// init_gui.hoc allows the choice of simulations to run associated with
// the paper: Axonal spheroids and conduction defects in Alzheimer’s
// disease reversed by PLD3 modulation. Peng Yuan, Mengyang
// Zhang, Lei Tong, Thomas M. Morse, Robert A. McDougal, Hui Ding,
// Diane Chan, Yifei Cai, Jaime Grutzendler
{
load_file("nrngui.hoc")
load_file("alz_axon_serial_GUI.hoc")
}
{
xpanel("Yuan, Zhang, Tong, et al")
  xlabel("Supplementary Material")
  xlabel("Extended Data Figure 2 examples")
  xlabel("Click on a button to run")
  xbutton("Ext. Fig. 2a)left Normal","ext_fig_2a_left()")
  xbutton("Ext. Fig. 2a)middle Delayed","ext_fig_2a_middle()")
  xbutton("Ext. Fig. 2a)left Blocked","ext_fig_2a_right()")
  xbutton("Ext. Fig. 2b) Blocked, then delayed AP from 20 Hz input","ext_fig_2b()")
  xlabel("Ext. Fig. 2e)top Single AP input long run (day)")
  xlabel("  Please see the readme for instructions")
  xlabel("Ext. Fig. 2e)bottom 20Hz AP input long run (day)")
  xlabel("  Please see the readme for instructions")
  xbutton("Quit","quit()")
xpanel(400,400)
}

ran_2b=0
proc ext_fig_2a_left() {
if (ran_2b) {
ic.amp=0.02
ic.dur=1
ic.del=100
objref ic_amp_vec
}
Can {L=1e-3
diam=1e-3}
tstop=150
init()
run()
if (ran_2b) {
Graph[0].xaxis(0,150)
Graph[0].xaxis(0)
Graph[0].exec_menu("View = plot")
}
}
proc ext_fig_2a_middle() {
Can {L=29
diam=29}
tstop=150
ic.dur=1
init()
run()
if (ran_2b) {
Graph[0].xaxis(0,150)
Graph[0].xaxis(0)
Graph[0].exec_menu("View = plot")
}
}
proc ext_fig_2a_right() {
Can {L=40
diam=40}
tstop=150
ic.dur=1
init()
run()
if (ran_2b) {
Graph[0].xaxis(0,150)
Graph[0].xaxis(0)
Graph[0].exec_menu("View = plot")
}
}
proc ext_fig_2b() {
Can {L=53
diam=53}
xopen("make_pulse.hoc")
ic.dur=1e7
{ic_amp_vec.play(&ic.amp, dt) }
tstop=1300
init()
run()
{
Graph[0].exec_menu("View = plot")
Graph[0].xaxis(3)        
Graph[0].xaxis(100, 1300)
Graph[0].yaxis(-80, 50)
}
ran_2b=-1 // -1 is true meaning will need to readjust axis for earlier figs
}
proc ext_fig_2e_top() {
print "instructions"
}
proc ext_fig_2e_bottom() {
print "instructions"
}