load_proc("nrnmainmenu")
// create a single compartment
create soma
// some fake values, make sure these correspond to others later
soma {
nseg = 1
//diam = 1.59e3 // [um], adjusted to make area 1 cm^2
//L = 1e4 // [um] = 1 cm
// 1cm^2 too large!!! Ra becomes big!
diam = 10 // [um], adjusted to make area 314 um^2
L = 10 // [um]
}
soma insert pas
//soma.cm = 18e-6 // [uF/cm^2]
//soma.g_pas = 3.2e-9 // S/cm^2
soma.cm = 5.72 // [uF/cm^2]
soma.g_pas = 1e-3 // [S/cm^2]
soma.e_pas = -88
// create the passive electrode
// apply voltage clamp
objectvar stim
stim = new VClamp(0.5)
stim {
amp0 = -70
dur0 = 10
amp1 = -90
dur1 = 100
amp2 = -70
dur2 = 10
}
// load the electrode model
//load_file("VC-electrode.ses")
{load_file("nrngui.hoc")}
objectvar save_window_, rvp_
objectvar scene_vector_[8]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List() scene_list_ = new List()}
{pwman_place(0,0,0)}
//Begin LinearCircuit[0]
{
load_file("lincir.hoc", "LinearCircuit")
}
{
ocbox_ = new LinearCircuit(1)
}
{object_push(ocbox_)}
{version(2)}
{mkelm(1, 150, 110, 2, 0)}
28
{mklabel(0, "Re", 0.077, 23.642)}
{mkelm(2, 130, 85, 2.5, -1.5708)}
0.0001
{mklabel(0, "Ce", 28.452, 1.7385)}
{mklabel(2, "", 15, 15)}
{mkelm(6, 130, 40, 2, 0)}
{mkelm(8, 230, 90, 2, 0)}
{mklabel(0, "soma(0.5)", 0.483, -19.1752)}
{sel.extra_info.set("soma", 0.5) sel.extra_info.name(sel)}
{mkelm(0, 200, 110, 3, 0)}
{mkelm(4, 110, 110, 2, 0)}
{mklabel(0, "VC", 0.711, 26.155)}
{sel.extra_info.restore()}
3
10 -70
100 -90
10 -70
{mkelm(6, 90, 90, 2, 0)}
{parasitic_ = 0 noconsist_ = 0}
{graphlist.append(new LincirGraph(this, 1))}
1
VC I (nA)
1 1 0.8 0.9 2
0 120 -1 1 // graph size
119 517 308.16 261.12 // box size
// end info
{g.exec_menu("Simulate") tool(2)}
{sel = nil}
{object_pop()}
{
{
save_window_=ocbox_.g
save_window_.size(0,300,0,200)
scene_vector_[2] = save_window_
ocbox_.g = save_window_
save_window_.save_name("ocbox_.g")
save_window_.label(150.077, 133.642, "Re", 1, 1, 0.5, 0.5, 1)
save_window_.label(158.452, 86.7385, "Ce", 1, 1, 0.5, 0.5, 1)
save_window_.label(145, 75, "", 1, 1, 0.5, 0.5, 1)
save_window_.label(230.483, 70.8248, "soma(0.5)", 1, 1, 0.5, 0.5, 1)
save_window_.label(110.711, 136.155, "VC", 1, 1, 0.5, 0.5, 1)
}
ocbox_.map("LinearCircuit[0]", 337, 414, 744, 405.12)
}
objref ocbox_
//End LinearCircuit[0]
{
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 = 120
xvalue("t","t", 2 )
tstop = 120
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(1279,584)
}
{
save_window_ = new Graph(0)
save_window_.size(4.0175,12.8925,-0.0278442,0.0259142)
scene_vector_[4] = save_window_
{save_window_.view(4.0175, -0.0278442, 8.875, 0.0537583, 517, 221, 300.48, 200.32)}
graphList[2].append(save_window_)
save_window_.save_name("graphList[2].")
save_window_.addvar("soma.i_cap( 0.5 )", 1, 1, 0.637061, 0.986262, 2)
save_window_.addvar("soma.i_pas( 0.5 )", 2, 1, 0.630671, 0.967093, 2)
}
{
save_window_ = new Graph(0)
save_window_.size(6.04,17.54,-0.0429,0.0841)
scene_vector_[5] = save_window_
{save_window_.view(6.04, -0.0429, 11.5, 0.127, 193, 223, 300.48, 200.32)}
graphList[2].append(save_window_)
save_window_.save_name("graphList[2].")
save_window_.addexpr("LinearCircuit[0].VC_I", 1, 1, 0.528434, 0.971885, 2)
save_window_.addexpr("soma.i_pas( 0.5 ) * area(0.5) * 1e-2", 2, 1, 0.307987, 0.947923, 2)
}
{
save_window_ = new Graph(0)
save_window_.size(0,130,-90,-70)
scene_vector_[7] = save_window_
{save_window_.view(0, -90, 130, 20, 842, 221, 300.48, 200.32)}
graphList[2].append(save_window_)
save_window_.save_name("graphList[2].")
save_window_.addvar("soma.v( 0.5 )", 1, 1, 0.8, 0.9, 2)
}
objref xvec, yvec, xline[10], yline[10], savefile
xvec=new Vector()
yvec = new Vector()
proc readGraph() { local graphindex, i, j
graphindex = $1
// copied from example
// TODO make this one read the graph name and then save the whole
// thing as a binary file to be read by trace
j =0
for (i=-1; (i = Graph[graphindex].getline(i, xvec, yvec)) != -1 ; j+=1 ) {
// xvec and yvec contain the line with Graph internal index i.
// and can be associated with the sequential index j.
print j, i, yvec.label
xline[j] = xvec.c
yline[j] = yvec.cl // clone label as well
}
}
proc saveCurrent() { local graphindex, i, j, n
graphindex = $1
strdef filename
i = Graph[graphindex].getline(-1, xvec, yvec)
print "Size: ", xvec.size()
// Build the filename with some more info like dt and dy
sprint(filename, "%s_dt_%fms_dy_1e-9nA_vclamp_-70_to_%d_mV.bin", $s2, xvec.x[1], LinearCircuit[0].VC_amp1)
savefile=new File(filename)
savefile.wopen()
n = yvec.vwrite(savefile)
print "Wrote ", n, " bytes to ", filename, ".\n"
savefile.close()
}
objectvar scene_vector_[1]
{doNotify()}
// simulate & save current into file
run()
saveCurrent(1, "Ic")
LinearCircuit[0].VC_amp1 = -50
run()
saveCurrent(1, "Ic")
// TODO: make a for loop and save all 4 steps