Search found 127 matches

by Keivan
Mon Jul 04, 2011 2:38 am
Forum: Anatomically detailed models
Topic: Probable bug in IClamp mechanism
Replies: 7
Views: 2677

Probable bug in IClamp mechanism

ICamp injects current from t=0 if delay (of IClamp) is less than 200 ms.
When delay is more than 200 ms everything works fine.

I can send you a test model if you want.

Code: Select all

NEURON -- VERSION 7.2 (522:60f37c136abb) 2011-06-02
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
by Keivan
Mon Jun 27, 2011 5:14 am
Forum: The GUI
Topic: 2 fitness generators in multirun fitter
Replies: 11
Views: 10906

Re: 2 fitness generators in multirun fitter

Thank you Raj I assume you want the value of 6 to emerge from your fitting procedure. That's exactly what I want. What I want is similar to a system of equations. you would have to combine the two fitness functions into a single fitness function. I don't know how to do this? how to combine a functio...
by Keivan
Sun Jun 26, 2011 4:28 pm
Forum: The GUI
Topic: 2 fitness generators in multirun fitter
Replies: 11
Views: 10906

Re: 2 fitness generators in multirun fitter

If I didn't understand what you wanted, I still don't. then let me explain again: forget about the dendrites. suppose my sigmoid function (gh()) is sth like this: gh(dist,gbarHBegin,gbarHEnd,Steep) = gbarHBegin + (gbarHEnd - gbarHBegin ) / (1.0 + exp((dHalf-dist)/Steep)) gbarHBegin determines the s...
by Keivan
Sun Jun 26, 2011 3:07 pm
Forum: Other questions
Topic: How to create a list of procedures
Replies: 4
Views: 1371

Re: How to create a list of procedures

WoW. You are very intelligent. Thanks This is the final code. It may help someone else. load_file("stdlib.hoc") begintemplate FList public add, list, exec objref FnList proc init() { FnList = new List() } proc add() {//adds a function name to the list FnList.append(new String($s1)) } proc list() { l...
by Keivan
Sun Jun 26, 2011 11:39 am
Forum: The GUI
Topic: 2 fitness generators in multirun fitter
Replies: 11
Views: 10906

Re: 2 fitness generators in multirun fitter

No. I want to fit the parameters of the model. this gbar_h = 6*gbarHBegin has some information about the distribution of Ih in the model. it is sth like my electrophysiological data in nature. Actually the "gbar_h = 6*gbarHBegin" should be sth like this (if calculate_error was a procedure calculates...
by Keivan
Sun Jun 26, 2011 3:03 am
Forum: Other questions
Topic: How to create a list of procedures
Replies: 4
Views: 1371

Re: How to create a list of procedures

Thank you ted. With your guidance I could write a simple FList class. load_file("stdlib.hoc") begintemplate FList public FCount, add, list, exec objref Fname[100], FnList proc init() { FCount =0 FnList = new List() } proc add() { //adds a function name to the list Fname[FCount] = new String($s1) FnL...
by Keivan
Sat Jun 25, 2011 12:55 pm
Forum: The GUI
Topic: 2 fitness generators in multirun fitter
Replies: 11
Views: 10906

Re: 2 fitness generators in multirun fitter

is there any chance to do this without modifying the multirun fitter?
by Keivan
Mon Jun 20, 2011 9:34 pm
Forum: The GUI
Topic: 2 fitness generators in multirun fitter
Replies: 11
Views: 10906

2 fitness generators in multirun fitter

I'm fitting parameters of my model to reproduce some dual patch data (hyperpolarization activated channels). gbar_h in my model changes with a sigmoid function (suppose variables of sigmoid functions are gbarHBegin and gbarHEnd. gbar_h of soma = gbarHBegin in my model). I can do this. now I want to ...
by Keivan
Mon Jun 20, 2011 1:18 am
Forum: Other questions
Topic: How to create a list of procedures
Replies: 4
Views: 1371

How to create a list of procedures

I work on a detailed neuron model fitted to data and I want to build a list of functions and use it to make a dynamic init() function. Every Channel in my model added to the model with a separate hoc file using a procedure. for example If I want to add HH to my model I make insert_hh.hoc file which ...
by Keivan
Tue Mar 15, 2011 5:19 am
Forum: Anatomically detailed models
Topic: How to set non-uniform v_init
Replies: 8
Views: 3276

Re: How to set non-uniform v_init

Thank you very much ted. :)
by Keivan
Mon Mar 14, 2011 4:24 pm
Forum: Anatomically detailed models
Topic: How to set non-uniform v_init
Replies: 8
Views: 3276

Re: How to set non-uniform v_init

I agree with what you said and your answer really helped me in some of my experiments. But still, I'm asking myself: maybe you do not understand my question? please let me explain more. consider the model is in the steady state and has a nonuniform RMP. I just want to save these values of RMP and lo...
by Keivan
Mon Mar 14, 2011 3:02 am
Forum: Anatomically detailed models
Topic: How to set non-uniform v_init
Replies: 8
Views: 3276

Re: How to set non-uniform v_init

Thank you Ted. Your code is actually helpful. But, I'm curious about a way to deal with membrane voltage like other range variables. I want to know how I can assign a value for membrane voltage for each region of the membrane (before start of the simulation). Also, I want a fast method; because I wo...
by Keivan
Sun Mar 13, 2011 4:54 pm
Forum: Anatomically detailed models
Topic: How to set non-uniform v_init
Replies: 8
Views: 3276

Re: How to set non-uniform v_init

yes. This is a question about initialization of the model. Density of hyperpolarization activated channels in dendrites are larger than soma. This may cause distal dendrites have a higher resting membrane potential (RMP). At the moment, it takes 200ms to reach asteady state. I'm looking for a way to...
by Keivan
Sat Mar 12, 2011 10:16 am
Forum: Anatomically detailed models
Topic: How to set non-uniform v_init
Replies: 8
Views: 3276

How to set non-uniform v_init

I'm trying to build a model with nonuniform v_init. I mean dendrites of model should have 2 mV higher resting membrane potential than the soma. Is it possible to do this?
by Keivan
Tue Feb 08, 2011 12:52 pm
Forum: Optimization
Topic: Bug in MulRunFitter patch from Aaron Luchko
Replies: 9
Views: 7678

Re: Bug in MulRunFitter patch from Aaron Luchko

Dear My friend
your patch did not fixed the problem. I will send you the simulation to see it for yourself.
news: this problem did not exist in my windows laptop.