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when I run the cell more than once in the same kernel, I get an error That's strange. What do you mean "run more than once in the same kernel"? just call h.run() again, and then execute the "plot results" code? That should work if you did it in plain python, without using Jupyte...

You're welcome. Many of the old GUI tools are quite powerful, and particularly useful for interactive exploration of model properties and simulation results in a way that complements Python's powerful introspection features.

You're almost there. I bet you forgot to declare that cell is an objref. Easy to do, especially if you're comfortable with Python which has dynamic typing. Just to make sure, I ran a couple of tests myself. Over the past couple of days I have been switching from CentoOS 7 to Rocky Linux 9, and as of...

Import3d won't do this. NEURON's InterViews based GUI has a "Section Parameters viewer" tool (AKA "shape name" tool) that is specifically designed for interactive browsing of a model cell's sections and segments. NEURON Main Menu toolbar / Tools / Distributed Mechanisms / Viewers...

In NMODL the assignment statement foo = bar() evaluates the value of bar() at the instant when the statement is executed, and passes that to foo. It does not make foo an alias for bar. If you want the value of foo to be calculated from function f0() when control variable c == 0, and from function f1...

Thanks for the followup. To help with further diagnosis:

What version of Windows are you using? 10 or 11 or something else?
Have you updated Windows recently?

Have you updated NEURON recently?

What version of NEURON are you using?

Decide whether you want to use h.run() or the sequence h.finiitalize h.continuerun If you prefer the latter, it's probably best to avoid inserting any other statements between them. If you prefer to call h.run(), there's no point in calling h.finiitalize, because h.run() executes hoc statements that...

how does pyr.hoc know how to assign each chunk of data in oh140807_A0_idJ.asc to the appropriate section category The Neurolucida file contains not only the morphometric data that specify cell topology and geometry, but also metadata (specified by the person or algorithm that did the actual measuri...

First, let me thank you for using NEURON. Now, about the problem you encountered, I need to ask a few questions. What version of Windows are you using? 10 or 11 or something else? Have you updated Windows recently? Have you updated NEURON recently? What version of NEURON are you using? (in a Command...

Thanks for the followup! Now I have a question for you:

Given the (to me at least) relatively nonspecific and noninformative error messages, what led you to check the mod file permissions? After all, nrnivmodl completed without complaint.

In an empty directory launch python 3 from the command line.
In Python execute
from neuron import h
If that works, execute
soma = h.Section("soma")
If something fails, at which step did that happen, and what was the error message?

NSF-Simons NITMB Fellows Program Applications due October 15, 2024 NITMB is seeking early-career researchers who have interest in transforming biological research and inspiring new mathematical discoveries. This opportunity is open to researchers who want to develop mathematical, theoretical, and c...

The Python tutorials illustrate a lot of useful things that can be done with code, and a particular approach to writing code that scales well as program complexity increases. But the KISS principle has its own advantages. Writing less code automatically means writing fewer typos and user-created bug...

Calcium is a key signal in many phenomena, some of which involve calcium diffusion from the site of ca entry (or site of release from organelles) to the site of ca action. Calcium accumulation mechanisms for such cases add even more overhead because more ODEs (or more complex kinetic schemes) are in...

Relax. Numerical integration is computationally expensive. Merely "READing" cai costs nothing by comparison. You could insert hundreds of mechanisms that READ cai into every section of a model cell, with no noticeable effect on run time--unless at least one of those mechanisms involved an ...