Search found 62 matches

by pascal
Wed Oct 10, 2018 11:04 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 3
Views: 1284

Re: Where to find squid.hoc associated with hh.mod

Thanks for the resources, Ted. I'll read through them and get back to you if I have any more questions.
by pascal
Tue Oct 09, 2018 5:43 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 3
Views: 1284

Re: Where to find squid.hoc associated with hh.mod

Okay, I believe I found it here: https://github.com/neurodroid/neurodroid/blob/master/nrn/squid.hoc Here is the code: /* Squid giant axon ap */ load_file("stdrun.hoc") /* Print v at every time step */ proc advance() { fadvance() print "ND ", v } create axon access axon insert hh gnabar_hh = gna gkba...
by pascal
Tue Oct 09, 2018 12:13 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Where to find squid.hoc associated with hh.mod
Replies: 3
Views: 1284

Where to find squid.hoc associated with hh.mod

I am learning to write my own MOD files, and I'm starting with hh.mod as a learning tool. The comment section in hh.mod says to see squid.hoc as an example of the hh mechanism's implementation...but I cannot find squid.hoc anywhere. It's not in my installation of NEURON, and I can't find it anywhere...
by pascal
Thu Oct 04, 2018 11:02 pm
Forum: Specific models
Topic: Weird "trap" function in Bazhenov 2002 model
Replies: 4
Views: 1388

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: 1388

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: 1388

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: 952

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: 952

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: 4982

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: 4982

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: 6155

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: 6155

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: 6155

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: 6155

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: 6155

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...