Search found 25 matches

by mzenker
Mon Nov 12, 2018 12:19 pm
Forum: Getting started
Topic: Porting AtolTool settings to GUI-less batch simulation
Replies: 5
Views: 1530

Re: Porting AtolTool settings to GUI-less batch simulation

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 ...
by mzenker
Mon Nov 12, 2018 8:14 am
Forum: Getting started
Topic: Porting AtolTool settings to GUI-less batch simulation
Replies: 5
Views: 1530

Re: Porting AtolTool settings to GUI-less batch simulation

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 ...
by mzenker
Fri Nov 09, 2018 10:12 am
Forum: Getting started
Topic: Porting AtolTool settings to GUI-less batch simulation
Replies: 5
Views: 1530

Porting AtolTool settings to GUI-less batch simulation

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...
by mzenker
Fri Oct 26, 2018 10:39 am
Forum: MSWin
Topic: Compile Neuron
Replies: 5
Views: 2366

Re: Compile Neuron

Thank you very much!!
by mzenker
Thu Oct 25, 2018 7:03 am
Forum: MSWin
Topic: Compile Neuron
Replies: 5
Views: 2366

Re: Compile Neuron

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...
by mzenker
Thu Oct 25, 2018 5:28 am
Forum: MSWin
Topic: downloading neuron on windows
Replies: 3
Views: 3291

Re: downloading neuron on windows

Hi,

the problem occurs when the python executable is not in your Path environment variable. If you type

Code: Select all

python
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
by mzenker
Wed Oct 24, 2018 6:47 am
Forum: NEURON + Python
Topic: More NEURON + Python documentation
Replies: 6
Views: 22304

Re: More NEURON + Python documentation

Almost all of the links (except Ramain's tutorial) are dead.
But I have found Andrew Davison's instructions here: http://andrewdavison.info/notes/
by mzenker
Wed Oct 24, 2018 4:34 am
Forum: Suggestions and Feedback
Topic: Search in forum not usable
Replies: 3
Views: 2111

Re: Search in forum not usable

It does. Thank you!
by mzenker
Wed Oct 24, 2018 4:33 am
Forum: MSWin
Topic: Compile Neuron
Replies: 5
Views: 2366

Re: Compile Neuron

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...
by mzenker
Tue Oct 23, 2018 11:04 am
Forum: MSWin
Topic: Compile Neuron
Replies: 5
Views: 2366

Compile Neuron

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...
by mzenker
Tue Oct 16, 2018 10:33 am
Forum: The GUI
Topic: Plot vector_y vs vector_x
Replies: 3
Views: 1858

Re: Plot vector_y vs vector_x

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)?
by mzenker
Tue Oct 16, 2018 4:35 am
Forum: The GUI
Topic: Plot vector_y vs vector_x
Replies: 3
Views: 1858

Plot vector_y vs vector_x

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...
by mzenker
Tue Oct 16, 2018 4:12 am
Forum: Suggestions and Feedback
Topic: Search in forum not usable
Replies: 3
Views: 2111

Search in forum not usable

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...
by mzenker
Wed Oct 10, 2018 4:26 am
Forum: Getting started
Topic: The math behind extracellular mechanisms
Replies: 21
Views: 16794

Re: The math behind extracellular mechanisms

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...
by mzenker
Tue Oct 09, 2018 4:47 am
Forum: Getting started
Topic: The math behind extracellular mechanisms
Replies: 21
Views: 16794

Re: The math behind extracellular mechanisms

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 |...