## Help in understanding the terms in a code

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ram1712
Posts: 12
Joined: Thu Nov 07, 2013 8:25 am

### Help in understanding the terms in a code

Hi,
I have this reference programme . The final section is a code which plots a voltage graph for soma,axon dendrite in a C-fibre

// graph
x = 0.5
objref g
g = new Graph()
g.size(0,tstop,-100,100)
for i = 0,idend-1 {
}

If possible can somebody please explain me this part of the code

2) what are the numbers (3,2), (2,2) used to plot soma and axon respectively??

The entire code for reference:-

idend = 1 // number of dendrites
create soma, dend[idend], axon
connect axon(0), soma(0) // connect the soma and axon
for i = 0,idend-1 {
connect dend(0), soma(1) // connect the soma and dendrite
}
// axon <=> soma <=> dendrite(s)

soma {
L = 30 // um
diam = 30 // um
nseg = 1
insert hh

// Ion Channels
insert fvnag3e // Nav 1.7 channel: endings of pain-sensing nerves
insert nav1p8 // Nav 1.8 channel: slow kinetics
insert nav1p9 // Nav 1.9 channel: preferentially expressed in pain fibers
insert ka // Ka channel: repetitive firing of neurons
insert km // Km channel: excitability of pain fibers
insert kdrs // Kdr channel: many specific K channels, slow
insert kdrf // Kdr channel: many specific K channels, fast
insert emdkna // KNa channel: slow After Hyperpolarization (AHP)
insert h // hyperpolarization-activated cationic channel
}

for i = 0,idend-1 dend {
// L = 100 um
diam = 1.5 // um
nseg = 23
insert pas
g_pas = 0.0002
e_pas = -65
}

axon {
nseg = 250
L = 12500 // um, 12.5cm
diam(0:0.8) = 1:1 // um
diam(0.8:0.84) = 1:0.25 // um
diam(0.84:1) = 0.25:0.25 // um
insert hh

// Ion Channels
insert fvnag3e // Nav 1.7 channel: endings of pain-sensing nerves
insert nav1p8 // Nav 1.8 channel: slow kinetics
insert nav1p9 // Nav 1.9 channel: preferentially expressed in pain fibers
insert ka // Ka channel: repetitive firing of neurons
insert km // Km channel: excitability of pain fibers
insert kdrs // Kdr channel: many specific K channels, slow
insert kdrf // Kdr channel: many specific K channels, fast
insert emdkna // KNa channel: slow After Hyperpolarization (AHP)
insert h // hyperpolarization-activated cationic channel
}

topology() // check branched architecture of model
forall psection() // generate a printoout of the gemoetry and biophysical properties of each section

// simulation control
dt = 0.025
tstop = 100

// stimulation electrode
objref stim
soma stim = new IClamp(0.5)
stim.amp = 10 // amplitude, nA
stim.del = 1 // delay, ms
stim.dur = 0.1 // duration, ms

// graph
x = 0.5
objref g
g = new Graph()
g.size(0,tstop,-100,100)
for i = 0,idend-1 {
}

run()
oren
Posts: 55
Joined: Fri Mar 22, 2013 1:03 am

### Re: Help in understanding the terms in a code

Hello ram,

g = new Graph() // create a new graph ( like figure in matlab)
addplot(g, 0) // add the graph to the graphList[0] so it will be updated each run.
g.size(0,tstop,-100,100) // sets the axis limits .size(xstart, xstop, ystart, ystop)

g.addvar("soma.v(x)",3,2) // (.., color_index, brush_index) test and see what colors you get as it says in the comments blue :-)

http://www.neuron.yale.edu/neuron/stati ... graph.html

and on other commands in here:
http://www.neuron.yale.edu/neuron/stati ... rence.html
ted
Posts: 5810
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

### Re: Help in understanding the terms in a code

Thanks, oren! Right on target.
ram1712
Posts: 12
Joined: Thu Nov 07, 2013 8:25 am

Thanks Oren