Search found 5936 matches

by ted
Thu Apr 15, 2021 4:42 pm
Forum: OS X
Topic: If you can't compile mod files . . .
Replies: 26
Views: 32891

Re: If you can't compile mod files . . .

why Spyder displays this message
implies launching from within Spyder. What does Spyder treat as the "working directory" and is there a way to make Spyder change that to the parent of the x86_64 directory?
by ted
Wed Apr 14, 2021 11:54 am
Forum: NEURON + Python
Topic: Myelin modeling
Replies: 3
Views: 388

Re: Myelin modeling

I am trying to model the double cable circuit used by Wårdell et al 2019 I have no suggestions, having never seen the paper. Presumably the authors describe their methodology sufficiently clearly that correspondences between their parameters and those of NEURON's extracellular "mechanism"...
by ted
Tue Apr 13, 2021 2:56 pm
Forum: General questions and discussions about computational neuroscience
Topic: Funding opportunites from NASA!
Replies: 0
Views: 881

Funding opportunites from NASA!

The NASA Human Research Program has released two funding opportunities for research relevant to the Space Radiation Element. Appendix E Flagship Opportunity: https://tinyurl.com/HERO20-HHP Space Radiation Topics: Topic 2. Computational Brain Modeling to Characterize the Effects of Space Radiation Ex...
by ted
Tue Apr 13, 2021 11:45 am
Forum: NEURON + Python
Topic: Impulse Response for all locations
Replies: 1
Views: 271

Re: Impulse Response for all locations

I know I can find the transfer impedance for a pure frequency What constitutes an impure frequency? What to do depends on whether you prefer to operate in the frequency domain or in the time domain. If you want to operate in the frequency domain, then for any pair of locations of interest you'll ha...
by ted
Tue Apr 13, 2021 1:08 am
Forum: NEURON + Python
Topic: Assigning values to a mechanism over all sections in anatomically detailed model
Replies: 3
Views: 325

Re: Assigning values to a mechanism over all sections in anatomically detailed model

Comments: 1. Iteration over all sections is required because ena is a range variable, not a global variable. 2. Iteration over all segments is not required because the syntax sectionname.rangevarname = somevalue assigns the value "somevalue" to the range variable in all segments of the ref...
by ted
Mon Apr 12, 2021 2:49 pm
Forum: NEURON + Python
Topic: Assigning values to a mechanism over all sections in anatomically detailed model
Replies: 3
Views: 325

Re: Assigning values to a mechanism over all sections in anatomically detailed model

It's pretty straightforward in Python too. Try to think about the problem as being "how to iterate over all sections." This is easiest with the idiom for sec in h.allsec(): one_or_more_statements Example: suppose you have just created a bunch of sections and you need to insert hh into all ...
by ted
Fri Apr 02, 2021 12:10 pm
Forum: OS X
Topic: Gui Freezing
Replies: 5
Views: 659

Re: Gui Freezing

Thanks for following up on that.
by ted
Fri Mar 26, 2021 9:43 am
Forum: NEURON + Python
Topic: Myelin modeling
Replies: 3
Views: 388

Re: Myelin modeling

What "myelin double circuit model" are you referring to? With regard to models of spike propagation in myelinated axons, many authors have published such models. Most of them use very simple representations of the electrical effects of the myelin sheath. Whether one is better than another ...
by ted
Wed Mar 24, 2021 10:26 am
Forum: NEURON + Python
Topic: initbatser.py
Replies: 3
Views: 243

Re: initbatser.py

Those files are from an exercise that was part of the 2018 NEURON Summer Course. Download and expand this file
https://neuron.yale.edu/ftp/neuron/2018emory/course.zip
and you'll find all the files for that particular exercise in course/bulletin_board_py
by ted
Tue Mar 23, 2021 6:53 pm
Forum: NEURON + Python
Topic: initbatser.py
Replies: 3
Views: 243

Re: initbatser.py

The programs initbatser.py and initplotfi.py both need to use a procedure called plotfi, but plotfi is not built into Python. Instead, it is a user-written procedure that is defined in plotfi.py, which is in the same directory as initbatser.py and initplotfi.py. The statement from plotfi import plot...
by ted
Tue Mar 23, 2021 11:00 am
Forum: Specific models
Topic: Adding multiple synaptic connections to the two-compartment model (Ladenbauer 2019)
Replies: 1
Views: 376

Re: Adding multiple synaptic connections to the two-compartment model (Ladenbauer 2019)

There's a lot of "stuff" (code complexity) in that implementation of the Izhikevich model. It would be easier to incorporate simple representations of excitatory and inhibitory synaptic transmission, similar to ExpSyn and/or Exp2Syn, into your January 26 twocomps model. ExpSyn-like excitat...
by ted
Mon Mar 22, 2021 9:11 am
Forum: NEURON Announcements
Topic: 8.0 release plan?
Replies: 3
Views: 408

Re: 8.0 release plan?

It will be released when it's ready.
by ted
Thu Mar 18, 2021 12:12 pm
Forum: Getting started
Topic: The math behind extracellular mechanisms
Replies: 23
Views: 26920

Re: The math behind extracellular mechanisms

Sorry about that. The site's architecture has changed several times over the years, and some old URLs were not updated. The updated link is https://neuron.yale.edu/neuron/static/p ... p2.htm#3.2
by ted
Thu Mar 18, 2021 12:06 pm
Forum: NEURON + Python
Topic: Kernel dies in Jupyter notebook when attempting to import NEURON
Replies: 3
Views: 781

Re: Kernel dies in Jupyter notebook when attempting to import NEURON

Thanks for that information.

I would also expect that nrnivmodl (or mknrndll) would generate an error message if it encountered duplicate SUFFIXes when compiling mod files.
by ted
Tue Mar 16, 2021 12:17 am
Forum: NEURON + Python
Topic: Kernel dies in Jupyter notebook when attempting to import NEURON
Replies: 3
Views: 781

Re: Kernel dies in Jupyter notebook when attempting to import NEURON

In my case, the source of the error was a naming conflict between mod files, where they shared the same user defined name.
Do you mean to say that the mod files had the same name? Or that their NEURON blocks contained identical
SUFFIX
or
POINT_PROCESS
or
ARTIFICIAL_CELL
statements?