Search found 23 matches

by afc
Thu Sep 29, 2016 7:50 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Mechanosensitive channels
Replies: 1
Views: 5313

Mechanosensitive channels

Dear all,

I was wondering if there is a turn around in NEURON, i.e, a complementary software or an extension of NEURON itself, that enables the embedding of a neuron in a physical space, allowing the studying of mechanosensitive channels?

Thank you all in advance!
by afc
Sat Jun 13, 2015 7:01 pm
Forum: Other questions
Topic: Electrotonic distance negative values
Replies: 12
Views: 2300

Re: Electrotonic distance negative values

Nevermind, I just found out how to do that:

Code: Select all

proc calcZ() {
  soma zz.loc(WHERE) 
  zz.compute(FREQ) 
  forall {
        fprint("%s\%s\%g\n", secname(),"L=", log(1/(zz.ratio(1))))
  }
Thank you!
by afc
Sat Jun 13, 2015 6:50 pm
Forum: Other questions
Topic: Electrotonic distance negative values
Replies: 12
Views: 2300

Re: Electrotonic distance negative values

You were right, it seems that was the case! Thank you very much. But still I wanted to keep analyzing the electrotonic structure of the cell, and I wanted to compare the active and passive electrotonic structure of it. Do you know how can I compute the passive electrotonic structure of the cell with...
by afc
Fri Jun 12, 2015 3:33 pm
Forum: Other questions
Topic: Electrotonic distance negative values
Replies: 12
Views: 2300

Re: Electrotonic distance negative values

Even if this is the case (I am checking it now), how can one interpret the negative values?
by afc
Fri Jun 12, 2015 2:22 pm
Forum: Other questions
Topic: Electrotonic distance negative values
Replies: 12
Views: 2300

Re: Electrotonic distance negative values

From 0 to ~20 Hz. Afterwards the results become positive.
by afc
Fri Jun 12, 2015 1:54 pm
Forum: Other questions
Topic: Electrotonic distance negative values
Replies: 12
Views: 2300

Re: Electrotonic distance negative values

When I do not use the "include dstate/dt contribution" the plot only has positive values, either for Vin or Vout. When I use the "include dstate/dt contribution" the plot shows negative values for both Vin and Vout.
by afc
Fri Jun 12, 2015 11:34 am
Forum: Other questions
Topic: Electrotonic distance negative values
Replies: 12
Views: 2300

Re: Electrotonic distance negative values

Thank you for the prompt reply!

I am computing it as:

Code: Select all

log(1/(zz.ratio(1)))
What I want to compute is the electrotonic distance (L) described here: http://www.neuron.yale.edu/neuron/stati ... l#citation.

Thank you!
by afc
Thu Jun 11, 2015 2:25 pm
Forum: Other questions
Topic: Electrotonic distance negative values
Replies: 12
Views: 2300

Electrotonic distance negative values

Dear all, I have a quick question that I could not answer myself: when I compute the electrotonic distance of some cells sometimes a number of dendritic branches of these cells show negative values (these cells have active conductances). Does this mean that there was no attenuation, and instead (pro...
by afc
Fri May 29, 2015 11:52 am
Forum: Other questions
Topic: Impedance Class bug
Replies: 1
Views: 1036

Impedance Class bug

Dear all, after updating to NEURON version 7.3-1, I am no longer able to compute the impedance class while taking into account the impedance contributions of gating state differential equations. Every time I try to do so, a "segmentation violation" warning appears, and this happens when I am running...
by afc
Wed Apr 29, 2015 6:47 pm
Forum: Other questions
Topic: What measure of electrotonic extent to use?
Replies: 5
Views: 4542

Re: What measure of electrotonic extent to use?

Dear Ted, once more thank you for the prompt reply! For the coincidence detector case: I understood that 25 Hz was a standard rule of thumb validated by some experiments done, but if I increase the synaptic input frequency that will affect the electrotonic structure of the cell, and in this case sho...
by afc
Wed Apr 29, 2015 12:38 pm
Forum: Other questions
Topic: Times of spikes vector
Replies: 1
Views: 1136

Times of spikes vector

Dear all, I want to analyse the spike train outputs from some single neuron models that I am simulating, the spike trains are recorded as the voltage traces at the axo-somatic compartment of these models. When I pick the vector generated by these simulations, what one obtains is the time course of t...
by afc
Wed Apr 29, 2015 12:05 pm
Forum: Other questions
Topic: What measure of electrotonic extent to use?
Replies: 5
Views: 4542

Re: What measure of electrotonic extent to use?

Dear Ted, I want to analyze the electrotonic properties of a neuron and because of that I found myself reading this post, so I think my question will fit this thread. As you said the best electrotonic measure to be used depends jointly on the properties of the cell and of the synaptic inputs, howeve...
by afc
Fri Jan 23, 2015 6:47 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Making nmodl files CVode Compatible
Replies: 14
Views: 4308

Re: Making nmodl files CVode Compatible

I used an installer, particularly the Debian/Ubuntu for 64 bit (amd86/x86_64) (version 7.3).
by afc
Thu Jan 22, 2015 9:16 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Making nmodl files CVode Compatible
Replies: 14
Views: 4308

Re: Making nmodl files CVode Compatible

Thank you so much for your prompt response!!

But just to be sure, How/Where should I add the extra line of code?

Thank you!
by afc
Wed Jan 21, 2015 3:34 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Making nmodl files CVode Compatible
Replies: 14
Views: 4308

Re: Making nmodl files CVode Compatible

Dear Ted, I followed your advice and I further analyzed the mod files from Mainen ZF, Sejnowski TJ (1996), I found out two "problems": 1) the cad.mod was modified to allow variable time step, but then afterwards the cnexp was replaced with derivimplicit. But i read in http://www.neuron.yale.edu/neur...