Search found 40 matches

by Darshan
Fri May 27, 2016 6:22 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Spatial discretization for radial diffusion of Ca
Replies: 7
Views: 7678

Re: Spatial discretization for radial diffusion of Ca

Hi Ted, Thanks for reply. I will get back to you once I have implemented and tested in the 'complete model' along with integral of BK current and their time course. That makes sense. At what time does it occur? The peak times with the models I used above fall within 1 ms of each other. I will test t...
by Darshan
Fri May 27, 2016 5:35 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Setting the basal level for Intracellular Calcium Concentrat
Replies: 22
Views: 18231

Re: Setting the basal level for Intracellular Calcium Concen

Hi Ted, As you suggested, I am using the cabpump.mod file. Needed one clarification on the factor (1+beta) in the COMPARTMENT statement. Is this factor used to take into account the rapid buffer approximation? I read about the theory in the book "Principles of Computational Modelling in Neurosc...
by Darshan
Sat May 07, 2016 8:33 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Spatial discretization for radial diffusion of Ca
Replies: 7
Views: 7678

Re: Spatial discretization for radial diffusion of Ca

Thank you Ted for the quick and detailed explanation. I was trying to implement equal shell widths for the models. I am using the cabpump.mod file which has a membrane pump, radial diffusion and buffering. I have used this formula for calculating the volume of a shell: PI*(r^2-rc^2)*1 where rc is th...
by Darshan
Fri May 06, 2016 2:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Spatial discretization for radial diffusion of Ca
Replies: 7
Views: 7678

Spatial discretization for radial diffusion of Ca

Hi, I am using a calcium accumulation mechanism with shells for modelling the calcium dynamics in a cell. The diameter of the soma is different from that of the dendrites and the axon. This implies that the shell widths are different for all the sections. If there are calcium activated mechanisms li...
by Darshan
Sun May 01, 2016 2:48 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Setting the basal level for Intracellular Calcium Concentrat
Replies: 22
Views: 18231

Re: Setting the basal level for Intracellular Calcium Concen

Thank you Ted.

I will do some computational analysis of the model to understand the model better. Will also try the MultipleRunFitter to get a good parameter fit.

Regards,
Darshan
by Darshan
Fri Apr 29, 2016 1:56 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Setting the basal level for Intracellular Calcium Concentrat
Replies: 22
Views: 18231

Re: Setting the basal level for Intracellular Calcium Concen

Hi, But if one wants to leave the rate constants unchanged and use the membrane's ion channels plus a "constant ca source" to force resting cai to a desired value, the question is how to find the required intensity of the "constant ca source." I'm going to have to think about thi...
by Darshan
Thu Jul 09, 2015 4:16 pm
Forum: MSWin
Topic: cannot review shell's command history!
Replies: 7
Views: 9118

Re: cannot review shell's command history!

Hi, I am using NEURON -- VERSION 7.4 (1343:d0b379734f36) 2015-06-08, which I compiled from the mercurial repository. I am facing a similar problem on the NEURON interpreter (terminal). I am not able to view the command history by using the UP arrow key. Is there a workaround for this? I am on Ubuntu...
by Darshan
Tue Apr 07, 2015 3:55 pm
Forum: Reaction-diffusion in NEURON
Topic: New reaction-diffusion model on ModelDB
Replies: 6
Views: 9644

Re: New reaction-diffusion model on ModelDB

Thanks Robert. It was actually taking the old python library. The reason for that was incorrect PYTHONPATH. Another error came up after this, which was because of unavailability of cython(pointed out by Robert. Thanks!). It was corrected by installing it using sudo apt-get install cython and then co...
by Darshan
Sat Apr 04, 2015 6:14 am
Forum: Reaction-diffusion in NEURON
Topic: New reaction-diffusion model on ModelDB
Replies: 6
Views: 9644

Re: New reaction-diffusion model on ModelDB

Hi Ted, Thanks for the quick reply. I compiled using the latest source code from the repository. Now, the first line on starting NEURON reads: NEURON -- VERSION 7.4 (1315:a35e721080fb) 2015-04-02. I compiled the code with nrnivmodl and it was successful with a few warnings. A seperate folder called ...
by Darshan
Fri Apr 03, 2015 2:54 am
Forum: Reaction-diffusion in NEURON
Topic: New reaction-diffusion model on ModelDB
Replies: 6
Views: 9644

Re: New reaction-diffusion model on ModelDB

Hi, Thanks for making the model available on ModelDb. I tried using the code by following the instructions in readme file. The mod files get compiled correctly. But when I run this 'run batch import *' I get the following error: File "cawave.py", line 183, in <module> cyt_er_membrane = rxd...