Search found 53 matches

by roybens
Tue Oct 26, 2021 12:56 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modifying cell capacitance (cm) via a mod file (also cai)
Replies: 2
Views: 348

Re: Modifying cell capacitance (cm) via a mod file (also cai)

Thank you!
Those are very helpful. I will look into them and report back.
Best,
Roy
by roybens
Mon Oct 25, 2021 3:34 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Modifying cell capacitance (cm) via a mod file (also cai)
Replies: 2
Views: 348

Modifying cell capacitance (cm) via a mod file (also cai)

Hi developers, I am trying to simulate an ultrasonic stimulation (US) of a neuron. There are several hypotheses what it would do some include modifications to the membrane's capacitance and an increase in internal Ca concentration. I would like to simulate this initially with a simple hh one section...
by roybens
Mon Nov 23, 2020 5:16 pm
Forum: Other questions
Topic: Simulating nanodomains to link SK/BK channels to specific Ca channels
Replies: 6
Views: 1246

Re: Simulating nanodomains to link SK/BK channels to specific Ca channels

Hi Ted,
Thanks so much this will keep me busy for a while. Do you know of anyone who implemented something similar in the past? Would be nice to have a template to start from...
by roybens
Fri Nov 20, 2020 6:09 pm
Forum: Other questions
Topic: Simulating nanodomains to link SK/BK channels to specific Ca channels
Replies: 6
Views: 1246

Simulating nanodomains to link SK/BK channels to specific Ca channels

Hello Forum members, We have a model with BK/SK channels (KCa calcium-activated potassium channels) and if I understand correctly they are sensitive to the internal [Ca] in the section. However BK/SK are linked to different Ca channels e.g. https://www.jneurosci.org/content/24/40/8818.short or https...
by roybens
Tue Jul 21, 2020 12:40 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 1537

Re: color or color_list procedures in PlotShape

Thanks so much!
This is very helpful.
by roybens
Thu Jul 16, 2020 11:42 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 1537

Re: color or color_list procedures in PlotShape

Hi ramcdougal, I am probably doing something wrong or there is a problem in my environment (though for any other purpose except this it is working totally fine) So i tried the code you sent on both my local machine (running windows NEURON 7.7) and i get the following error: runfile('E:/GitHub/MoreGi...
by roybens
Tue Jul 07, 2020 5:59 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 1537

Re: color or color_list procedures in PlotShape

This is very helpful,
I will try both methods, and report back if I get into any problems.
Thanks ramcdougal!
by roybens
Mon Jul 06, 2020 4:58 pm
Forum: NEURON + Python
Topic: color or color_list procedures in PlotShape
Replies: 5
Views: 1537

color or color_list procedures in PlotShape

Hi, I am trying to plot the morphology of a neuron with a different color for each section. I am trying to use the PlotShape (really nice it is working with matplotlib now). The code i am running is: from neuron import h from matplotlib import pyplot mosinit_hoc = '/global/homes/r/roybens/Cori/Neuro...
by roybens
Fri Feb 01, 2019 12:41 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 3238

Re: eca calculation

Thanks Micheal,
Now the results i got from ion_style does make sense.
Best
Roy
by roybens
Thu Jan 31, 2019 5:54 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 3238

Re: eca calculation

:-) thanks Ted, ill continue investigating!
by roybens
Thu Jan 31, 2019 2:40 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 3238

Re: eca calculation

I am a bit confused trying to figure this out. From the program reference i get this: The oldstyle value is previous internal setting of c_style + 4*cinit + 8*e_style + 32*einit + 64*eadvance. c_style: 0, 1, 2, 3. Concentrations respectively treated as UNUSED, PARAMETER, ASSIGNED, or STATE variables...
by roybens
Thu Jan 31, 2019 1:54 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 3238

Re: eca calculation

Thank, Ted!
This is very helpful.
by roybens
Wed Jan 30, 2019 7:01 pm
Forum: Other questions
Topic: eca calculation
Replies: 10
Views: 3238

eca calculation

Hi, I wanted to ask how does NEURON knows when to calculate eca from cai and cao or not to. For example in Mainen's model https://senselab.med.yale.edu/modeldb/showmodel.cshtml?model=2488&file=%2Fcells%2F#tabs-1 the eca is always 140. But when using one of the BBP models from their portal it is ...
by roybens
Fri Jun 15, 2018 4:23 pm
Forum: Other questions
Topic: Getting the full topology (segments level) from hoc
Replies: 18
Views: 8985

Re: Getting the full topology (segments level) from hoc

Hi again, I am back in trying to apply this method on a more complicated model - one of the BBP pyramidal neurons https://bbp.epfl.ch/nmc-portal/downloads. For some reason when applying this method to Mainen's model (1996) it works well but when applying to BBP it does not work at all and it is like...