Search found 5842 matches

by ted
Mon Oct 26, 2020 9:47 am
Forum: Other questions
Topic: Neurolucida text morphology changes when using import3D
Replies: 3
Views: 376

Re: Neurolucida text morphology changes when using import3D

Yes, there are many lessons to learn from this, like how to write code that is difficult for anyone else to use.
by ted
Thu Oct 22, 2020 11:00 am
Forum: Other questions
Topic: Neurolucida text morphology changes when using import3D
Replies: 3
Views: 376

Re: Neurolucida text morphology changes when using import3D

I'll have to reproduce this for myself. Please send the necessary morphometric data file(s) to ted dot carnevale at yale dot edu
by ted
Thu Oct 22, 2020 10:58 am
Forum: Other questions
Topic: Some questions on plot [Ca2+]i vs. distance
Replies: 2
Views: 345

Re: Some questions on plot [Ca2+]i vs. distance

Read the Programmer's Reference documentation of the RangeVarPlot class https://neuronsimulator.github.io/nrn/new_doc/visualization/rvarplt.html#rangevarplot . First, some definitions. Parent section and child section: The statement connect foo, bar connects section foo to section bar. bar is the pa...
by ted
Mon Oct 12, 2020 4:55 pm
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 954

Re: Installing on Ubuntu 20.04 (GUI not working)

Under Mint 19.3 (a Debian/Ubuntu variant) I did a fresh install of NEURON 8.x by executing pip3 install neuron as an ordinary user. However, when I tried checking a mod file for units inconsistencies, I found that the command modlunit failed. So did idraw but nrniv and nrnivmodl both worked. modluni...
by ted
Tue Oct 06, 2020 2:37 pm
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 954

Re: Installing on Ubuntu 20.04 (GUI not working)

If you want to load the GUI,
from neuron import h, gui

or
from neuron import h
h.load_file('nrngui.hoc')

Does that take care of the problem?
by ted
Tue Oct 06, 2020 11:17 am
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 954

Re: Installing on Ubuntu 20.04 (GUI not working)

I then installed using tar.gz file of 7.6.7 version
So what's the current status? Does 7.6.7 work?
by ted
Sun Oct 04, 2020 11:23 am
Forum: UNIX/Linux
Topic: Installing on Ubuntu 20.04 (GUI not working)
Replies: 7
Views: 954

Re: Installing on Ubuntu 20.04 (GUI not working)

After installing the package
Did you do
sudo pip3 install neuron
or did you install from a .deb package?
If you used a .deb package, from where did you get it?
by ted
Fri Oct 02, 2020 11:25 am
Forum: NEURON + Python
Topic: External Stimuli not working
Replies: 1
Views: 640

Re: External Stimuli not working

1. Is the model cell excitable? Attach an IClamp to the soma and apply a 1 ms current pulse that starts at t = 1 ms. Record and plot the current generated by the IClamp and v at the point of attachment. Adjust amplitude of the current pulse until a spike is elicited. Can't elicit a spike? Verify tha...
by ted
Thu Oct 01, 2020 12:34 am
Forum: UNIX/Linux
Topic: Configure fonts, etc in GUI
Replies: 2
Views: 273

Re: Configure fonts, etc in GUI

Under Windows it's easy. Assuming that an instance of the PWManager class exists (it will exist if you started NEURON by executing nrngui, or if your code has executed a load_file("nrngui.hoc") statement), then an instance of the PWManager class will exist and you can use its scale() funct...
by ted
Wed Sep 30, 2020 11:33 am
Forum: NEURON + Python
Topic: implement Randles circuit in NEURON
Replies: 3
Views: 359

Re: implement Randles circuit in NEURON

Further comments: 1. The linear circuit could be implemented with the Linear Circuit builder. 2. The simulation of neural activity and calculation of PHI_REC(t) do not have to be done in the same session. Instead, the simulation and calculation of PHI_LFP(t) could be done once, and PHI_LFP(t) saved ...
by ted
Wed Sep 30, 2020 12:01 am
Forum: NEURON + Python
Topic: implement Randles circuit in NEURON
Replies: 3
Views: 359

Re: implement Randles circuit in NEURON

I'm not clear how to do this in the real-time simulation of NEURON. Let's use proper terminology. You mean "time domain simulation" not "real-time simulation." It's clear that you know the difference between time domain and frequency domain, but some who read this thread may not...
by ted
Tue Sep 29, 2020 11:05 am
Forum: Other questions
Topic: spatial discretization, and saving results
Replies: 1
Views: 251

Re: spatial discretization, and saving results

1) I noticed in the gui a user can specify d_X in the geometry --> is there an equivalent way to do this when working in python? The d_X rule for spatial discretization is set nseg to the smallest odd number such that L/nseg <= d_X Code to do this is built into the CellBuilder. If you want to do it...
by ted
Mon Sep 14, 2020 3:17 pm
Forum: NEURON + Python
Topic: Frequency dependent activation of g protein models
Replies: 2
Views: 3518

Re: Frequency dependent activation of g protein models

Yes, ModelDB would be a good place to start looking. Also, do you know of one or more published articles that provides a mathematical description of the exact phenomenon you want to represent in your model?
by ted
Mon Sep 14, 2020 3:10 pm
Forum: NEURON + Python
Topic: injecting continuous normally distributed noise in python
Replies: 2
Views: 1383

Re: injecting continuous normally distributed noise in python

I've been trying to insert normally distributed noise onto my cells via IClamp . . . I have a vector of say 1x1000 (1 per ms) that I want to set as the amp value. Your code was heading in the right direction. Just a few changes and it will work. Here's a toy example (just a single cell) that might ...
by ted
Mon Sep 14, 2020 1:47 pm
Forum: NEURON + Python
Topic: Connect multiple cells using connection probabilities
Replies: 4
Views: 4143

Re: Connect multiple cells using connection probabilities

I'm trying to connect multiple neuron cells . . . I need to take into account the connection probabilities between the cells. So I was thinking of multiplying the connection probability by the number of dendrites in the post synaptic cell. Why would that be useful? Is the number of dendrites presen...