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.