Search found 6362 matches

by ted
Tue Dec 03, 2024 12:40 pm
Forum: The GUI
Topic: voltage propagation in the whole cell
Replies: 5
Views: 19704

Re: voltage propagation in the whole cell

Well, you're on the right track, but this can be done without explicit, formal use of callbacks. And the resulting code could be easily understood by all, even those who are new to Python. Some of the following discussion is for the benefit of others who may read this thread but have less experience...
by ted
Thu Nov 14, 2024 11:19 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to call my ionic current variable implemented in NMODL in HOC
Replies: 12
Views: 4032

Re: How to call my ionic current variable implemented in NMODL in HOC

Here is the primary consideration: reusing code that is known to have serious problems is inadvisable for many reasons. It wastes the time and effort of whoever reuses it, because it jeopardizes publication of results, not to mention support of current or future work. And it's not good for computati...
by ted
Wed Nov 13, 2024 2:37 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How to call my ionic current variable implemented in NMODL in HOC
Replies: 12
Views: 4032

Re: How to call my ionic current variable implemented in NMODL in HOC

Well, maybe not so quickly, allowing for intrusions like a grant application. Here at last are properly written implementations of AMPAergic and NMDAergic synaptic transmission https://www.neuron.yale.edu/ftp/ted/neuron/ampanmda.zip along with demonstration programs that illustrate usage via hoc and...
by ted
Mon Nov 11, 2024 12:43 pm
Forum: Getting started
Topic: h.run vs h.continuerun(h.tstop)
Replies: 6
Views: 4554

Re: h.run vs h.continuerun(h.tstop)

Assuming that the time course of seg's extracellular potential is specified by the vector pair gvec and stim_t_vec, then the correct syntax for Vector.play is gvec.play(seg._ref_e_extracellular, stim_t_vec) This should force seg.e_extracellular to follow the time course specified by the vector pair ...
by ted
Thu Oct 31, 2024 6:17 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How to call my ionic current variable implemented in NMODL in HOC
Replies: 12
Views: 4032

Re: How to call my ionic current variable implemented in NMODL in HOC

< revised from initial post > The chief problem with the models of NMDAergic and AMPAergic synaptic transmission used and published by Basak and Narayanan (2018) is they are implemented as point processes but their parameters and variables have units that are appropriate not for point processes but ...
by ted
Tue Oct 22, 2024 1:37 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How to call my ionic current variable implemented in NMODL in HOC
Replies: 12
Views: 4032

Re: How to call my ionic current variable implemented in NMODL in HOC

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)...
by ted
Mon Oct 21, 2024 11:33 am
Forum: Adding new mechanisms and functions to NEURON
Topic: How to call my ionic current variable implemented in NMODL in HOC
Replies: 12
Views: 4032

Re: How to call my ionic current variable implemented in NMODL in HOC

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 ...
by ted
Thu Oct 17, 2024 2:28 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: How to call my ionic current variable implemented in NMODL in HOC
Replies: 12
Views: 4032

Re: How to call my ionic current variable implemented in NMODL in HOC

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, ...
by ted
Thu Oct 10, 2024 1:12 pm
Forum: Other questions
Topic: Multicompartment Soma
Replies: 2
Views: 2000

Re: Multicompartment Soma

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...
by ted
Mon Oct 07, 2024 4:44 pm
Forum: Getting started
Topic: h.run vs h.continuerun(h.tstop)
Replies: 6
Views: 4554

Re: h.run vs h.continuerun(h.tstop)

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...
by ted
Fri Oct 04, 2024 10:31 am
Forum: Anatomically detailed models
Topic: Determining distance from soma along apical dendrite
Replies: 7
Views: 4454

Re: Determining distance from soma along apical dendrite

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.
by ted
Thu Oct 03, 2024 4:04 pm
Forum: Anatomically detailed models
Topic: Determining distance from soma along apical dendrite
Replies: 7
Views: 4454

Re: Determining distance from soma along apical dendrite

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...
by ted
Sun Sep 29, 2024 1:13 pm
Forum: Anatomically detailed models
Topic: Determining distance from soma along apical dendrite
Replies: 7
Views: 4454

Re: Determining distance from soma along apical dendrite

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...
by ted
Sun Sep 29, 2024 12:30 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Updating the derivative in a NET_RECEIVE block
Replies: 1
Views: 1515

Re: Updating the derivative in a NET_RECEIVE block

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...
by ted
Thu Sep 26, 2024 11:20 pm
Forum: MSWin
Topic: NEURON cann't open hoc
Replies: 5
Views: 3203

Re: NEURON cann't open hoc

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?