Search found 26 matches

by Feanor
Thu Nov 23, 2023 4:44 pm
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 4
Views: 29717

Re: Cell membrane with PMCA pump

Hi ramcdougal, Could you explain the derivation of the scale factor here? Why is the electron charge in the factor? I would have guessed Avogadro's number would have something to do with it. Why 1e-14? um2 is 1e-12 m2, is that related? e = 1.60217662e-19 scale = 1e-14 / e # rate constant is in terms...
by Feanor
Fri Sep 17, 2021 2:17 pm
Forum: Anatomically detailed models
Topic: Error in loading morphology from swc file
Replies: 4
Views: 7943

Re: Error in loading morphology from swc file

OK, I can mark this as resolved now ... I restarted the computer and the same code works now. I have NO idea what happened.
by Feanor
Fri Sep 17, 2021 2:05 pm
Forum: Anatomically detailed models
Topic: Error in loading morphology from swc file
Replies: 4
Views: 7943

Re: Error in loading morphology from swc file

Strange indeed. Maybe something in this code I am using has changed throughout different NEURON versions? Hopefully something easy to spot. Here is the code. It is a class that creates a spiny projection neuron (also medium spiny neuron, hence the class name MSN). I am pasting just the beginning of ...
by Feanor
Fri Sep 17, 2021 11:04 am
Forum: Anatomically detailed models
Topic: Error in loading morphology from swc file
Replies: 4
Views: 7943

Error in loading morphology from swc file

Hello everyone! I just installed NEURON 8.0 on a fresh installation of Ubuntu 20, and am trying to run already existing code. While loading a morphology of a spiny projection neuron I get the following error which did not appear on my previous installation of Ubuntu and NEURON. I am wondering if I h...
by Feanor
Fri Sep 17, 2021 10:57 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 6774

Re: undefined symbol: nrnpython_start

How (not) helpful. Under Linux Mint (a close cousin of Ubuntu), pip install of NEURON simply adds .local/bin to PATH, and everything works properly without the user having to do anything to PATH. Yes, I also got the impression that the user does not need to do anything after "pip3 install neur...
by Feanor
Fri Sep 17, 2021 7:30 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 6774

Re: undefined symbol: nrnpython_start

I installed Ubuntu 20 anew and I think I realized how an earlier version ended up getting installed. After installing NEURON with pip3 install neuron I didn't add it to the path. At trying to compile mod files Ubuntu prompts me to install neuron-dev with sudo apt which was version 7.6.3. I must have...
by Feanor
Wed Sep 15, 2021 12:07 pm
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 6774

Re: undefined symbol: nrnpython_start

Hi again Ted! It seems I have been editing the previous post while you were writing your answer. (I also realized while re-reading your first response that the entire output is not there and went on to edit the post to include NEURON's version. Also commented there that I installed NEURON according ...
by Feanor
Wed Sep 15, 2021 4:37 am
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 6774

Re: undefined symbol: nrnpython_start

Hi Ted! Thank you very much for your quick reply. Here is the output: NEURON -- VERSION 7.6.3 master (85d62db) 2018-11-21 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2018 See http://neuron.yale.edu/neuron/credits loading membrane mechanisms from /home/daniel/Documents/PhD Studies/Work/Pl...
by Feanor
Mon Sep 13, 2021 4:25 pm
Forum: NEURON + Python
Topic: undefined symbol: nrnpython_start
Replies: 8
Views: 6774

undefined symbol: nrnpython_start

Hello everyone, I am trying to load compiled mechanisms with: h.nrn_load_dll('./mod/x86_64/.libs/libnrnmech.so') and am getting this error: dlopen failed - /usr/lib/x86_64-linux-gnu/libnrniv.so.0: undefined symbol: nrnpython_start Anybody has an idea what this means and how to fix it? I read online ...
by Feanor
Thu Mar 07, 2019 8:59 am
Forum: Other questions
Topic: See what a vector is recording from ?
Replies: 4
Views: 2974

Re: See what a vector is recording from ?

OK, thank you.
by Feanor
Wed Feb 06, 2019 12:14 pm
Forum: Other questions
Topic: See what a vector is recording from ?
Replies: 4
Views: 2974

Re: See what a vector is recording from ?

It is a very good friend, indeed, but this time I couldn't find the answer in the documentation of the Vector class.
by Feanor
Fri Jan 18, 2019 12:17 pm
Forum: Other questions
Topic: See what a vector is recording from ?
Replies: 4
Views: 2974

See what a vector is recording from ?

Hello to everyone,

my question is about the following scenario. Say we have a vector that is recording from some variable. Is there a way to check what the vector is recording from, like, an attribute or a method in the vector class that returns this information?

Best regards
by Feanor
Thu Jul 06, 2017 5:39 am
Forum: NEURON + Python
Topic: DIfferent results with Neuron + Python and with HOC
Replies: 3
Views: 12363

Re: DIfferent results with Neuron + Python and with HOC

Thank you so much! I wouldn't have guessed.

Daniel
by Feanor
Mon Jun 26, 2017 12:11 pm
Forum: NEURON + Python
Topic: DIfferent results with Neuron + Python and with HOC
Replies: 3
Views: 12363

DIfferent results with Neuron + Python and with HOC

Hello to all! When trying out a ball-and-stick model, one written using nrnpython and the other using HOC, I get different results from each of them. I think I have written the equivalent code statements in each example, and I can't see what is going wrong. The codes are below, and I can send the fi...
by Feanor
Sat May 30, 2015 7:17 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMDA_S cannot be used with CVODE
Replies: 2
Views: 7249

Re: NMDA_S cannot be used with CVODE

The answer to the question - I didn't find any at the time, but yes, I didn't look thoroughly. Alternatively, yes, starting with the AMPA_S mechanism sounds like the way to go. Thank you!