Search found 89 matches

by pascal
Thu Oct 04, 2018 11:02 pm
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 3169

Re: Weird "trap" function in Bazhenov 2002 model

Fair enough, thanks. I just wanted a sanity check to make sure I wasn't missing something.
by pascal
Thu Oct 04, 2018 10:42 am
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 3169

Re: Weird "trap" function in Bazhenov 2002 model

Good question. I should have mentioned in my original post that yes, I have checked the source code you referenced (written in C++), and it incorporates this exact trap function. It's so bizarre that it makes the function discontinuous. I'll try emailing the authors one more time...
by pascal
Wed Oct 03, 2018 11:27 am
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 3169

Weird "trap" function in Bazhenov 2002 model

I am trying to code the Bazhenov 2002 sleep model in NEURON (ModelDB link: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=28189 ), and I have run across a very strange "trap" function for the fast sodium current in the cortical pyramidal cells. The details of this current are found in ...
by pascal
Tue Sep 25, 2018 4:29 pm
Forum: Specific models
Topic: No capacitance in cortical cells from Bazhenov (2002)
Replies: 2
Views: 2376

Re: No capacitance in cortical cells from Bazhenov (2002)

Good to know, thanks, Ted. I will use the same specific capacitance for the soma as for the dendrite, then compare to Bazhenov et al's results.
by pascal
Tue Sep 25, 2018 12:23 pm
Forum: Specific models
Topic: No capacitance in cortical cells from Bazhenov (2002)
Replies: 2
Views: 2376

No capacitance in cortical cells from Bazhenov (2002)

I am interested in coding Bazhenov's sleep model ("Sleep-wake transitions in corticothalamic system," 2002) in NEURON. (ModelDB link: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=28189#tabs-2 ) In getting started, however, I immediately stumbled upon a curious feature of the model: t...
by pascal
Tue Aug 01, 2017 4:33 pm
Forum: Parallel NEURON
Topic: Parameter sweep with distributed parallel network
Replies: 2
Views: 5967

Re: Parameter sweep with distributed parallel network

Okay, this post https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=3213&p=13373&hilit=subworlds#p13373 helped me figure out the solution: I need to include a destructor in my "Net" class definition. I just added def __del__(self): pc.gid_clear() to my Net class (which contains everything needed t...
by pascal
Tue Jul 25, 2017 4:20 pm
Forum: Parallel NEURON
Topic: Parameter sweep with distributed parallel network
Replies: 2
Views: 5967

Parameter sweep with distributed parallel network

I have written some fairly complex distributed network code in which different groups of cells are hosted on different processors (i.e. NOT bulletin board style parallelization). My current simulations are not large enough to require parallel code (I currently run them with just one processor), but ...
by pascal
Fri Jun 09, 2017 7:11 pm
Forum: Other questions
Topic: Getting the 'xtra' mechanism to work without 'extracellular'
Replies: 9
Views: 8678

Re: Getting the 'xtra' mechanism to work without 'extracellu

All right, finally figured out the solution. Much thanks to Ted and Robert for their help with this. For some reason beforestep_py.mod messes with i_membrane_'s location in memory, and this problem can be avoided by instead using cvode's extra_scatter_gather method to call the function which compute...
by pascal
Sun May 07, 2017 12:10 pm
Forum: Other questions
Topic: Getting the 'xtra' mechanism to work without 'extracellular'
Replies: 9
Views: 8678

Re: Getting the 'xtra' mechanism to work without 'extracellu

Hmmm...I solved the reproducibility problem by commenting out from neuron import gui and replacing it with h('load_file("nrngui.hoc")') . Apparently these two statements are not identical? In any case, I still have the flat-line problem. Here is the result I consistently get: http://i.imgur.com/tq4Q...
by pascal
Sat May 06, 2017 6:15 pm
Forum: Other questions
Topic: Getting the 'xtra' mechanism to work without 'extracellular'
Replies: 9
Views: 8678

Re: Getting the 'xtra' mechanism to work without 'extracellu

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...
by pascal
Fri May 05, 2017 9:16 am
Forum: Other questions
Topic: Getting the 'xtra' mechanism to work without 'extracellular'
Replies: 9
Views: 8678

Re: Getting the 'xtra' mechanism to work without 'extracellu

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 pointers, im and e...
by pascal
Fri Apr 28, 2017 8:58 am
Forum: Other questions
Topic: Getting the 'xtra' mechanism to work without 'extracellular'
Replies: 9
Views: 8678

Re: Getting the 'xtra' mechanism to work without 'extracellu

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...
by pascal
Thu Apr 27, 2017 3:33 pm
Forum: Other questions
Topic: Getting the 'xtra' mechanism to work without 'extracellular'
Replies: 9
Views: 8678

Re: Getting the 'xtra' mechanism to work without 'extracellu

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 debug the act...
by pascal
Wed Apr 26, 2017 10:11 pm
Forum: Other questions
Topic: Getting the 'xtra' mechanism to work without 'extracellular'
Replies: 9
Views: 8678

Getting the 'xtra' mechanism to work without 'extracellular'

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 modifications to ...
by pascal
Wed Apr 19, 2017 11:38 am
Forum: Other questions
Topic: Purpose of interpxyz.hoc in extracellular_stim_and_rec code
Replies: 3
Views: 5350

Re: Purpose of interpxyz.hoc in extracellular_stim_and_rec c

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