Search found 36 matches

by Darshan
Sun Aug 04, 2019 1:07 pm
Forum: Reaction-diffusion in NEURON
Topic: Altering Total Concentration During a Simulation
Replies: 2
Views: 540

Re: Altering Total Concentration During a Simulation

Hi, If you are interested in clamping concentration to a particular value using a mod mechanism, see this code: https://github.com/darshanmandge/Tools/tree/master/ConcClamp. Screenshot here: https://github.com/darshanmandge/Tools/blob/master/README.md (2. Ionic Concentration Clamp) Cheers, Darshan
by Darshan
Tue Jun 04, 2019 7:55 pm
Forum: Hot tips
Topic: conversion units
Replies: 5
Views: 1666

Re: conversion units

Thank you for clearing these doubts!
by Darshan
Mon Jun 03, 2019 1:33 am
Forum: Hot tips
Topic: conversion units
Replies: 5
Views: 1666

Re: conversion units

Hi, I have a doubt in mA/cm2 to nA conversion: if I want to convert the current density INA [mA/cm2] in nA I should divide the current in mA/cm2 by the factor (area*(0.01)): INA/(area*(0.01)) True, assuming that area is in units of um2. Shouldn't the current in mA/cm2 be multiplied by (area*0.01) to...
by Darshan
Tue Mar 12, 2019 4:11 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 2443

Re: NMODL Compile Error: Assertion failed!

Thanks for the prompt reply and example of CONDUCTANCE keyword.
by Darshan
Tue Mar 12, 2019 2:39 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 2443

Re: NMODL Compile Error: Assertion failed!

Thanks again for the elaborate explanation. So, if those statements (minf, ninf) are in BREAKPOINT, are they undergoing unnecessary recalculations? I guess by moving them to the DERIVATIVE block will save some simulation time which might be more evident in long or large-scale simulations, Also, I co...
by Darshan
Tue Mar 12, 2019 1:52 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 2443

Re: NMODL Compile Error: Assertion failed!

Thank you Michael. Using the recursive multiplication approach works for these expressions when using derivimplicit. I also tried using function and LOCAL. It gave me the same results both of them (though not desirable). I have to fix the parameter values. I will use functions for greater power valu...
by Darshan
Mon Mar 11, 2019 3:11 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 2443

Re: NMODL Compile Error: Assertion failed!

Thanks. This shortcut for copying text works perfectly fine. I guess the key assigned for copy was changed to 'return' in newer NEURON versions.

I will also post here if I find a solution/workaround to the compilation error.

Best Wishes,
Darshan
by Darshan
Mon Mar 11, 2019 1:26 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 2443

Re: NMODL Compile Error: Assertion failed!

Thank you Ted for your prompt reply! 1. I expanded the terms for adpi' and atpi' expressions: atpi' = ((nu - atpi* (1+(k2^2)*(adpi^2)+2*k2*adpi))/tauc) adpi' = ((atpi*(1+(k2^2)*(adpi^2)+2*k2*adpi) - eta*adpi)/tauc) and also changed the "k" which I declared as constant earlier to "k2". Forgot that "k...
by Darshan
Sat Mar 09, 2019 1:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: NMODL Compile Error: Assertion failed!
Replies: 10
Views: 2443

NMODL Compile Error: Assertion failed!

Hi, I was trying to translate this code given here: https://www.math.fsu.edu/~bertram/software/islet/JTB_04.ode for pancreatic beta-cells, published by Wierschem and Bertram, J. Theor. Biol., 228:513-521, 2004. Here is the nmodl code I made: TITLE weirshem and Bertram 2004 UNITS { (molar) = (1/liter...
by Darshan
Sat Nov 17, 2018 2:28 am
Forum: Reaction-diffusion in NEURON
Topic: Reaction-Diffusion in HOC
Replies: 5
Views: 17791

Re: Reaction-Diffusion in HOC

Hi, I get the following error when I run the working example given in the first post: C:\nrn\bin\nrniv.exe: cai not a section variable in D:/NEURON_Tools/rxd_hoc/rxd_hoc.hoc near line 32 g.addvar("ca", &soma.cai(0.5), 1, 1) NEURON -- VERSION 7.6.2 master (f5a1284) 2018-08-15 Duke, Yale, and the Blue...
by Darshan
Thu Sep 27, 2018 10:52 am
Forum: Anatomically detailed models
Topic: Using Impedance Class for model with Ca accumulation
Replies: 8
Views: 2238

Re: Using Impedance Class for model with Ca accumulation

Thanks for your help, Ted!

Darshan
by Darshan
Tue Sep 25, 2018 5:23 am
Forum: Anatomically detailed models
Topic: Using Impedance Class for model with Ca accumulation
Replies: 8
Views: 2238

Re: Using Impedance Class for model with Ca accumulation

Ok. So, there is no change in cai in the model and it may not be the reason for the message. I will try find the source of error. Meanwhile, I will use a workaround for calculating transfer impedance similar to as discussed in the above posts: injecting current (1 nA) and recording the resulting (pe...
by Darshan
Mon Sep 24, 2018 2:14 pm
Forum: Anatomically detailed models
Topic: Using Impedance Class for model with Ca accumulation
Replies: 8
Views: 2238

Re: Using Impedance Class for model with Ca accumulation

Sorry for not being clear on the source of mod files. I obtained the cachan.mod and capmp.mod from C:\nrn\examples\nrniv\nmodl of my NEURON 7.6.2 setup. Also uploaded here: https://drive.google.com/drive/folders/1ZGvLL3qKvjmCe7klT9rwk6L93qY-xQuh?usp=sharing The SUFFIX in capmp.mod is capr. I don't h...
by Darshan
Mon Sep 24, 2018 12:12 pm
Forum: Anatomically detailed models
Topic: Using Impedance Class for model with Ca accumulation
Replies: 8
Views: 2238

Re: Using Impedance Class for model with Ca accumulation

Thanks Ted for the detailed explanation for the "Warning". I will look into my model for the source of that error. Below is the code I used for the toy model: load_file("nrngui.hoc") v_init=-65 create soma soma{ nseg =9 insert hh insert cachan insert capr } finitialize(v_init) objref zz zz = new Imp...
by Darshan
Sat Sep 22, 2018 8:44 am
Forum: Anatomically detailed models
Topic: Using Impedance Class for model with Ca accumulation
Replies: 8
Views: 2238

Using Impedance Class for model with Ca accumulation

Hi Ted, I have a model with calcium accumulation mechanism. I wanted to measure transfer impedance at different locations of the cell using the Impedance class. While doing so I get a following error: cmplx_spFactor error: Singular The model does not have the extracellular and LinearMechanism. Accor...