Search found 5648 matches

by ted
Thu Nov 21, 2019 1:47 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL: COMPARTMENT statement in the KINETIC section
Replies: 2
Views: 103

Re: NMODL: COMPARTMENT statement in the KINETIC section

If you actually have a copy of The NEURON Book , see the discussion in 9.10.1 Modeling diffusion with kinetic schemes . Any reader of this thread who does not have the book may download this earlier draft of chapter 9 https://www.neuron.yale.edu/ftp/ted/book/revisions/chap9indexedref.pdf and read Mo...
by ted
Thu Nov 21, 2019 1:33 pm
Forum: OS X
Topic: NEURON not working properly after update to Catalina and major troubleshooting!
Replies: 3
Views: 131

Re: NEURON not working properly after update to Catalina and major troubleshooting!

Not related to the problem that triggered this thread, but something you need to know: for your ODE-described calcium accumulation mechanism, use derivimplicit rather than cnexp. See Integration methods for SOLVE statements https://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592 in the Hot tips a...
by ted
Thu Nov 21, 2019 1:25 pm
Forum: NEURON + Python
Topic: How to get synapse offset/position
Replies: 5
Views: 136

Re: How to get synapse offset/position

If it is absolutely essential to place "something" at a very particular location along a neurite, then represent the neurite by two sections connected in series, assign each section whatever length you need, and place the "something" at their junction point. Then you are free to use whatever values ...
by ted
Thu Nov 21, 2019 11:30 am
Forum: Getting started
Topic: How to reconstruct the 3D points of a morphology imported by Import3D
Replies: 7
Views: 234

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

If a section.parentseg().x = 0.5 and parent_section.n3d = 21, does that mean that section is connected to parent_section somewhere around the 10th-11th 3d xyz point? No. Reflect on the fact that what governs the placement of xyzdiam measurements along the length of an unbranched neurite are the irr...
by ted
Thu Nov 21, 2019 11:06 am
Forum: NEURON hacks
Topic: NMODL file in different folder
Replies: 9
Views: 2026

Re: NMODL file in different folder

On Linux it generates a folder x86_64 . . . The documentation mentions that nrn_load_dll works for Linux, but I don't see a dll file? The file you want to load is x86_64/.libs/libnrnmech.so You realize that, by doing this, you are writing code that will not work under MSWin or MacOS. And unless you...
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: 203

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: 234

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: 203

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: 122

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: 2026

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: 168

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: 117

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: 203

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: 663

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: 198

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 ...