Search found 22 matches

by maxwellphenderson
Wed Apr 09, 2014 9:33 am
Forum: NEURON + Python
Topic: Exponential overflow error
Replies: 1
Views: 1905

Exponential overflow error

I was having an issue similar to the one mentioned in: http://www.neuron.yale.edu/phpbb/viewtopic.php?f=31&t=2130 I am not doing any parallelization so I think that the issue must be stemming from an overflow in a mod file. I am using simplified exc. and inh. neurons from ModelDB (#3817 http://sense...
by maxwellphenderson
Thu Oct 24, 2013 11:32 am
Forum: NEURON + Python
Topic: Issue importing NEURON into Python
Replies: 3
Views: 2613

Re: Issue importing NEURON into Python

Ah, I think it came down to a silly issue with my PYTHONPATH after all! Every time I ssh into a node, my PYTHONPATH got wiped (because apparently I didn't set it in my profile file). Thanks for the help, everything looks like it is working great now! :)
by maxwellphenderson
Tue Oct 22, 2013 3:04 pm
Forum: NEURON + Python
Topic: Issue importing NEURON into Python
Replies: 3
Views: 2613

Issue importing NEURON into Python

Hello, I have for a long time using NEURON on my computer to run various experiments. Some of my experiments have gotten too large / taking too long, so I am attempting to install and run NEURON on a cluster of computers (Linux). I am trying to first install it on a single node of our cluster of com...
by maxwellphenderson
Wed Feb 27, 2013 11:52 am
Forum: NEURON + Python
Topic: Cannot get the syntax correct for creating a gap junction
Replies: 10
Views: 3493

Re: Cannot get the syntax correct for creating a gap junctio

Everything is now working correctly and even built my own version of a gap.mod file! Thanks for the help! :)
by maxwellphenderson
Sun Feb 24, 2013 3:41 pm
Forum: NEURON + Python
Topic: Cannot get the syntax correct for creating a gap junction
Replies: 10
Views: 3493

Re: Cannot get the syntax correct for creating a gap junctio

To add a bit more (again), the closest I could make was #create sections soma = h.Section() soma1 = h.Section() # Insert gap junction gap_junction = h.gap(0.9999, sec=soma) gap_junction.r = 1.0 # Connect gap junction to pre-synaptic cell h.setpointer(gap_junction._ref_vgap, '_ref_v', soma1(0.0001)._...
by maxwellphenderson
Sun Feb 24, 2013 2:52 pm
Forum: NEURON + Python
Topic: Cannot get the syntax correct for creating a gap junction
Replies: 10
Views: 3493

Re: Cannot get the syntax correct for creating a gap junctio

Thanks so much for the help with setting the path correctly! After I fixed that, I ran nrnivmodl and everything worked correctly! :) Now my only remaining issues come back to original syntax issues... when I run the code: g = h.gap() print g The output I get is: NEURON -- Release 7.1 (359:7f113b76a9...
by maxwellphenderson
Sat Feb 23, 2013 3:35 pm
Forum: NEURON + Python
Topic: Cannot get the syntax correct for creating a gap junction
Replies: 10
Views: 3493

Re: Cannot get the syntax correct for creating a gap junctio

Hmm... I think I am having some problems with how I installed NEURON, possibly. I installed NEURON without interviews (which I am guessing is probably ok?). I installed everything into a folder called 'neuron' (as suggested for obvious reasons in the installation information). When I try to follow t...
by maxwellphenderson
Fri Feb 22, 2013 7:59 pm
Forum: NEURON + Python
Topic: Cannot get the syntax correct for creating a gap junction
Replies: 10
Views: 3493

Re: Cannot get the syntax correct for creating a gap junctio

One final word - I have been poking around different stuff, and the error that I get when I try g = h.gap(0.5, sec = soma) is AttributeError: 'hoc.HocObject' object has no attribute 'gap' So I guess I'm trying to figure out if I am calling this wrong, or if something didn't load / install correctly ...
by maxwellphenderson
Fri Feb 22, 2013 4:47 pm
Forum: NEURON + Python
Topic: Cannot get the syntax correct for creating a gap junction
Replies: 10
Views: 3493

Re: Cannot get the syntax correct for creating a gap junctio

Also just to add a bit more: I have found that the file gap.mod exists and currently is in the directory:

/neuron/nrn/share/examples/nrniv/nmodl

I also copied it and put it in the same directory as netstim.mod because I found other point process mod files there. Doesn't appear to have helped.
by maxwellphenderson
Fri Feb 22, 2013 3:54 pm
Forum: NEURON + Python
Topic: Cannot get the syntax correct for creating a gap junction
Replies: 10
Views: 3493

Cannot get the syntax correct for creating a gap junction

Hello, I have found several examples for creating gap junctions using hoc; some form of: gap_ = new Gap(0.5) I cannot find the way to do this using Python. I have tried variations and have been looking around for a while in the documentation but not really finding what I needed. Thanks for the help!
by maxwellphenderson
Tue Feb 12, 2013 10:45 am
Forum: NEURON + Python
Topic: Issues using NetStim
Replies: 3
Views: 3097

Re: Issues using NetStim

Thanks for getting back to me! I applied a more rigorous method checking my code one step at a time and eventually found my error. The following code ended up working for me to produce random stimulus: stimNc = h.NetStim() stimNc.noise = 1 stimNc.start = 0 stimNc.number = 100 stimNc.interval = 5 syn...
by maxwellphenderson
Fri Feb 01, 2013 4:11 pm
Forum: NEURON + Python
Topic: Issues using NetStim
Replies: 3
Views: 3097

Issues using NetStim

Hello, I am having an issue creating NetStim objects in my neural networks. Basically, I am testing the dynamics of different neural networks and I want to give all neurons some random stimulus over the entire simulation. NetStim seems to be built for that, however; it is not appearing to work in my...
by maxwellphenderson
Wed Mar 14, 2012 12:09 pm
Forum: NEURON + Python
Topic: Ring shaped network question
Replies: 1
Views: 1529

Ring shaped network question

Hey, I had a question concerning some behavior with some code I wrote to make ring-shaped neural networks with different numbers of neurons. Just as you would expect (and like the example in Translating network models to parallel hardware in NEURON), each neuron has two synapses and NC - one to each...
by maxwellphenderson
Wed Jan 18, 2012 10:52 am
Forum: NEURON + Python
Topic: Question about connectivity using pt3dadd
Replies: 3
Views: 1919

Re: Question about connectivity using pt3dadd

Thanks for the reply! Very helpful.
by maxwellphenderson
Wed Jan 18, 2012 10:20 am
Forum: NEURON + Python
Topic: Question about connectivity using pt3dadd
Replies: 3
Views: 1919

Question about connectivity using pt3dadd

I had a question concerning the construction of neurons with complicated geometries using the pt3dadd command. I was curious about how the tool handles bifurcations, or what the best method of dealing with them would be. Basically, say I have a list of 3D coordinates and diameters for points outlini...