www.neuron.yale.edu

Sounds like a cosmetic problem to me... You are right, of course. I use it as it is now. I thought that not running all those plots during the simulation would save me some time in an unattended run (don't know it it's true), so while I was at it I wanted to run without the GUI completely. But the ...

Thank you for your reply and additional hints! Also, on-screen rendering of the GUI's graphical elements can be suppressed by including -nogui in the command line, e.g. nrngui -nogui foo.hoc, without affecting numerical results. How do I do that from within Python? The AtolTool window opens even if ...

Hi, I want to port a model from use with the GUI to a batch mode controlled by Python. Everything seems to work except for the variable timestepping settings which were done using the AtolTool (see https://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=3232 ). I have the following code in my .ses fi...

Thank you very much!!

Thank you, Michael, for pointing me to the documentation. For the records: it can be found at https://github.com/neuronsimulator/nrn . However, I have given up for the moment. I get an "invalid package name" error when I try to configure, and I feel that it will not be the last one. And I am not sur...

Hi,

the problem occurs when the python executable is not in your Path environment variable. If you type in a terminal and get the python prompt, it should be OK. Else you have to locate python.exe and add that directory to your Path.

HTH,
Matthias

Almost all of the links (except Ramain's tutorial) are dead.
But I have found Andrew Davison's instructions here: http://andrewdavison.info/notes/

It does. Thank you!

Hi, I am one step further: export PATH=/cygdrive/c/ProgrammePlus/MinGW/bin:$PATH export PATH=/cygdrive/c/ProgrammePlus/MinGW/msys/1.0/bin:$PATH fixed the "command not found" messages. Now I have a different problem: bash-4.4$ ./configure --prefix=`pwd` /usr/bin/sed: -e expression #1, char 1: unknown...

Hi, I would like to use an extracellular mechanism with more than 2 layers. In the documentation it says that this is possible if I recompile Neuron. So I have downloaded nrn-7.6.2.tar.gz here: https://www.neuron.yale.edu/neuron/getstd . Since I just want to change the number of extracellular layers...

Thank you for the quick reply!

ted wrote: ↑

Tue Oct 16, 2018 10:18 am

If the x and y values are updated in the course of a simulation, use
NEURON Main Menu / Graph / Phase plane

That is what I have tried. But I don't manage to display my vectors there. Is there a description somewhere how to do it with the GUI (if possible)?

Hi, I want to make a plot using vectors for x and y coordinates. I have built them myself, i.e. they do not figure in the standard NEURON variables. So I don't have access using "plot what?" in a plot window. I have found the vec.plot on the documentation. But how do I build such a plot using the GU...

Hi, normally it is good practice to search in the forum before asking questions. However, very often a search query gets rejected with a message like the following: The following words in your search query were ignored because they are too common words: plot gui vector (In this case I really want to...

OK, this explains the "mysterious" term. Since in the post it was written Starting from scratch, treating the potential at each node as "relative to ground," and using these definitions (...) v, vext[0], and vext[1] are the potentials indicated in the diagram that is part of NEURON's documentation o...

Hi Ted, I am confused. I don't understand how you derive your equations, and I get different ones if I do it. I paste here the picture from the documentation: Ra o/`--o--'\/\/`--o--'\/\/`--o--'\/\/`--o--'\o vext + v | | | | --- --- --- --- | | | | | | | | --- --- --- --- | | | | | | | | i_membrane |...