Search found 5857 matches

by ted
Thu Feb 25, 2021 11:11 am
Forum: The GUI
Topic: Convert a channel from .mod to the channel builder to modify gating in the GUI
Replies: 4
Views: 58

Re: Convert a channel from .mod to the channel builder to modify gating in the GUI

Chapter 14 of the NEURON Book contains some information about GUI programming in NEURON that might help: https://www.neuron.yale.edu/ftp/ted/boo ... ndexed.pdf
by ted
Thu Feb 25, 2021 11:06 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 78

Re: Loading a morphology as a hoc file

I am trying to load a morphology as a hoc file in GUI I think I understand this up to the word "file." Specifically, you're saying that you have a hoc file that contains statements that will create and connect sections and assign the correct length and diameter properties to them. I'm gue...
by ted
Wed Feb 24, 2021 10:40 pm
Forum: The GUI
Topic: Convert a channel from .mod to the channel builder to modify gating in the GUI
Replies: 4
Views: 58

Re: Convert a channel from .mod to the channel builder to modify gating in the GUI

Lots of other things to do, little time. The Channel Builder's source code is in nrn/share/nrn/lib/hoc/chanbild.hoc and the subdirectory nrn/share/nrn/lib/hoc/chanbild. Have fun!
by ted
Wed Feb 24, 2021 10:45 am
Forum: Getting started
Topic: recording axial current
Replies: 6
Views: 9314

Re: recording axial current

Is there a way to write a code for these in a mod file? Nope. hoc or Python. The example in my old post is in hoc. I am trying to measure the axial current between every segment in an object. How do you plan to deal with branch points? The notion of "axial current between every segment" b...
by ted
Wed Feb 24, 2021 10:40 am
Forum: The GUI
Topic: Convert a channel from .mod to the channel builder to modify gating in the GUI
Replies: 4
Views: 58

Re: Convert a channel from .mod to the channel builder to modify gating in the GUI

The principal strengths of the Channel Builder over NMODL as a means for implementing ion channels are 1. It makes syntax errors impossible (unlike NMODL, which practically invites them). Anything it allows you to do will probably work. 2. Its menu of formulas for voltage gating offers only physical...
by ted
Tue Feb 23, 2021 10:43 am
Forum: Hot tips
Topic: Plotting the lateral current of any segment
Replies: 2
Views: 50

Re: Plotting the lateral current of any segment

1. Making duplicate posts is as a violation of forum etiquette--not just here in the NEURON Forum, but in all moderated fora. Your duplicate post has been deleted. 2. The term for what you are calling "lateral current" is "axial current" or "longitudinal current." It ha...
by ted
Mon Feb 22, 2021 9:57 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to find EXp2Syn
Replies: 2
Views: 71

Re: How to find EXp2Syn

If you mean "where is exp2syn.mod" the answer is 1. if you installed by compiling the latest development code from the github repository, look in nrn/src/nrnoc 2. if you used a binary installer, download the tar.gz file that contains the source code for the standard distribution from the l...
by ted
Sat Feb 20, 2021 2:49 pm
Forum: Getting started
Topic: run funtion error
Replies: 3
Views: 91

Re: run funtion error

Is the code in your first post your entire program? If yes, then the problem is most likely that grclist.object(0) doesn't exist.
by ted
Sat Feb 20, 2021 2:45 pm
Forum: Other questions
Topic: computing impedances...
Replies: 17
Views: 15948

Re: computing impedances...

Do you have an idea? Without more information, let alone access to your code, I can't begin to guess whether the cause of problem is in your code or in NEURON. Did any error message appear in the interpreter window? Did you initialize the model before launching the impedance GUI tool? What version ...
by ted
Thu Feb 18, 2021 9:46 am
Forum: Other questions
Topic: McCulloch-Pitts or Boolean neurons in NEURON?
Replies: 2
Views: 75

Re: McCulloch-Pitts or Boolean neurons in NEURON?

I am collaborating with a biologist who would like to incorporate Boolean switching elements (like McCulloch-Pitts units) into a network model. Some biologist. McCulloch-Pitts! Maybe thinking about gene expression, or perhaps "high-level phenomena" like learning or social interaction. Is ...
by ted
Thu Feb 18, 2021 9:32 am
Forum: Getting started
Topic: run funtion error
Replies: 3
Views: 91

Re: run funtion error

Where is the complete multiline printout that constitutes the complete error message?
by ted
Wed Feb 10, 2021 9:59 am
Forum: NEURON + Python
Topic: Mechanisms in nrnmech.dll do not seem to be loading in python script
Replies: 5
Views: 164

Re: Mechanisms in nrnmech.dll do not seem to be loading in python script

As for the suggestion you made, I will be doing that from now on, especially if my work is to be published as this will just make it user friendly to anyone who decides to use it Excellent. Future potential users will appreciate that and be more likely to cite your work. BTW, we're always on the lo...
by ted
Tue Feb 09, 2021 5:42 pm
Forum: NEURON + Python
Topic: Mechanisms in nrnmech.dll do not seem to be loading in python script
Replies: 5
Views: 164

Re: Mechanisms in nrnmech.dll do not seem to be loading in python script

Thank you for your prompt reply. Also, and I should have written this sooner, thank you for using NEURON in your work. Previously you demonstrated that NEURON running by itself can discover and load a nrnmech.dll file from the current working directory ("Checking if the nrnmech.dll is loaded in...
by ted
Tue Feb 09, 2021 4:26 pm
Forum: NEURON + Python
Topic: Mechanisms in nrnmech.dll do not seem to be loading in python script
Replies: 5
Views: 164

Re: Mechanisms in nrnmech.dll do not seem to be loading in python script

You have already done a lot of important tests. Here's one more test I'd like you to do. Create a new empty directory. Put a copy of the NMODL file that defines klt (looks like that would be klt.mod) in that directory. Run mknrndll in that directory and check the printed messages to make sure there ...