Search found 5771 matches

by ted
Wed Jan 01, 2020 7:48 pm
Forum: NEURON + Python
Topic: Associative arrays in HOC
Replies: 5
Views: 796

Re: Associative arrays in HOC

As long as Python is installed, you can use Python dictionaries from inside HOC
This looks like the way to go--avoids trying to use hoc to replicate existing Python functionality.
by ted
Wed Jan 01, 2020 2:34 pm
Forum: NEURON + Python
Topic: Converting HOC extracellular to Python
Replies: 3
Views: 643

Re: Converting HOC extracellular to Python

As ramcdougal notes, the hoc statement insert extracellular xraxial=Rpn0 xg=1e10 xc=0 will affect xraxial[0], xg[0], and xc[0] of the currently accessed section. extracellular's "0" layer is the one that is right next to the external surface of the section, and it's usually the one whose parameters ...
by ted
Wed Jan 01, 2020 11:43 am
Forum: Getting started
Topic: replicate Waxman's model
Replies: 4
Views: 1775

Re: replicate Waxman's model

I wonder if I use a finer scale (Δx=10um, n_seg=200, compared with Waxman: Δx=200um, n_seg=10),apply Crank-Nicholson method with an integration time increment Δt=5 us, then I should get a more accurate result, is that right? That's not going to resolve the differences between their results and the ...
by ted
Wed Jan 01, 2020 11:00 am
Forum: Getting started
Topic: replicate Waxman's model
Replies: 4
Views: 1775

Re: replicate Waxman's model

On re-reading Brill et al. 1977 I saw that my interpretation of "internodal conduction time" was incorrect. They define it as "the difference in times at which the rising phase crossed 50 mV at two consecutive nodes." This means that spike time measurement must be made at the centers of two consecut...
by ted
Tue Dec 31, 2019 2:51 pm
Forum: Getting started
Topic: replicate Waxman's model
Replies: 4
Views: 1775

Re: replicate Waxman's model

First let me apologize for this delayed reply. I've zipped my file (for the first two figures)and sent to your email I received your email message, but it had no attachment. Try again? The model used by Waxman et al. 1978 is based on what they used for Brill, Waxman, Moore, and Joyner (1977) Conduct...
by ted
Sun Dec 22, 2019 9:36 pm
Forum: Anatomically detailed models
Topic: altering length and diameter over a subset
Replies: 1
Views: 575

Re: altering length and diameter over a subset

for i=1, 8 {
forsec all_dendrite {L=L/i} <--- you changed the length of every section in "all_dendrite"

forsec all { nseg = int((L/(0.1*lambda_f(100))+.999)/2)*2 + 1 } <--- now you're changing nseg in every section in "all"
...

analysis()
}
by ted
Sun Dec 22, 2019 9:29 pm
Forum: Suggestions and Feedback
Topic: Accessibility of documentation
Replies: 1
Views: 563

Re: Accessibility of documentation

Fixed on Friday.

--Ted
by ted
Wed Dec 18, 2019 9:10 pm
Forum: Anatomically detailed models
Topic: Is there any way to bifurcate axon?
Replies: 3
Views: 607

Re: Is there any way to bifurcate axon?

That ModelDB entry actually contains several models. One is very simple (defined by demofig2.hoc)--uses two compartments to represent the entire cell. This is probably not the model that you mean. The other models are based on anatomical data from real cells. However, none of that data includes any ...
by ted
Tue Dec 17, 2019 1:22 pm
Forum: Anatomically detailed models
Topic: Is there any way to bifurcate axon?
Replies: 3
Views: 607

Re: Is there any way to bifurcate axon?

To answer your question, I need to know which model you mean. The URL you posted is broken. Forget about the URL--just tell me its accession number. Click on the model entry's "Model Information" tab and you'll see the accession number just below the tab.
by ted
Tue Dec 17, 2019 1:18 pm
Forum: NEURON + Python
Topic: Video Tutorial on how to compile .mod file and incorporate it with Python for simulation
Replies: 1
Views: 670

Re: Video Tutorial on how to compile .mod file and incorporate it with Python for simulation

Interesting tutorial. Thanks for posting it! It's no surprise that "how to compile mod files" is a Frequently Asked Question. NEURON's web site has a list of answers to to this and many other frequently asked questions. At www.neuron.yale.edu click on the Documentation link. A popup appears that con...
by ted
Mon Dec 16, 2019 11:30 am
Forum: NEURON + Python
Topic: Associative arrays in HOC
Replies: 5
Views: 796

Re: Associative arrays in HOC

Nope, hoc doesn't have dicts. You might be able to fake it with a pair of Lists.
by ted
Mon Dec 16, 2019 11:28 am
Forum: Parallel NEURON
Topic: Periodically saving results during simulation
Replies: 3
Views: 1113

Re: Periodically saving results during simulation

If runlength specifies the number of ms that you want the simulation to advance,
ParalelContext.psolve(t + runlength)
should do it.
by ted
Fri Dec 13, 2019 11:02 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Accessing state variables of one mechanisn in another mechanism
Replies: 4
Views: 746

Re: Accessing state variables of one mechanisn in another mechanism

The example is to be read as an illustration of the use of pointers to link variables in different mechanisms. Period. There's nothing about pointers that requires that any point processes be involved at all. If mechanism B has some variable y whose value is actually computed in mechanism A, then re...
by ted
Thu Dec 12, 2019 10:49 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 1022

Re: Precise 3D morphology

it seems to be very precise What seems to be very precise? Spine location, detailed shape of spine heads, what? The people at MicroBrightField are very helpful. Address questions about Neurolucida to them and they'll be glad to tell you what you want to know. Or search the Internet for neurolucida ...
by ted
Wed Dec 11, 2019 11:05 am
Forum: Anatomically detailed models
Topic: Precise 3D morphology
Replies: 6
Views: 1022

Re: Precise 3D morphology

Fine spatial detail doesn't matter much for electrical signals, which have length constants on the order of tens or hundreds of microns. It can be important for chemical signals, especially intracellular calcium and second messengers, not to mention ions and neurotransmitters in tissue extracellular...