www.neuron.yale.edu

Before digging into implementational details, it is a good idea to verify that what we know, or think we know, makes sense. This is especially important when it comes to mathematical formulas and units. A synapse generates a current that is specified in "absolute units" (e.g. nA in NEURON)...

I modified the two synaptic NMODL files by declaring USEION na WRITE inas USEION k WRITE iks In a USEION statement, the variable name declared in the USEION clause dictates the form of the names declared in the READ and WRITE clauses. Also, NEURON only "knows" about na, k, and ca, so any ...

There may be some ways to reduce complexity, but I'll have to ask some questions. Here's a big suggestion (I don't know why Lavzin et al. didn't do this): The mod files for several mechanisms generate nonspecific currents. Presumably you want to attribute those currents to corresponding ion fluxes, ...

Interesting questions. I was wondering if it makes any sense in some cases (such as mine) to model a multicompartment soma. Depends on the temporal and spatial scales that are relevant to the phenomena you are studying. For structures roughly the size of somas in vertebrates, there is no need to use...

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?