Search found 22 matches
- Wed Apr 09, 2014 9:33 am
- Forum: NEURON + Python
- Topic: Exponential overflow error
- Replies: 1
- Views: 3077
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://s...
- Thu Oct 24, 2013 11:32 am
- Forum: NEURON + Python
- Topic: Issue importing NEURON into Python
- Replies: 3
- Views: 5072
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! :)
- Tue Oct 22, 2013 3:04 pm
- Forum: NEURON + Python
- Topic: Issue importing NEURON into Python
- Replies: 3
- Views: 5072
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...
- Wed Feb 27, 2013 11:52 am
- Forum: NEURON + Python
- Topic: Cannot get the syntax correct for creating a gap junction
- Replies: 10
- Views: 6439
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! :)
- Sun Feb 24, 2013 3:41 pm
- Forum: NEURON + Python
- Topic: Cannot get the syntax correct for creating a gap junction
- Replies: 10
- Views: 6439
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)._...
- Sun Feb 24, 2013 2:52 pm
- Forum: NEURON + Python
- Topic: Cannot get the syntax correct for creating a gap junction
- Replies: 10
- Views: 6439
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...
- Sat Feb 23, 2013 3:35 pm
- Forum: NEURON + Python
- Topic: Cannot get the syntax correct for creating a gap junction
- Replies: 10
- Views: 6439
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...
- Fri Feb 22, 2013 7:59 pm
- Forum: NEURON + Python
- Topic: Cannot get the syntax correct for creating a gap junction
- Replies: 10
- Views: 6439
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 ...
- Fri Feb 22, 2013 4:47 pm
- Forum: NEURON + Python
- Topic: Cannot get the syntax correct for creating a gap junction
- Replies: 10
- Views: 6439
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.
/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.
- Fri Feb 22, 2013 3:54 pm
- Forum: NEURON + Python
- Topic: Cannot get the syntax correct for creating a gap junction
- Replies: 10
- Views: 6439
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!
- Tue Feb 12, 2013 10:45 am
- Forum: NEURON + Python
- Topic: Issues using NetStim
- Replies: 3
- Views: 4628
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...
- Fri Feb 01, 2013 4:11 pm
- Forum: NEURON + Python
- Topic: Issues using NetStim
- Replies: 3
- Views: 4628
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...
- Wed Mar 14, 2012 12:09 pm
- Forum: NEURON + Python
- Topic: Ring shaped network question
- Replies: 1
- Views: 2331
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...
- Wed Jan 18, 2012 10:52 am
- Forum: NEURON + Python
- Topic: Question about connectivity using pt3dadd
- Replies: 3
- Views: 2972
Re: Question about connectivity using pt3dadd
Thanks for the reply! Very helpful.
- Wed Jan 18, 2012 10:20 am
- Forum: NEURON + Python
- Topic: Question about connectivity using pt3dadd
- Replies: 3
- Views: 2972
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...