Search found 5895 matches

by ted
Tue Mar 02, 2021 10:52 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 284

Re: Loading a morphology as a hoc file

Everything between begintemplate celltemplate and endtemplate celltemplate defines a class. If those statements include one or more "create" statements and "connect" statements, it's a cell class. If that's the case, what you have is a hoc file that defines a cell class but doesn...
by ted
Mon Mar 01, 2021 3:58 pm
Forum: Parallel NEURON
Topic: Parallel version of a model
Replies: 6
Views: 273

Re: Parallel version of a model

This model entry's README file should really provide instructions for parallel execution.
by ted
Mon Mar 01, 2021 3:41 pm
Forum: Parallel NEURON
Topic: Parallel version of a model
Replies: 6
Views: 273

Re: Parallel version of a model

You'll want to use the command line when dealing with parallelized code. Double clicking on a hoc file will result in serial execution. The syntax for parallel execution is mpiexec -n N nrniv -mpi foo.hoc where N is the number of cores to use in the simulation and foo.hoc is the name of the parallel...
by ted
Mon Mar 01, 2021 2:40 pm
Forum: Parallel NEURON
Topic: Parallel version of a model
Replies: 6
Views: 273

Re: Parallel version of a model

When I tried to run the parallel version
And how did you do that?
by ted
Sun Feb 28, 2021 1:51 pm
Forum: NEURON + Python
Topic: hoc file is not a template
Replies: 6
Views: 253

Re: hoc file is not a template

Hi Alexandra, I just tested the model and I was able to instantiate the izh2003 cell. I'm on Mac OS . . . After compiling the mod files, I was able to execute nrngui izhi2004a.hoc without problems. Also, starting nrngui without any command line options, I was able to create an instance of Izhi2003a...
by ted
Sun Feb 28, 2021 1:42 pm
Forum: NEURON + Python
Topic: hoc file is not a template
Replies: 6
Views: 253

Re: hoc file is not a template

With regard to the problem that occasioned your first post in this thread, which opened with I want to instantiate the izhekevic neuron Izhi2003a.hoc attached, but I get the error: "Izhi2003a is not a template" That post included the output that NEURON printed to its terminal, from which I...
by ted
Sun Feb 28, 2021 11:32 am
Forum: NEURON hacks
Topic: space plot of voltage changes every repetition
Replies: 1
Views: 211

Re: space plot of voltage changes every repetition

Do you mean that you're not getting the same results each time you run a simulation?
by ted
Sun Feb 28, 2021 11:31 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 284

Re: Loading a morphology as a hoc file

The mod files have nothing to do with the problems you're having. Could not open C:/Users/Jackie.MEDICINE/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anaconda3 (64-bit)/Anaconda Prompt.lnk Could not open C:/Users/Jackie.MEDICINE/AppData/Roaming/Microsoft/Windows/Start Menu/Programs/Anacond...
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: 394

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: 284

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: 394

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: 9552

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: 394

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: 191

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...