Search found 97 matches

by neuromau
Tue Apr 02, 2013 5:19 pm
Forum: UNIX/Linux
Topic: NEURON on Trestles
Replies: 1
Views: 6145

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: 11927

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...
by neuromau
Thu Apr 19, 2012 3:49 pm
Forum: Other questions
Topic: Precision of t in fadvance
Replies: 5
Views: 2377

Re: Precision of t in fadvance

generates spike events at deterministic intervals (at least for starts), right?
Yes
parameter "period" in ms or seconds?
It's in ms.

Thanks for your help!
by neuromau
Thu Apr 19, 2012 1:36 pm
Forum: Other questions
Topic: Precision of t in fadvance
Replies: 5
Views: 2377

Re: Precision of t in fadvance

Right now I have something to the effect of: period = 125 baserate = 10 // maximum firing rate (ms, interval) amp = 45 // half of the range between min and max firing rate (ms, interval) tstop = 1000 freq = 1000/period // Hz numinrns = 3 double phasepref[numinrns] phasepref[0] = .1 phasepref[1] = .3...
by neuromau
Thu Apr 19, 2012 12:53 pm
Forum: Other questions
Topic: Precision of t in fadvance
Replies: 5
Views: 2377

Re: Precision of t in fadvance

Do you want to generate a train of spike events whose ISIs are directly or inversely proportional to sin(2*PI*f*t)? Were you thinking of doing this by altering a NetStim's interval parameter in the course of a simulation, e.g. at some user-specified times t0, t1 . . . ti ?
Yes and Yes.
by neuromau
Wed Apr 18, 2012 8:38 pm
Forum: Other questions
Topic: Precision of t in fadvance
Replies: 5
Views: 2377

Precision of t in fadvance

Hello, I'm using a sinusoidally varying netstim in my model and so I added code to fadvance() to update the interval of the netstim. I only want to update the interval every so often and so I added code to check the value of t before resetting the interval. However, the check doesn't work because ca...
by neuromau
Tue Mar 20, 2012 3:03 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 7365

Re: Using ions in multiple mechanisms

It has not been published yet. I'll post a note in this thread when it gets uploaded.

~ Marianne
by neuromau
Fri Aug 26, 2011 10:45 pm
Forum: Other questions
Topic: array variable in template
Replies: 1
Views: 1566

array variable in template

I made a template that creates a soma as an array variable: begintemplate grr proc init() { load_file("mytest.hoc") } endtemplate grr objref mycell mycell = new grr() quit() where mytest.hoc contains: create soma[5] for i = 0, 4 soma[i] { print i } print soma[0].L This code works just fine, printing...
by neuromau
Thu Apr 28, 2011 9:05 pm
Forum: UNIX/Linux
Topic: NEURON on Ranger
Replies: 2
Views: 3631

Re: NEURON on Ranger

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 WORK file system: cdw 2. Create a directory called test: mkdir test 3. Move to the test directory: cd test 4. In the t...
by neuromau
Thu Apr 28, 2011 9:00 pm
Forum: UNIX/Linux
Topic: NEURON on Ranger
Replies: 2
Views: 3631

NEURON on Ranger

Hello, Michael Hines installed NEURON on Ranger for me and so I'm posting the instructions here for other users of Ranger. Ranger is a Linux cluster at the University of Texas which, according to the website (1), has "62,976 compute cores, 123 TB of total memory and 1.7 PB of raw global disk space."...
by neuromau
Wed Dec 15, 2010 5:57 pm
Forum: Anatomically detailed models
Topic: SWC files with a single "soma" point
Replies: 13
Views: 13576

Re: SWC files with a single "soma" point

what are those big red zigzag lines that I see in Import3D? Attempts to trace the boundaries of hippocampal cortical layers? Yes, that was my assumption. It has a compartment type of '10', which doesn't correspond to any of the real compartment types, and other cells in the database have similar (o...
by neuromau
Tue Dec 14, 2010 11:12 pm
Forum: Anatomically detailed models
Topic: SWC files with a single "soma" point
Replies: 13
Views: 13576

SWC files with a single "soma" point

If such swc files are common, I would expect Import3D to already have a policy for dealing with them. Have you such a file, and what did Import3D do? Yes, I downloaded the file from http://neuromorpho.org/neuroMorpho/dableFiles/amaral/CNG%20version/c10261.CNG.swc . The first two data lines of it lo...
by neuromau
Tue Dec 14, 2010 9:17 pm
Forum: Anatomically detailed models
Topic: SWC files with a single "soma" point
Replies: 13
Views: 13576

SWC files with a single "soma" point

After reading some of the other threads in this forum, it seems that I would be better served by just adding a line to the swc file such that the soma is specified as a cylinder with L = diam = 2*sphere_radius. The only other uncertainty I had was the orientation of this cylinder. This (CA1 pyramida...
by neuromau
Tue Dec 14, 2010 4:45 pm
Forum: Anatomically detailed models
Topic: SWC files with a single "soma" point
Replies: 13
Views: 13576

SWC files with a single "soma" point

The question is bound to arise again and again. Yes, I just had related question! Based on an entry in the Neuromorpho FAQ at http://neuromorpho.org/neuroMorpho/myfaq.jsp , the single point for the soma is indeed meant to specify a spherical soma: Soma can be a single point or more than one point. ...
by neuromau
Tue Oct 12, 2010 3:21 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Using ions in multiple mechanisms
Replies: 11
Views: 7365

Re: Using ions in multiple mechanisms

I tried this for the mechanism in the other post and am a bit stuck, working backwards from the target equation and forwards from the starting equation (my math skills are rusty...) I think that the -dt*tadj/ntau term would be small enough that I can use the approximation "as h --> 0, exp(h) --> h ...