Search found 5205 matches

by ted
Mon Jun 18, 2018 10:38 am
Forum: Parallel NEURON
Topic: Parallel simulations of ephaptic connections
Replies: 2
Views: 107

Re: Parallel simulations of ephaptic connections

Referring back to your post from March 13 I've read about how pc.source_var and pc.target_var are used for gap junctions. . . . they copy v from source onto target, so that seems to be a one-directional coupling to me which is why two source_var - target_var pairs are used to parallelize gap junctio...
by ted
Sun Jun 17, 2018 4:41 pm
Forum: Anatomically detailed models
Topic: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between them
Replies: 6
Views: 63

Re: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between t

What I'm doing is making a simulation of fiber tract stimulation. I decided to work at the most basic level, with individual neurons. The hypothesis is this: stimulating the fiber tract using focused ultrasound is a viable neuromodulation modality for altering the functional plasticity between the ...
by ted
Sun Jun 17, 2018 3:36 pm
Forum: NEURON + Python
Topic: Manual Installation of NEURON Python module on Linux Mint 18
Replies: 6
Views: 46

Re: Manual Installation of NEURON Python module on Linux Mint 18

For this particular installation, I did sudo python3 setup.py install I use NEURON and idraw from the command line, so in .bashrc I inserted PATH= $PATH:/usr/local/iv/x86_64/bin:/usr/local/nrn/x86_64/bin If you plan to launch Python and import nrn, you'll need to specify PYTHONPATH A correct stateme...
by ted
Sun Jun 17, 2018 11:24 am
Forum: NEURON + Python
Topic: Manual Installation of NEURON Python module on Linux Mint 18
Replies: 6
Views: 46

Re: Manual Installation of NEURON Python module on Linux Mint 18

I just installed NEURON under Mint18.3 just 2 weeks ago, and setup.py ran without problems. I started with the latest development source code from Github and allowed NEURON to be installed into its default location /usr/local/nrn. Of couse that required invoking sudo for the make install steps, and ...
by ted
Fri Jun 15, 2018 9:44 pm
Forum: NEURON + Python
Topic: Manual Installation of NEURON Python module on Linux Mint 18
Replies: 6
Views: 46

Re: Manual Installation of NEURON Python module on Linux Mint 18

I am trying to do a manual installation of the NEURON Python module
What NEURON Python module? One you picked up somewhere, or what?
by ted
Wed Jun 13, 2018 10:02 am
Forum: NEURON + Python
Topic: Neuron code
Replies: 20
Views: 125

Re: Neuron code

Is it known that squid even have a low threshold calcium current?
by ted
Mon Jun 11, 2018 1:44 pm
Forum: Anatomically detailed models
Topic: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between them
Replies: 6
Views: 63

Re: Making whole cells out of Mcintyre myelinated axon model (2002) and testing short and long-term plasticity between t

I'm currently developing a detailed model of 2 (up to 5) connected neurons that need to have myelinated axons. Why do they need myelinated axons? Is some aspect of the structure or function of myelinated axons essential for the hypothesis that you plan to evaluate with your model? I will stimulate ...
by ted
Mon Jun 11, 2018 12:46 pm
Forum: Getting started
Topic: Equation that models the entire tree
Replies: 1
Views: 50

Re: Equation that models the entire tree

Your answer awaits you in the scientific literature of the 1970s and early 1980s. Rall was an author on some of them, but not all. Tell us what you find.
by ted
Sun Jun 10, 2018 11:44 pm
Forum: Other questions
Topic: Numerical methods in NEURON
Replies: 6
Views: 75

Re: Numerical methods in NEURON

OK, we're talking about different things. The model is described by the set of ODEs y ' = f ( y ,t) ( bold terms are vectors). The simplest method for calculating a(n approximate) numerical solution to this is the explicit Euler method y (t+dt) = y (t) + dt * f ( y ,t) where the first term on the ri...
by ted
Sun Jun 10, 2018 4:43 pm
Forum: NEURON + Python
Topic: Neuron code
Replies: 20
Views: 125

Re: Neuron code

that means the basic equation is Fick's second law Actually the basic equation is conservation of mass. Rewriting in english rate of change of total mass of solute S in compartment C = (sum of all fluxes of S into C)/(volume of C) Diffusion is only one of many possible mechanisms that can generate ...
by ted
Sun Jun 10, 2018 4:20 pm
Forum: Other questions
Topic: Numerical methods in NEURON
Replies: 6
Views: 75

Re: Numerical methods in NEURON

In my understanding, when NEURON integrate one step, it first setup a matrix GV=I, where G is the Hines matrix representing the conductance, I is the current vector (including axial current, injected current and current of ion channels) and V is the vector of v_new (membrane voltages in next time s...
by ted
Thu Jun 07, 2018 10:27 pm
Forum: NEURON + Python
Topic: Neuron code
Replies: 20
Views: 125

Re: Neuron code

You generally want to use an odd value for nseg
For more about this, and how to choose an appropriate value for nseg, see Use an odd value for nseg viewtopic.php?f=28&t=3637
by ted
Thu Jun 07, 2018 6:10 pm
Forum: Anatomically detailed models
Topic: importing .asc (Neurolucida ASCII) files with Python
Replies: 1
Views: 43

Re: importing .asc (Neurolucida ASCII) files with Python

Example provided by Robert McDougal: Suppose you had a Neurolucida ASCII file called C011098A-P4.asc from neuron import h, gui h.load_file('import3d.hoc') class MyCell: def __init__(self): morph_reader = h.Import3d_Neurolucida3() morph_reader.input('C011098A-P4.asc') i3d = h.Import3d_GUI(morph_reade...
by ted
Tue Jun 05, 2018 3:34 pm
Forum: Hot tips
Topic: Synaptic plasticity
Replies: 0
Views: 51

Synaptic plasticity

NEURON doesn't come with synaptic mechanisms that have built-in plasticity. However, you can use it to implement whatever kind of synaptic plasticity you like. For example: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=3815 implements the short term plasticity mechanism described by T...
by ted
Mon May 28, 2018 9:22 pm
Forum: NEURON + Python
Topic: Best way(s) to advance() in Python
Replies: 3
Views: 92

Re: Best way(s) to advance() in Python

Actually the use of fadvance is key, not just minor. But then I only promised "something like," not a real, working solution.

(Can one call "weasel words" on oneself?)