www.neuron.yale.edu

I'm glad you posted that code. These are good questions: Now the proc setrates() is called on every time step. However, I wonder what is the impact of this on the calculation speed. Is this similar to the NMODL mechanisms where the rates are usually called on every timestep? Similar in effect. (unle...

Apart from moving a reconstructed cell is there an easy way to rotate it in 3D space? You can view it from different angles. See http://www.neuron.yale.edu/neuron/static/courses/2008/course/zclass/shape.htm which is from this tutorial on how to analyze the electrotonic properties of a cell http://w...

I've never had any difficulty removing .i686 directories under MSWin 2K or XP. Who knows
what limitations exist when trying to do that via a login under Citrix.

Very strange.

I am using Windows.

Sounds like you're using Linux--why do you have i686 folders? Are you compiling NEURON
from source code? Under Linux, rm -rf i686 should remove i686 and any subdirs.

If the model's geometry was defined with pt3d specification, you can import it into a
CellBuilder, then save the CellBuilder to a session file. If geometry was defined using
the stylized (L, diam) specification, you're out of luck.

eacheon wrote:Why did this get removed in NEURON 5.8?

??
It works in 5.8. Have you encountered an instance in which it doesn't?

You have stumbled upon something that is an accident of history. In NEURON's early incarnations, hoc had scalars, doubles (arrays), sections, and strdefs (strings). Object-oriented programming was added later, and with it came objrefs. Consequently doubles, sections, and strdefs "aren't quite o...

when I try to run the same simulation outside the runFitter I get quite a different response Then the assumption that you have "run the same simulation" is false, i.e. an instance of mismatch between what's in your head and what's in the computer. Such mismatches are often cases of the &q...

That's much better than what I suggested. Today I learned something new and useful--
thanks!

The Graph class has a label() method, but the xy values are not "model coordinates"-- they are "relative position within the displayed window" i.e. they range from 0 to 1 where 0,0 and 1,1 are the LL and UR corners of the window itself, respectively. You could still used it; just...

You're raising a provocative question. I'm surprised--or maybe not surprised--that this hasn't yet received comments. Model reduction is a very broad topic. One could say that a form of model reduction happens every time someone cooks up a conceptual model that can be mapped into a computational mod...

Use a different random number seed for each instance and/or simulation run. See http://www.neuron.yale.edu/neuron/static/docs/help/neuron/general/classes/random.html A reasonable strategy is to create a set of seeds in advance. For the sake of reproducibility, you may also want to record a log file ...

I think there should be one central repository for NEURON knowlegde. Depends on the meaning of "one central repository." One thing it should not mean: stuffing everything into a wiki. wiki has obvious strengths for certain kinds of documentation, but it also has undeniable weaknesses that...

You're right, most of those Google hits don't really describe the mechanism of anode break excitation. Anode break is an "old" term, from long before microelectrodes were invented. Physiologists used extracellular electrodes to stimulate nerves. Stimulus electrodes were applied to the outs...

Google finds 627 hits. At least a dozen of those should explain it fairly well. The first page
of Google's hits even includes one on this forum. There might also be something on
Wikipedia, but I didn't bother to check.