Search found 5842 matches

by ted
Tue Dec 01, 2020 11:32 am
Forum: General questions and discussions about computational neuroscience
Topic: General validation of NEURON?
Replies: 4
Views: 420

Re: General validation of NEURON?

An interesting question, not least because it seems skew to NEURON's primary design goal: to serve as a tool for implementing and performing experiments on computational models of biological neurons and networks. Every computational model is only an expression, in computational form, of a conceptual...
by ted
Mon Nov 23, 2020 9:53 pm
Forum: Other questions
Topic: Simulating nanodomains to link SK/BK channels to specific Ca channels
Replies: 5
Views: 415

Re: Simulating nanodomains to link SK/BK channels to specific Ca channels

Or maybe Biophysical Journal. A couple of PubMed searches turned up many interesting papers; you might find this one to be helpful: @Article{Montefusco2019, author = {Montefusco, Francesco and Pedersen, Morten G}, title = {From local to global modeling for characterizing calcium dynamics and their e...
by ted
Mon Nov 23, 2020 5:52 pm
Forum: Other questions
Topic: Simulating nanodomains to link SK/BK channels to specific Ca channels
Replies: 5
Views: 415

Re: Simulating nanodomains to link SK/BK channels to specific Ca channels

Can't say that I've seen anybody else do this, but it should work. Would start small--first just a cluster of P/Q channels with local ion accumulation that equilibrates with bulk cytoplasm, then add a cluster of BK channels with its own local volume that equilibrates with bulk cytoplasm, then couple...
by ted
Mon Nov 23, 2020 5:39 pm
Forum: NEURON + Python
Topic: Recording voltage across elements and using external stim Linear Circuit Builder
Replies: 1
Views: 247

Re: Recording voltage across elements and using external stim Linear Circuit Builder

I was wondering if it's possible to record voltage across an element in the Linear Circuit Builder. You can only record voltages relative to ground. If neither terminal of a two terminal device is grounded, you have to capture the time course of potential at each end into a pair of vectors, then af...
by ted
Sun Nov 22, 2020 3:26 pm
Forum: Other questions
Topic: Simulating nanodomains to link SK/BK channels to specific Ca channels
Replies: 5
Views: 415

Re: Simulating nanodomains to link SK/BK channels to specific Ca channels

This could be done in NMODL as a point process. Such an implementation might represent interactions within a "complex of elements" that consists of a cluster of P/Q channels, a nearby SER cistern, and a nearby cluster of BK channels. Done properly, this would allow any segment to have as m...
by ted
Fri Nov 20, 2020 10:26 am
Forum: Other questions
Topic: Enable/Disable NetStim objects at run time
Replies: 1
Views: 173

Re: Enable/Disable NetStim objects at run time

Good question. Before dealing with it-- Instead of from neuron import h import neuron do this: from neuron import h h.load_file("stdgui.hoc") import h gives Python access to everything built into the NEURON executable (the program that is launched by executing nrniv at the command line). P...
by ted
Wed Nov 18, 2020 10:42 pm
Forum: NEURON + Python
Topic: Modelling of subcellular signalling
Replies: 1
Views: 181

Re: Modelling of subcellular signalling

When I insert the ion channels with pointer they will occupy a whole compartment although I would only want a segment to be modulated. A segment is a compartment. Perhaps you meant to say "When I insert the ion channels with pointer they will occupy a whole section" but that doesn't expla...
by ted
Thu Nov 12, 2020 4:53 pm
Forum: NEURON hacks
Topic: Flushing Output to Disk
Replies: 1
Views: 279

Re: Flushing Output to Disk

Look in the Hot tips area of the Forum for Simulations that generate lots of data
by ted
Wed Nov 04, 2020 5:46 pm
Forum: Modeling networks
Topic: fsyn()
Replies: 2
Views: 315

Re: fsyn()

Aha, I violated the principle of RTFM. Sure enough, searching the Programmers' Reference for fsyn turns up a section on "Obsolete Stimuli" that mentions the (obsolete) function prstim() which is described as "obsolete. Print the info about fstim, fclamp, and fsyn". My own dusty p...
by ted
Wed Nov 04, 2020 5:18 pm
Forum: NEURON hacks
Topic: Implementing Superposition to "custom" waveforms in NMODL
Replies: 6
Views: 384

Re: Implementing Superposition to "custom" waveforms in NMODL

Sounds like you have take on a challenging task. I'm fresh out of ideas for how to accomplish it.
by ted
Wed Nov 04, 2020 5:09 pm
Forum: Modeling networks
Topic: fsyn()
Replies: 2
Views: 315

Re: fsyn()

Never heard of fsyn(). Doubtless some user-written function. Is it defined in any of the files that are part of that model entry where you found it?
by ted
Tue Nov 03, 2020 9:51 pm
Forum: NEURON Announcements
Topic: NEURON Virtual Course
Replies: 0
Views: 252

NEURON Virtual Course

What: The one-day NEURON course presented as a series of short webinars. When: The webinars will run from 1 PM to 3 PM New York time on Monday and Tuesday, Nov. 16 and 17, and on Monday and Tuesday, Nov. 23 and 24, 2020 Speakers: Ted Carnevale and Robert McDougal Registration is on a first-come, fi...
by ted
Mon Nov 02, 2020 10:27 pm
Forum: NEURON hacks
Topic: Implementing Superposition to "custom" waveforms in NMODL
Replies: 6
Views: 384

Re: Implementing Superposition to "custom" waveforms in NMODL

For this particular problem, what do you want your array of precalculated values to drive? Probability of transmitter release as a function of time? Transmitter concentration in the synaptic cleft? The detailed time course of synaptic conductance? If none of these, then what? The use of the array to...
by ted
Mon Nov 02, 2020 9:12 am
Forum: NEURON hacks
Topic: Implementing Superposition to "custom" waveforms in NMODL
Replies: 6
Views: 384

Re: Implementing Superposition to "custom" waveforms in NMODL

I am unsure exactly how NEURON maintains this superposition of waveforms. I assume it is something that happens "behind the scenes" and is hidden from the NMODL level. There is no hidden magic. It arises naturally from the numerical integration of the differential equation(s) that govern ...
by ted
Wed Oct 28, 2020 12:44 pm
Forum: Getting started
Topic: Compiling Mod Files on Catalina
Replies: 8
Views: 668

Re: Compiling Mod Files on Catalina

Thank you for reporting how you fixed the problem.

So "Command Line Tools for XCode 12", which you installed first, isn't the same as "Xcode 12.1", which fixed the problem?