Search found 5857 matches

by ted
Fri Mar 05, 2021 12:04 pm
Forum: Getting started
Topic: Help with fixing errors to run modeldb neurons
Replies: 6
Views: 54

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: 54

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: 81

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: 57

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: 57

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: 69

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: 93

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"?
by ted
Tue Mar 02, 2021 10:52 am
Forum: Anatomically detailed models
Topic: Loading a morphology as a hoc file
Replies: 9
Views: 81

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: 69

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: 69

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: 69

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: 93

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: 93

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: 38

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: 81

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...