www.neuron.yale.edu

Posted: **Thu Jul 05, 2007 10:25 am**

Hi everybody,

I am just staring with Neuron. I tried to create a soma with hh conductances. When I insert everything in the console, the model runs properly (i.e. I see the action potentials). However, when I load directly the .hoc file, I only see an step in voltage in response to a current step.

Code: Select all


/*soma.hoc */

load_proc("nrnmainmenu")

tstop = 500
v_init = -70
celsius = 37


create soma
access soma
{nseg=1 L=30 diam=30 Ra=123.0}

insert hh

objectvar stimulator
stimulator = new IClamp(0.5)
stimulator.del = 100
stimulator.dur = 200
stimulator.amp = 0.5

/* additional menus*/
nrnmainmenu()
nrncontrolmenu()
newPlotV()

If I load the corresponding hoc file, I can see the inserted mechanisms and hh properties (with forall psection()), but the model does not work properly. Would anybody be so kind to assist me here with the code.

Another question. Do i have to open/close Neuron every time that I want to load the modified the hoc file?.This is a little bit disturbing...

Thank you very much in advance.

Posted: **Thu Jul 05, 2007 1:52 pm**

1. See https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=177

2. Work through the tutorials on the Documentation page.

3. As much as possible, use the GUI to specify model properties and
control simulations.

4. Use the d_lambda rule (selectable from the Cell Builder at the click of
a button, but also usable from hoc--see the FAQ list) to specify spatial
discretization.

5. If it is ever necessary to write hoc code, structure your program as
follows:

Code: Select all

load_file("nrngui.hoc")
specify model topology (create sections, connect sections)
specify model geometry (stylized (L, diam) or pt3d method as appropriate)
specify instrumentation (IClamps, SEClamps, other Point Processes, graphs)
specify simulation flow control (RunControl panel is sufficient for most purposes)

6. Avoid load_proc()--it's very slow under MSWin, so unless you swear never
to use MSWin or exchange code with MSWin users, it's more bother than
it's worth.

7. Avoid writing your own "main computational loop" (i.e. a "for" or "while"
loop that calls fadvance() to march the simulation through time)--use the
standard run system's run() to launch simulations.

8. Use topology(), psection(), and especially the GUI's Model View tool to
discover what is actually in a model and verify a close match between
the model in the computer and the model in your mind. Especially if there
is a mismatch between what the model does and what you expected it to do.

Nin wrote:When I insert everything in the console, the model runs properly (i.e. I see the action potentials). However, when I load directly the .hoc file, I only see an step in voltage in response to a current step.
. . .
If I load the corresponding hoc file, I can see the inserted mechanisms and hh properties (with forall psection()), but the model does not work properly.

See item 8 above.

Do i have to open/close Neuron every time that I want to load the modified the hoc file?

It is mandatory if class definitions ("templates") have been altered.
It is the safest policy if the changes alter the structure of the model's
system equations (e.g. by affecting model topology), or remove
mechanisms or objects whose parameters and/or variables are
referenced elsewhere.

Posted: **Thu Jul 05, 2007 2:14 pm**

Model-specific comments:
1. HH doesn't work well at 37 deg C. Standard temp for the HH squid axon model
is 6.3 deg C. At high temp, gna inactivates so quickly, and gk activates so
rapidly, that excitability is severely compromised.
2. Because of 1, at 37 deg C the model can only produce a partially
regenerative depolarizing bump, and eliciting that requires use of a very
brief stimulus with carefully adjusted amplitude. 4 nA x 0.1 ms will bring this
out (rises about 10 mV above the charging transient caused by the injected
current). With larger peak current, the regenerative bump becomes difficult
to distinguish from the charging transient. Prolonged depolarization with
0.5 nA only elicits a nonregenerative bump (v sags back toward ek because
of activation of gk).
3. Standard resting potential for the HH model is -65 mV at 6.3 deg C (about
-65.8 mV at 37 deg C). Settting vinit to -70 only forces the model away from
its resting potential, requiring several ms after start of a run for things to
settle.

Posted: **Thu Jul 05, 2007 3:09 pm**

Dear Ted,

thank you very much for your wisdom advices (and specially for the model-specific comments). The problem was solved changing just the temperature (and I changed V_init as well). I've just started with Neuron, and I need to become more familiar with it (I own the book, by the way).

Actually, I was trying to build a model of the backpropagation of action potentials in the dendrites, and its amplification by the calcium channels located distally. I started with the most simplistic concept to start working with it (and learn a little bit the language).

My most sincere gratitude for your help.

Nin

www.neuron.yale.edu

single spiking soma.

single spiking soma.

Re: single spiking soma.