www.neuron.yale.edu

Thanks, Ted. Good point on using modlunit. When I did so, I found that I needed to use 'nanoamps' instead of 'nA'. Also, I needed to change er = rx * im to er = (1000) * rx * im , which makes sense since er is in microvolts, rx is in megohms, and im is in nanoamps. (Although, weirdly, modlunit conti...

All right, I figured out what was causing the segmentation fault in h.finitialize: I wasn't linking the ex pointer within xtra.mod. This post was helpful: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=16&t=3403&p=14429&hilit=segmentation+finitialize#p14429 xtra.mod defines two pointe...

Model setup is laying the groundwork for this to happen, because print statements show the program gets to h.run and then chokes with Segmentation fault (core dumped) . I'm having a hard time debugging from here, because usually when NEURON chokes within h.run, it gives an error message that indicat...

Hmmm...I see what you're getting at now. Upon further investigation, the simulation was not actually choking within setelec, but rather somewhere within h.run(). The error message associated with this is simply "Segmentation fault (core dumped)". So yes, it would seem I need to somehow deb...

I am trying to get a minimal model working in which I record the LFP of one cell using 'xtra', without the 'extracellular' mechanism, as described here https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=3389&p=14342&hilit=extracellular+recording+parallel#p14342 . I have made the modif...

Got it, interpxyz.hoc applies very generally to stylized and 3d models. Thanks.

Hi Ted, I want to make sure I understand why interpxyz.hoc is necessary in your extracellular_stim_and_rec code (found here: http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=168 ). In particular, it seems to my naive eyes that define_shape() already calculates the interpolated 3D coordinate...

Whoops, apparently this question has already been asked here: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=8&t=3627 (In my defense, I searched for n3d and n3d() , and nothing came up in either case.) I thought I had tried calling define_shape() before printing out the 3D coordinates, but ap...

I am having trouble with a very basic issue: getting NEURON to tell me the 3D location of a cell. The "Conceptual Overview of Sections" documentation has the following snippet of code to print out the 3D coordinates of a cell: forall delete_section() create a, b, c, d, e connect b(0), a(1)...

All right, I figured out the fix from this post: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=3160 I had to replace the line pc.source_var(cell.soma(0.5)._ref_v, source_src_gid) with pc.source_var(cell.soma(0.5)._ref_v, source_src_gid,sec=cell.soma) According to the link above, sec=cell...

I am trying to implement Traub's parallel gap junction code (see https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=82894&file=\nrntraub\hoc\parlib2.hoc#tabs-2 ) in Python. So far I have the following for par_gap_create and par_gap_create1 (implemented as methods within a "Net&quo...

I am also trying to implement gap junctions in a parallel model, and I have a question about the Traub implementation (at https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=82894&file=\nrntraub\hoc\parlib2.hoc#tabs-2 , as stated above). The code looks like this: gap_src_gid = 2 proc pa...

That is very helpful--thank you!

Ah, I did end up finding a good example in this portion of the tutorial: http://neuron.yale.edu/neuron/static/docs/neuronpython/ballandstick2.html . Thanks. Following the tutorial, I was able to clean up my code by using the wholetree method (rather than adding each individual section to the Section...

I am writing one of my first programs in NEURON + Python, and I want to make sure that I am correctly iterating over just the sections within a newly-created object. (I realized that using for sec in h.allsec() iterates over all sections in the entire program, which is not what I want.) My toy class...