Search found 5673 matches

by ted
Wed Nov 20, 2019 10:36 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 319

Re: Calcium diffusion and shells

Thanks, that will be a useful tip for others who may read this thread.
by ted
Wed Nov 20, 2019 10:32 am
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 456

Re: How to reconstruct the 3D points of a morphology imported by Import3D

Your post actually contains signs of multiple problems. I'm using the Import3D tool on a .asc file. I'm then using the n3d, x3d, y3d, and z3d functions on a section to iterate over what I presume are the 3D positions of all the segments in that section You realize that * a section's first and last 3...
by ted
Tue Nov 19, 2019 9:43 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 319

Re: Calcium diffusion and shells

Check to see if the readline library exists on your computer. If it doesn't, download and install it, then uninstall and reinstall NEURON. How? Depends on your Linux distribution. For distributions that use rpm for package management, rpm -q readline and rpm -ivh readline are your friends. Debian-re...
by ted
Mon Nov 18, 2019 10:39 am
Forum: NEURON hacks
Topic: How can I set coupling conductance explicitly to separate incoming from outgoing current?
Replies: 1
Views: 198

Re: How can I set coupling conductance explicitly to separate incoming from outgoing current?

For hypothesis testing purposes I'd like to have one compartment in the multi-compartment cell transmitting currents to all the connected compartments but not receiving current from all compartments. Is that doable in NEURON? If I correctly understand what you want (and I'm assuming that you aren't...
by ted
Sun Nov 17, 2019 2:59 pm
Forum: NEURON hacks
Topic: NMODL file in different folder
Replies: 9
Views: 2321

Re: NMODL file in different folder

I'm distributing models as part of a python package. During a post-install script I'd like to compile all of the mod files that are in a subfolder of the package, and I'd like NEURON to be able to find the resulting .dll from any folder on that machine. Right now it only seems to look in the curren...
by ted
Sun Nov 17, 2019 2:49 pm
Forum: Anatomically detailed models
Topic: measurments of area by section
Replies: 2
Views: 270

Re: measurments of area by section

I'm trying to obtain the surface of the different compartments. I understood that to obtain it for a section I should write totalarea_soma = 0 soma for (x,0) totalarea_soma += area(x) # take into account the number of nseg True. soma for (x,0) statement is equivalent to the following pseudocode: fo...
by ted
Fri Nov 15, 2019 8:03 am
Forum: Getting started
Topic: math operation
Replies: 1
Views: 233

Re: math operation

a\b
triggers an error message because \ is not recognized as an operator. Python thinks it is a line continuation mark. hoc doesn't recognize it at all. Search the Programmer's Reference for the term operator, or read Python's own reference materials.
by ted
Thu Nov 14, 2019 8:20 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Calcium diffusion and shells
Replies: 5
Views: 319

Re: Calcium diffusion and shells

See chapter 9 of the NEURON Book. If you don't have the book, get this preprint https://www.neuron.yale.edu/ftp/ted/book/revisions/chap9indexedref.pdf If you installed NEURON from source code, see nrn/share/examples/nrniv/nmodl/cadif.mod which may be slightly different from the example in the book. ...
by ted
Fri Nov 08, 2019 4:45 pm
Forum: Reaction-diffusion in NEURON
Topic: The equilibrium between the FS and external
Replies: 20
Views: 1094

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: 315

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: 20
Views: 1094

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: 315

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: 20
Views: 1094

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: 212

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: 254

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.