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by ted
Fri Nov 08, 2019 4:45 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 13
Views: 267

Re: The equilibrium between the FS and external

That's a very good question. NEURON's computational engine can calculate ionic equilibrium potentials in the course of a simulation. If your model includes an NMODL-specified "ion accumulation mechanism" (a mechanism with a USEION statement that WRITEs the intra- or extracellular concentration of on...
by ted
Fri Nov 08, 2019 10:32 am
Forum: Getting started
Topic: model view
Replies: 3
Views: 50

Re: model view

No, NEURON works with Python 2.7 as well. But there's not much point in configuring NEURON to use 2.7 because the people who develop Python are terminating support for 2.7 in 2020. If I were you, I'd uninstall both NEURON and Python, then I'd install the latest stable Python 3.x, and after that I'd ...
by ted
Thu Nov 07, 2019 1:37 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 13
Views: 267

Re: The equilibrium between the FS and external

Don't worry about that--you don't have to repost anything. The new thread will go in this same discussion area, because it's about using rxd.
by ted
Thu Nov 07, 2019 8:59 am
Forum: Getting started
Topic: model view
Replies: 3
Views: 50

Re: model view

Recent distributions of NEURON require Python to be installed in order for Model View to work. If Python is not already installed on your computer, suggest uninstalling NEURON completely (if you're using Windows, run c:\nrn\uninstall.exe and then be sure to c:\nrn and its contents if that directory ...
by ted
Wed Nov 06, 2019 10:08 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 13
Views: 267

Re: The equilibrium between the FS and external

This thread will be split into two threads. The "new" thread will contain the posts on and after November 5. Reason: The posts starting with November 5 are on a different topic than the earlier posts. Basic Forum etiquette: 1. Do not make duplicate posts. 2. Questions or answers that diverge from th...
by ted
Wed Nov 06, 2019 10:02 pm
Forum: Reaction-diffusion in NEURON
Topic: Tracking External and Internal Na & K concentration
Replies: 2
Views: 48

Re: Tracking External and Internal Na & K concentration

This thread will be deleted.
Reason: duplicate post of a question.
by ted
Tue Nov 05, 2019 8:41 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: adrunge not thread safe
Replies: 2
Views: 50

Re: adrunge not thread safe

Good that warning turned up. Always specify an appropriate method. runge, adrunge, adams etc. are not appropriate. See
Integration methods for SOLVE statements viewtopic.php?f=28&t=592
in the Forum's Hot tips area. Those recommendations are current.
by ted
Tue Nov 05, 2019 10:10 am
Forum: NEURON + Python
Topic: How to add synapses to an Adex model
Replies: 4
Views: 112

Re: How to add synapses to an Adex model

It's an artificial spiking cell. It ignores the membrane potential and membrane currents of whatever section to which it is attached, and makes no contribution to that section's membrane currents. It also ignores the weight associated with whatever NetCons deliver events to it. Although it contains ...
by ted
Fri Nov 01, 2019 2:11 pm
Forum: Getting started
Topic: Spike configuration at internode sections of myelinated axon
Replies: 5
Views: 91

Re: Spike configuration at internode sections of myelinated axon

In myelinated sections, there are no transmembrane currents then why the intracellular potential changes instead of remaining at -65mV? Here's a hint at an answer: The cytoplasm in the myelinated internode acts like a resistor that the flow of current from one end of the internode to the other. Acc...
by ted
Thu Oct 31, 2019 11:40 am
Forum: UNIX/Linux
Topic: PyNeuron + Ubuntu + Python 3.6
Replies: 5
Views: 116

Re: PyNeuron + Ubuntu + Python 3.6

Install NEURON. If your program makes use of NEURON's GUI or standard run system, make sure that its main Python file (the one you call to launch your model/simulation) starts with the line from neuron import h, gui If it doesn't, that file should start with the line from neuron import h Then at the...
by ted
Thu Oct 31, 2019 10:44 am
Forum: UNIX/Linux
Topic: PyNeuron + Ubuntu + Python 3.6
Replies: 5
Views: 116

Re: PyNeuron + Ubuntu + Python 3.6

If you're having problems with PyNeuron, ask the developer of PyNeuron for help. NEURON's license allows third parties to fork their own project from it, and create whatever they want with it. But they're responsible for supporting what they create. If you need to use NEURON, you should completely u...
by ted
Wed Oct 30, 2019 11:04 am
Forum: Getting started
Topic: Spike configuration at internode sections of myelinated axon
Replies: 5
Views: 91

Re: Spike configuration at internode sections of myelinated axon

Enthusiasm is good, asking good questions is good, but this thread is quickly becoming an informal short course on cellular neurophysiology plus circuit theory plus physics--all diverging from the primary aim of the NEURON Forum, which is to address questions about NEURON. Anyone else who wants to, ...
by ted
Tue Oct 29, 2019 9:30 pm
Forum: Getting started
Topic: Spike configuration at internode sections of myelinated axon
Replies: 5
Views: 91

Re: Spike configuration at internode sections of myelinated axon

The term "spike configuration" will not be understood by neuroscientists. Perhaps you mean "spike waveform"?
by ted
Mon Oct 28, 2019 2:29 pm
Forum: Getting started
Topic: construct a single myelinated axon
Replies: 8
Views: 276

Re: construct a single myelinated axon

if I want to see the spike propagation along a myelinated axon, can I refer to the work done(the effect of changing the diameter of the axon on the capacitance) by Moore using pas instead of extracellular Yes, if your intent is to see intracellular potential relative to ground. If the model uses ex...
by ted
Mon Oct 28, 2019 1:09 pm
Forum: The GUI
Topic: saving recordings automatically
Replies: 1
Views: 124

Re: saving recordings automatically

It's called programming. If you've never done it before, it's time to start learning, hire somebody to do it for you, or develop a collaboration with somebody who knows how. We strongly suggest Python for all new programming projects. Fortunately, it's easy to use GUI-built models with Python. Here'...