Search found 10 matches

by bdut
Thu Jan 16, 2020 1:40 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding cilia with an added mechanism to a dendrite
Replies: 2
Views: 121

Re: Adding cilia with an added mechanism to a dendrite

Sorry Ted for not being clear. Yes, each is a section. One section(cilium) has a mechanism attached to it. This mechanism has 8 differential equations that signify various components of signal transduction. I have added one more section(cilium) to this model with the same mechanism. There are no err...
by bdut
Mon Jan 06, 2020 3:17 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Adding cilia with an added mechanism to a dendrite
Replies: 2
Views: 121

Adding cilia with an added mechanism to a dendrite

I have a neuron model with soma, dendrite and cilium. The cilium has a mechanism added that gives variation of 8 variables with time. I need to add one more cilium to this model. But, when I add 1 more cilium with the same mechanism, both the cilia show error in graphs of the variables after 0.5 sec...
by bdut
Fri Dec 13, 2019 2:05 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Accessing state variables of one mechanisn in another mechanism
Replies: 4
Views: 306

Re: Accessing state variables of one mechanisn in another mechanism

Thank you for the details, Ted. I have gone through the modeldb entry you indicated, But, this code has a POINT PROCESS which is accessed by 2 .mod files. Is there a way to interact between the 2 mechanisms directly, without the POINT PROCESS?

Thanks and regards
by bdut
Sun Dec 01, 2019 11:35 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Accessing state variables of one mechanisn in another mechanism
Replies: 4
Views: 306

Accessing state variables of one mechanisn in another mechanism

I have a mechanism that has a state variable cAMP. Is it possible to access this state variable in another mechanism (.mod file)? The second mechanism has a state variable depending on cAMP.

Thanks
by bdut
Sat Sep 21, 2019 1:44 am
Forum: Getting started
Topic: matlab-neuron
Replies: 3
Views: 3806

Re: matlab-neuron

Hello,

Adding to this thread, is there a way to call a Matlab user-defined function from .mod/ .hoc file? I am working on Neuron 7.7.2 and Matlab2019.

Thank you
by bdut
Fri Sep 20, 2019 11:36 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 687

Re: Solving 8 interdependent differential equations

I have mailed you the zip of the code. It can be used with a single compartment model. Thank you for your timely help.
by bdut
Fri Sep 20, 2019 1:20 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 687

Re: Solving 8 interdependent differential equations

I have changed to derivimplicit, but there is no change. I printed the values for the PROCEDURE formulas and found they are not being calculated. kG: -1.#IND, rG: -1.#IND t: 5, syncAMP: -1.#IND, Icng: -1.#IND, inhcng: -1.#IND, JNCX: -1.#IND, cc1: -1.#IND, ck1: -1.#IND, cx1: -1.#IND, IClCa: -1.#IND, ...
by bdut
Thu Sep 19, 2019 10:37 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 687

Re: Solving 8 interdependent differential equations

Thank you Ted for your reply. STATE block declares all of the variables on LHS of the ODE's. BREAKPOINT contains below code: BREAKPOINT { hv1 = 1/(1+(exp(-(t-1)/sharpness))) hv2 = 1/(1+(exp(-(t-2)/sharpness))) ipulse = hv1 - hv2 od = ostim * ipulse SOLVE blrrate METHOD cnexp printf("t: %g, blr: %g, ...
by bdut
Thu Sep 19, 2019 12:53 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Solving 8 interdependent differential equations
Replies: 6
Views: 687

Solving 8 interdependent differential equations

In my .mod file, I have 8 DEs to be solved, and all are interdependent. DERIVATIVE block is as follows: DERIVATIVE blrrate { calcParameters(blr, aG, cAMP, aCaMK, Vcilia, CaCaM, Ca, IX) blr' = k1 * od * (Rtot - blr) - r1 * blr aG' = kG * (Gtot - aG) - rG cAMP' = syncAMP - pd * cAMP Ca' = inf * Icng -...