Search found 5895 matches

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: 167

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: 180

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: 16196

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: 187

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: 180

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: 331

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: 331

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: 331

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 ...
by ted
Mon Feb 01, 2021 1:53 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: A pump MOD file and no concentration inside
Replies: 3
Views: 210

Re: A pump MOD file and no concentration inside

I was missing the "mass balance equation".
That'll do it.

Be sure to check your revised mod file with modlunit to verify that units are consistent, and if they aren't, apply the necessary scale factors.
by ted
Sun Jan 31, 2021 10:04 am
Forum: Adding new mechanisms and functions to NEURON
Topic: A pump MOD file and no concentration inside
Replies: 3
Views: 210

Re: A pump MOD file and no concentration inside

The concentration of a solute y in a compartment will not change unless there is a mass balance equation that relates y' (the rate of change of concentration in that compartment) to the net flux of y into that compartment. The mass balance equation can be specified in an NMODL file or by a statement...
by ted
Tue Jan 26, 2021 12:16 pm
Forum: Specific models
Topic: How to model spike and reset condition Ladenbauer 2019
Replies: 5
Views: 309

Re: How to model spike and reset condition Ladenbauer 2019

Now some comments about stability. The authors concocted the mathematical form of the instantanously activating regenerative current (second term on the right hand side of their Eq. 3) simply to produce threshold and spiking behavior. Instantaneously activating regenerative currents can pose special...
by ted
Tue Jan 26, 2021 11:45 am
Forum: Specific models
Topic: How to model spike and reset condition Ladenbauer 2019
Replies: 5
Views: 309

Re: How to model spike and reset condition Ladenbauer 2019

Before addressing the stability issue, here are some problems with the source code for twocomps that need to be fixed. These were discovered by checking the file with modlunit. UNITS block: F is unknown. If you meant farad, insert the declaration (F) = (farad) INITIAL block: (mv) needs to be deleted...
by ted
Thu Jan 21, 2021 10:05 am
Forum: Parallel NEURON
Topic: Efficient way of debugging Python scripts with MPI library
Replies: 4
Views: 261

Re: Efficient way of debugging Python scripts with MPI library

My suggestions pertain to development and debugging of NEURON models. It looks like your question is centered on MPI itself or NEURON's internals.
by ted
Wed Jan 20, 2021 9:24 am
Forum: Parallel NEURON
Topic: Efficient way of debugging Python scripts with MPI library
Replies: 4
Views: 261

Re: Efficient way of debugging Python scripts with MPI library

General suggestions that you probably already know: 1. Do as much development/debugging as possible on a multicore desktop machine. Defer executing code on specialized parallel hardware until absolutely necessary. 2. Write code that will produce the same results regardless of the number of hosts on ...
by ted
Tue Jan 19, 2021 11:08 am
Forum: Anatomically detailed models
Topic: The effect of changed dt and steps_per_ms
Replies: 3
Views: 271

Re: The effect of changed dt and steps_per_ms

First, an important fact: NEURON's temporal discretization parameter is dt, not steps_per_ms. steps_per_ms is a parameter that specifies the interval at which graphs are updated. Of course, steps_per_ms and dt must be compatible with each other--for example, if dt == 0.025 ms, then steps_per_ms can ...