Search found 5815 matches

by ted
Thu Dec 03, 2020 2:13 pm
Forum: General questions and discussions about computational neuroscience
Topic: General validation of NEURON?
Replies: 4
Views: 29

Re: General validation of NEURON?

Two other places to check: both the Allen Institute and the European Human Brain Project have used NEURON extensively in their research. It seems likely that at least some of that work would have involved validation of the many models they have been building. And of course anyone who happens to read...
by ted
Wed Dec 02, 2020 11:04 am
Forum: Getting started
Topic: Instantiate cell from Destexhe et al 1996 Thalamocortical and Thalamic Reticular Network
Replies: 1
Views: 19

Re: Instantiate cell from Destexhe et al 1996 Thalamocortical and Thalamic Reticular Network

Welcome, new NEURON user! Make it easy for yourself. Start by eliminating complexity. 1. Forget about Jupyter until you can use the model cell from plain old python. If you can't do that, you'll never get it going in a Jupyter notebook. 2. If you import neuron then every time you want to use some fe...
by ted
Wed Dec 02, 2020 10:32 am
Forum: General questions and discussions about computational neuroscience
Topic: General validation of NEURON?
Replies: 4
Views: 29

Re: General validation of NEURON?

modelers who have published a series of papers on one or more related models
Potential examples include the hippocampus models from I. Soltesz's lab, and the neocortical rhythmogenesis modeling by Stephanie Jones at Brown.
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: 29

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: 74

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: 74

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: 43

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: 74

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 many such c...
by ted
Fri Nov 20, 2020 10:26 am
Forum: Other questions
Topic: Enable/Disable NetStim objects at run time
Replies: 1
Views: 39

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). Probably th...
by ted
Wed Nov 18, 2020 10:42 pm
Forum: NEURON + Python
Topic: Modelling of subcellular signalling
Replies: 1
Views: 44

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 explain everyth...
by ted
Thu Nov 12, 2020 4:53 pm
Forum: NEURON hacks
Topic: Flushing Output to Disk
Replies: 1
Views: 47

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: 63

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 paper archives includ...
by ted
Wed Nov 04, 2020 5:18 pm
Forum: NEURON hacks
Topic: Implementing Superposition to "custom" waveforms in NMODL
Replies: 6
Views: 117

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: 63

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: 60

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...