Search found 5895 matches

by ted
Mon Mar 22, 2021 9:11 am
Forum: NEURON Announcements
Topic: 8.0 release plan?
Replies: 3
Views: 224

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: 26340

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: 188

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: 188

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: 182

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: 182

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: 111

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: 182

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: 229

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).
by ted
Fri Mar 05, 2021 12:24 am
Forum: Getting started
Topic: Help with fixing errors to run modeldb neurons
Replies: 6
Views: 229

Re: Help with fixing errors to run modeldb neurons

When trying to see if somebody else's code executes, the first thing to do is try executing the code. Don't start tinkering with it or you may break something that didn't need fixing--or worse, destroy a clue to a problem that rendered the original code's results invalid. The first message "One...
by ted
Wed Mar 03, 2021 2:53 pm
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 284

Re: Loading a morphology as a hoc file

A nice consequence of defining a cell class: you can use it to make as many instances as you like. Each instance will have its own name, membrane potentials, ionic currents, etc.. Very useful for modeling networks. Example: objref pyrlist pyrlist = new List() for i = 0,9 pyrlist.append(new Pyr()) //...
by ted
Wed Mar 03, 2021 11:32 am
Forum: Anatomically detailed models
Topic: NEURON changes dendrite diameter to default value
Replies: 4
Views: 250

Re: NEURON changes dendrite diameter to default value

That's an ugly bug. No matter what I do, I'm not seeing what you did. I tried nrngui geom_test.hoc nrngui followed by execution of load_file("geom_test.hoc") at the oc> prompt nrngui followed by use of GUI (NEURON Main Menu / File / load hoc, then clicking on geom_test.hoc) and each produc...
by ted
Tue Mar 02, 2021 12:51 pm
Forum: Anatomically detailed models
Topic: NEURON changes dendrite diameter to default value
Replies: 4
Views: 250

Re: NEURON changes dendrite diameter to default value

Can't begin to guess what's going on. Would have to reproduce this in order to discover what's happening. Zip up the hoc file and email it to
ted dot carnevale at yale dot edu
and I'll tell you what I find out.
by ted
Tue Mar 02, 2021 12:49 pm
Forum: Parallel NEURON
Topic: Parallel version of a model
Replies: 6
Views: 273

Re: Parallel version of a model

When I run the serial code, I double click the .hoc file, then the GUI appears and I control the duration of simulations and see the real-time for each simulation. Is there any way I can do that with the parallel execution? Read about "time" in the Programmer's Reference. 2nd) The first t...
by ted
Tue Mar 02, 2021 12:31 pm
Forum: NEURON + Python
Topic: hoc file is not a template
Replies: 6
Views: 253

Re: hoc file is not a template

I want to plot/recreate the voltage output of the different izhikevic cells.The GUI loads successfully but as I select spike patters for the izhikevic neuron I get the error
How were you "selecting spike patterns"?