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_[4]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List()  scene_list_ = new List()}
{pwman_place(0,0,0)}

//Begin PointProcessManager
{
load_file("pointman.hoc")
}
{
soma ocbox_ = new PointProcessManager(0)
}
{object_push(ocbox_)}
{
mt.select("IClamp") i = mt.selected()
ms[i] = new MechanismStandard("IClamp")
ms[i].set("del", 0, 0)
ms[i].set("dur", 1000, 0)
ms[i].set("amp", 0.001, 0)
mt.select("IClamp") 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", 203, 500, 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 = 80
xvalue("t","t", 2 )
tstop = 100
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
dt = 40
xvalue("dt","dt", 1,"setdt()", 0, 1 )
steps_per_ms = 0.025
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
xvalue("Real Time","realtime", 0,"", 0, 1 )
xpanel(139,90)
}
{
xpanel("soma(0 - 1) (Parameters)", 0)
xlabel("soma(0 - 1) (Parameters)")
xlabel("nseg = 1")
soma.L = 5.64
xvalue("L","soma.L", 1,"define_shape()", 0, 0 )
soma.diam = 5.64
xvalue("diam","soma.diam", 1,"", 0, 0 )
soma.cm = 1
xvalue("cm","soma.cm", 1,"", 0, 0 )
soma.g_pas = 5e-05
xvalue("g_pas","soma.g_pas", 1,"", 0, 0 )
soma.e_pas = -70
xvalue("e_pas","soma.e_pas", 1,"", 0, 0 )
xpanel(437,266)
}
{
save_window_ = new Graph(0)
save_window_.size(0,100,-70,-50)
scene_vector_[3] = save_window_
{save_window_.view(0, -70, 100, 20, 444, 2, 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)
}

//Begin VariableTimeStep
{
ocbox_ = NumericalMethodPanel[0]
}
{object_push(ocbox_)}
{
atol_ = 0.001  CVode[0].atol(atol_)
restore(201, 1)
}
{object_pop()}
{
ocbox_.map("VariableTimeStep", 436, 516, 272.64, 113.28)
}
objref ocbox_
//End VariableTimeStep

objectvar scene_vector_[1]
{doNotify()}

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