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76.817 302.116 -36.395 0.54
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{object_pop()}
{
}
{object_push(subsets)}
{first = 0}
{ tobj = snlist.object(0)}
{consist()}
{object_pop()}
{
}
{object_push(geom)}
{
first = 0
tobj = new GeoSpec(7)
tobj.value = 0.3
bild.subsets.snlist.object(0).geo.append(tobj)
set_default()
}
{object_pop()}
{
}
{object_push(memb)}
{first=0}
{
tobj = new FakeMechStan(0)
tobj.value = 200
tobj.set_default()
tobj = new MStanWrap(tobj, 0)
bild.subsets.snlist.object(0).ml.append(tobj)
}
{
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 MechanismStandard("pas")
tobj.set("g_pas", 2.5e-05, 0)
tobj.set("e_pas", -70, 0)
tobj = new MStanWrap(tobj, 1)
bild.subsets.snlist.object(0).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 = 1
bild.topol.circles_off = 1
output_index = 0  output_x = 1
}
{object_pop()}
{
cexport()
}
{object_pop()}
{
save_window_=ocbox_.gtopol
save_window_.size(-248.177,248.177,-20,380)
scene_vector_[2] = save_window_
ocbox_.gtopol = save_window_
save_window_.save_name("ocbox_.gtopol")
}
{
ocbox_.map("CellBuild[0]", 62, 486, 822.72, 374.4)
}
objref ocbox_
//End CellBuild[0]


//Begin PointProcessManager
{
load_file("pointman.hoc")
}
{
soma ocbox_ = new PointProcessManager(0)
}
{object_push(ocbox_)}
{
mt.select("AlphaSynapse") i = mt.selected()
ms[i] = new MechanismStandard("AlphaSynapse")
ms[i].set("onset", 0, 0)
ms[i].set("tau", 1, 0)
ms[i].set("gmax", 0.002, 0)
ms[i].set("e", 0, 0)
mt.select("AlphaSynapse") i = mt.selected() maction(i)
hoc_ac_ = 0.5
sec.sec move() d1.flip_to(0)
}
{object_pop() doNotify()}
{
ocbox_ = ocbox_.v1
ocbox_.map("PointProcessManager", 379, 3, 208.32, 326.4)
}
objref ocbox_
//End PointProcessManager

{
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 = 10
xvalue("t","t", 2 )
tstop = 10
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 = 0.0200002
xvalue("Real Time","realtime", 0,"", 0, 1 )
xpanel(74,82)
}
{
save_window_ = new Graph(0)
save_window_.size(0,10,-70,-60)
scene_vector_[4] = save_window_
{save_window_.view(0, -70, 10, 10, 612, 5, 300.48, 200.32)}
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()}

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