Search found 5871 matches

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: 1
Views: 10

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: 374

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: 1
Views: 54

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: 46

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: 46

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: 47

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: 60

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: 25915

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: 83

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: 83

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?
by ted
Sat Mar 13, 2021 12:14 pm
Forum: Getting started
Topic: Find all point processes
Replies: 5
Views: 86

Re: Find all point processes

Thanks, but I'm just standing on the shoulders of giants. More credit goes to those who are responsible for the hard work of software development (not to mention getting support for such development). The list at http://neuron.yale.edu/neuron/credits lags behind the growth of the development team.
by ted
Thu Mar 11, 2021 1:10 pm
Forum: Getting started
Topic: Find all point processes
Replies: 5
Views: 86

Re: Find all point processes

It's always good to use meaningful names so a program automatically documents itself. One more hint: you can verify the existence or nonexistence of objects by using h.allobjects("classname") to discover the names of all instances of the named class (as well as the reference count for each...
by ted
Tue Mar 09, 2021 4:14 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: netstim and randomness
Replies: 1
Views: 53

Re: netstim and randomness

Very good question. The answer is yes, but "yes" doesn't tell you how to do it, or what complications might arise. For example, did you know that, by default, there is only a single pseudorandom number generator, and that everything that needs a "random" number will get its numbe...
by ted
Tue Mar 09, 2021 3:15 pm
Forum: Getting started
Topic: Find all point processes
Replies: 5
Views: 86

Re: Find all point processes

Why not hose the whole model and rebuild it from scratch? Seriously. That's the only bulletproof way to avoid undesired persistence of object instances (an instance persists until its reference count is 0). You might say, "oh, but undesired persistence will never happen because I will never cre...
by ted
Fri Mar 05, 2021 12:04 pm
Forum: Getting started
Topic: Help with fixing errors to run modeldb neurons
Replies: 6
Views: 108

Re: Help with fixing errors to run modeldb neurons

First thing I would do--if I was moving code from a windows box to a mac, I'd get rid of all nrnmech.dll, .o, and .c files that were generated on the PC. Then I'd try nrnivmodl on the Mac. Maybe that doesn't apply to you (maybe you did a fresh download from ModelDB).