Search found 95 matches

by neuromau
Sat Sep 07, 2013 2:27 pm
Forum: MSWin
Topic: NEURON installation was fine, now somewhat broken [resolved]
Replies: 1
Views: 6239

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: 4601

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: 4601

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: 6241

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: 6241

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: 6241

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: 5653

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: 1159

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: 1110

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: 1110

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: 7094

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: 5926

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 ...
by neuromau
Tue Apr 02, 2013 5:19 pm
Forum: UNIX/Linux
Topic: NEURON on Trestles
Replies: 1
Views: 5926

NEURON on Trestles

Trestles is a supercomputer provided by the San Diego Supercomputing Center. It has over 10,000 cores. There are multiple ways to gain access to Trestles. One is via the Neuroscience Gateway as detailed in the post Run parallel simulations via the Neuroscience Gateway . Another is via an allocation...
by neuromau
Mon Mar 25, 2013 6:38 pm
Forum: UNIX/Linux
Topic: NEURON on Stampede
Replies: 2
Views: 11600

NEURON on Stampede

Stampede is a supercomputer provided by the University of Texas. It has over 6,400 16-core nodes. Over 90% of Stampede resources are dedicated to XSEDE , NSF's mechanism for providing supercomputing resources to researchers. For information on obtaining an XSEDE allocation, visit their new allocati...