Search found 22 matches

by bscoventry
Mon Feb 13, 2017 11:07 pm
Forum: UNIX/Linux
Topic: nrnivmodl No rule to make target
Replies: 2
Views: 8739

Re: nrnivmodl No rule to make target

Michael,

Thank you for your help. Your suggestion fixed the second issue. However, the first issue persisted. So I utilized the scorched earth approach and deleted and redownloaded the model. This seemed to fix it. While disconcerting, atleast it worked. Thank you!

Brandon
by bscoventry
Fri Jan 06, 2017 11:05 am
Forum: UNIX/Linux
Topic: nrnivmodl No rule to make target
Replies: 2
Views: 8739

nrnivmodl No rule to make target

Hi all, I ran into an interesting problem while trying to compile mod files on an Ubuntu distribution. I was previously able to compile these files just fine, then I compiled NEURON into a Python package as per Hines et al 2009. Since then, when compiling mod files, I get the following error: :~/Opt...
by bscoventry
Mon Mar 23, 2015 11:03 am
Forum: NEURON + Python
Topic: h.FInitializeHandler Crashing
Replies: 5
Views: 1623

Re: h.FInitializeHandler Crashing

Perfect, works great now! Thank you for all your help!

Brandon
by bscoventry
Sat Mar 21, 2015 3:18 pm
Forum: NEURON + Python
Topic: h.FInitializeHandler Crashing
Replies: 5
Views: 1623

Re: h.FInitializeHandler Crashing

Hi all, So I tried the fix but now I'm running into another kind of hard to crack error. Running fih2 = h.FInitializeHandler(loadspikes, (numE,numI,rpE,rpI,h.nclistA,h.nclistB,h.nclistC,h.nclistD)) Executes just fine. However, something is wrong as h.finitialize throws a HOC runtime error. Running f...
by bscoventry
Fri Mar 20, 2015 5:00 pm
Forum: NEURON + Python
Topic: h.FInitializeHandler Crashing
Replies: 5
Views: 1623

Re: h.FInitializeHandler Crashing

Dr. Hines,

Fantastic thank you, I'll give this a shot and report back.

Brandon
by bscoventry
Tue Mar 17, 2015 11:17 am
Forum: NEURON + Python
Topic: h.FInitializeHandler Crashing
Replies: 5
Views: 1623

h.FInitializeHandler Crashing

Hi all, For cluster purposes, I'm currently porting all my MATLAB/NEURON code to Python. I seem to have run into a snag with the h.FInitializeHandler step. I am simply trying to load spike times into a target cell. Beginning with loading of AMPA, NMDA, and GABA conductances: for iii in range(numE): ...
by bscoventry
Mon Feb 16, 2015 4:00 pm
Forum: NEURON + Python
Topic: Compiling NEURON/Python
Replies: 4
Views: 1685

Re: Compiling NEURON/Python

Hi Ted,

Thank you so much for your helpful tips. Step 3 is where I was amiss, I thought NEURON mknrndll would suffice. Using PyNEURONS mknrndll solved the problem. Thank you again!

Brandon
by bscoventry
Mon Feb 16, 2015 10:59 am
Forum: NEURON + Python
Topic: Compiling NEURON/Python
Replies: 4
Views: 1685

Re: Compiling NEURON/Python

Hi Ted, Thank you for the reply. Maybe I don't need to. I guess I should clarify: I'm trying to run NEURON as a Python module. I have tried to use other precompiled packages (PyNEURON) and while the basic functionality worked, I could not PyNEURON to read in an DLL files for mechanisms, so I thought...
by bscoventry
Sun Feb 15, 2015 9:51 pm
Forum: NEURON + Python
Topic: Compiling NEURON/Python
Replies: 4
Views: 1685

Compiling NEURON/Python

Hi all, I have been using Matlab calls to run NEURON. While this works for small simulations, the amount of data overhead for our models has caused our run times to be off the scales for simulations. I'm hoping to run python and Neuron so that variables can be shared between NEURON and our control p...
by bscoventry
Thu Oct 03, 2013 2:40 pm
Forum: Getting started
Topic: Recording Conductances using Vector Record
Replies: 2
Views: 1048

Recording Conductances using Vector Record

Hi all, I am currently using Rudolph and Destexhe's Ornstein-Uhlenbeck noise process in my model(from ModelDB). I would like to record the excitatory and inhibitory conductances so that I can plot a sample path plot. Looking at the .mod file, it appears the g_e and g_i are range variables. However, ...
by bscoventry
Wed May 29, 2013 2:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Problems with randomizing point process noise
Replies: 5
Views: 1505

Re: Problems with randomizing point process noise

Hi Ted!

You're right, that was pretty simple. I'm not exactly new to neuron, but there are always a few things I miss, haha. I just wanted to let you know that the code is now up and running, and I've also now able to keep a log of the variation. Thank you for all your help!

Brandon
by bscoventry
Tue May 28, 2013 1:50 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Problems with randomizing point process noise
Replies: 5
Views: 1505

Re: Problems with randomizing point process noise

Hi all, Ok, I'm following the same idea listed here, albeit slightly differently to suit my needs. Unforntunately I can't quite understand why a particular procedure is not working. So, again here is the mod file code I'm using. In particular I'm trying to use the new_seed function: COMMENT --------...
by bscoventry
Mon May 27, 2013 1:05 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Problems with randomizing point process noise
Replies: 5
Views: 1505

Re: Problems with randomizing point process noise

Hi Ted,

Ok, that is what I was thinking I needed to do. Thank you for your input. I'll try this and let you know how it works out.

Best,
Brandon
by bscoventry
Thu May 23, 2013 4:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Problems with randomizing point process noise
Replies: 5
Views: 1505

Problems with randomizing point process noise

Hi all, I have a question regarding the initialization of the normrand function. I believe that the random number sequence is based only on the initial state of the random number generator seed. I am using a piece of code to generate synaptic noise in a neuron(modified from Destexhe's 2005 model in ...
by bscoventry
Tue Apr 09, 2013 4:45 pm
Forum: NEURON + Python
Topic: PyNEURON will not load DLL files
Replies: 17
Views: 20436

Re: PyNEURON will not load DLL files

Hi all,

So, I just got an error that I've never gotten before, but seems pertinent to the question at hand:

LoadLibrary("nrnmech.dll") failed with error 193

This came up when I loaded neuron via import neuron.

Brandon