Search found 25 matches
- Mon Nov 12, 2018 12:19 pm
- Forum: Getting started
- Topic: Porting AtolTool settings to GUI-less batch simulation
- Replies: 5
- Views: 3023
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 ...
- Mon Nov 12, 2018 8:14 am
- Forum: Getting started
- Topic: Porting AtolTool settings to GUI-less batch simulation
- Replies: 5
- Views: 3023
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 ...
- Fri Nov 09, 2018 10:12 am
- Forum: Getting started
- Topic: Porting AtolTool settings to GUI-less batch simulation
- Replies: 5
- Views: 3023
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 .se...
- Fri Oct 26, 2018 10:39 am
- Forum: MSWin
- Topic: Compile Neuron
- Replies: 5
- Views: 4287
Re: Compile Neuron
Thank you very much!!
- Thu Oct 25, 2018 7:03 am
- Forum: MSWin
- Topic: Compile Neuron
- Replies: 5
- Views: 4287
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 ...
- Thu Oct 25, 2018 5:28 am
- Forum: MSWin
- Topic: downloading neuron on windows
- Replies: 3
- Views: 5280
Re: downloading neuron on windows
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
the problem occurs when the python executable is not in your Path environment variable. If you type
Code: Select all
python
HTH,
Matthias
- Wed Oct 24, 2018 6:47 am
- Forum: NEURON + Python
- Topic: More NEURON + Python documentation
- Replies: 6
- Views: 25975
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/
But I have found Andrew Davison's instructions here: http://andrewdavison.info/notes/
- Wed Oct 24, 2018 4:34 am
- Forum: Suggestions and Feedback
- Topic: Search in forum not usable
- Replies: 3
- Views: 6652
Re: Search in forum not usable
It does. Thank you!
- Wed Oct 24, 2018 4:33 am
- Forum: MSWin
- Topic: Compile Neuron
- Replies: 5
- Views: 4287
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 ...
- Tue Oct 23, 2018 11:04 am
- Forum: MSWin
- Topic: Compile Neuron
- Replies: 5
- Views: 4287
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...
- Tue Oct 16, 2018 10:33 am
- Forum: The GUI
- Topic: Plot vector_y vs vector_x
- Replies: 3
- Views: 3122
Re: Plot vector_y vs vector_x
Thank you for the quick reply!
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)?
- Tue Oct 16, 2018 4:35 am
- Forum: The GUI
- Topic: Plot vector_y vs vector_x
- Replies: 3
- Views: 3122
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 us...
- Tue Oct 16, 2018 4:12 am
- Forum: Suggestions and Feedback
- Topic: Search in forum not usable
- Replies: 3
- Views: 6652
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...
- Wed Oct 10, 2018 4:26 am
- Forum: Getting started
- Topic: The math behind extracellular mechanisms
- Replies: 21
- Views: 23127
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 NEUR...
- Tue Oct 09, 2018 4:47 am
- Forum: Getting started
- Topic: The math behind extracellular mechanisms
- Replies: 21
- Views: 23127
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 |...