Search found 97 matches

by neuromau
Wed Oct 02, 2013 8:55 pm
Forum: MSWin
Topic: Incomplete directory tree within NEURON
Replies: 4
Views: 7233

Incomplete directory tree within NEURON

Hello, this may be a Cygwin issue and not a NEURON issue; I'm not sure. I'm on a 64-bit Windows 8 Machine using the NEURON 7.3 GUI. I have a main folder where I keep all my NEURON models; each model is in its own subdirectory. Lately when I open the NEURON 7.3 GUI and use the commands under the File...
by neuromau
Sat Sep 07, 2013 3:38 pm
Forum: MSWin
Topic: NEURON installation was fine, now somewhat broken [resolved]
Replies: 1
Views: 6539

Re: NEURON installation was fine, now somewhat broken

Also, I saw this in ivocmain.cpp: #if defined(CYGWIN) sprintf(nrn_props, "%s/%s", neuron_home, "lib/nrn.def"); #else sprintf(nrn_props, "%s\\%s", neuron_home, "lib\\nrn.def"); #endif So I tried removing my CYGWIN environmental variable and now the NEURON installation works again for numbers 2, 3, an...
by neuromau
Sat Sep 07, 2013 2:27 pm
Forum: MSWin
Topic: NEURON installation was fine, now somewhat broken [resolved]
Replies: 1
Views: 6539

NEURON installation was fine, now somewhat broken [resolved]

Hello, I have the 32-bit Cygwin installation on my Windows 8 machine. It's been working fine for months. Then, yesterday it began exhibiting problems. I think the only thing I did yesterday was install Java JDK and NeuroConstruct, and alter the NeuroConstruct settings so that it could find and work ...
by neuromau
Wed Jul 24, 2013 3:35 pm
Forum: Modeling networks
Topic: Accessing functions in a cell template with a NetStim
Replies: 2
Views: 4778

Re: Accessing functions in a cell template with a NetStim

Short answer is yes, MyNetStim must have a public is_art() if you want thecell.is_art() to succeed. Okay, I added the following to my MyNetStim.mod file and recompiled, now I can use "thecell.is_art()" with an object created by the pc.gid2cell function: FUNCTION is_art() { is_art=1 } what purpose d...
by neuromau
Tue Jul 23, 2013 1:59 pm
Forum: Modeling networks
Topic: Accessing functions in a cell template with a NetStim
Replies: 2
Views: 4778

Accessing functions in a cell template with a NetStim

Hi, I have an artificial cell template that contains a NetStim. I added an "is_art" function to this cell template, but when I try to access it from the parallel context, NEURON is looking for it to be part of the NetStim within the cell template, instead of just a function available as part of the ...
by neuromau
Thu Jul 11, 2013 1:45 pm
Forum: MSWin
Topic: Running NEURON from Cygwin
Replies: 3
Views: 6892

Re: Running NEURON from Cygwin

Also, not sure if this is related, but if I try to run

Code: Select all

mknrndll
from the Cygwin terminal, even after exporting NEURONHOME, I get:
sh: /lib/mknrndl2.sh: No such file or directory

But it works if I run that command from the rxvt shell.
by neuromau
Thu Jul 11, 2013 1:02 pm
Forum: MSWin
Topic: Running NEURON from Cygwin
Replies: 3
Views: 6892

Re: Running NEURON from Cygwin

Thanks, I will give those a try!
by neuromau
Tue Jul 09, 2013 7:33 pm
Forum: MSWin
Topic: Running NEURON from Cygwin
Replies: 3
Views: 6892

Running NEURON from Cygwin

Hi, I installed the precompiled 32-bit NEURON for Windows on a 64-bit Windows 7 Machine and added it to the path. Then, from the rxvt shell, I just enter 'nrniv' and it starts and runs my code fine. However, if I try to run it from the Cygwin terminal, when I enter nrniv, I get an error: NEURON -- R...
by neuromau
Fri Jun 21, 2013 7:20 pm
Forum: MSWin
Topic: problem with installation of NEURON on Windows 8 64 bit
Replies: 1
Views: 5890

problem with installation of NEURON on Windows 8 64 bit

Hi, I just tried installing both NEURON 7.3 Windows installers on a 64-bit Windows 8 machine: 64 bit MinGW The installation looked successful, but when I tried to launch NEURON Demo or nrngui, a terminal window blinked open and closed really fast, and nothing else happened. I tried uninstalling, del...
by neuromau
Thu Jun 20, 2013 8:11 pm
Forum: Other questions
Topic: Modeling data resources
Replies: 0
Views: 2137

Modeling data resources

Here are some resources that have data useful for detailed modeling: The NeuroElectro website displays cellular electrophysiology data from multiple articles, very nicely. For a variety of properties (resting membrane potential, membrane time constant, input resistance, rheobase, etc), it graphs the...
by neuromau
Wed May 22, 2013 8:58 pm
Forum: Other questions
Topic: Adding a length scale bar to a Shape plot
Replies: 2
Views: 1309

Re: Adding a length scale bar to a Shape plot

Awesome, thank you!
by neuromau
Tue May 21, 2013 8:03 pm
Forum: Other questions
Topic: Adding a length scale bar to a Shape plot
Replies: 2
Views: 1309

Adding a length scale bar to a Shape plot

I would like to add a length scale bar to a shape plot, and a label ("100 um"): create soma, dend connect dend(0), soma(1) objref ss ss = new Shape() ss.label(0.1,.1,"100 um") I thought perhaps I should use ss.beginline(x1,0.1) and ss.line(x2,0.1), but that didn't work for me (plus unsure of the uni...
by neuromau
Fri Apr 12, 2013 8:04 pm
Forum: Optimization
Topic: Optimizing PROCEDURE equations in mod files
Replies: 5
Views: 7713

Optimizing PROCEDURE equations in mod files

Hi, I have a cell model that contains a channel mechanism. I want to use the Multiple Run Fitter to adjust some equations in a PROCEDURE block of the channel definition. Before I get to that, I have to settle a more general issue, though. I can't seem to manually update the variable values in these ...
by neuromau
Tue Apr 02, 2013 5:31 pm
Forum: UNIX/Linux
Topic: NEURON on Trestles
Replies: 1
Views: 6189

Re: NEURON on trestles

Testing the installation and running job scripts are covered in the reply to this post. To test the installation of NEURON, we can create the following test program. 1. Move to the HOME file system: cd $HOME 2. Create a directory called test: mkdir test 3. Move to the test directory: cd test 4. In ...