www.neuron.yale.edu

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...

Oh I see, that explanation makes perfect sense. Thank you very much for the help. And yes, this model has been used to generate published results. I am currently going back and re-running with gmax_IhPyrKop = 0.1, and I will see whether this affects simulation results. Thank you both again for the h...

I am translating a hoc model (that I inherited) into Python, and I am having some trouble with a custom mod file. The hoc code references the mod file (which defines a mechanism named "IhPyrKop") in the following way: insert IhPyrKop soma{ gh_IhPyrKop = 0.1 v50_IhPyrKop = -82 } The only pr...

Great, thanks so much for the thorough explanation. I feel like when it comes to NEURON's integration schemes, I now harbor fewer unknown unknowns, more known unknowns, and maybe even one or two known knowns. :-)

Thanks, this works perfectly now. I really appreciate the help. I am curious why importing gui automatically creates an instance of CVode. I know CVode implements adaptive time step numerical integration, with a separate "stream" for each neuron in the simulation. Is CVode the default nume...