Search found 13 matches

by mart
Wed Mar 01, 2017 10:22 am
Forum: Adding new mechanisms and functions to NEURON
Topic: HCN channels modulation by cAMP
Replies: 3
Views: 6430

Re: HCN channels modulation by cAMP

Ok, thanks.
I clearly haven't looked carefully enough.
I will come back with more specific doubts after having a look to the references you mentioned.

Sorry for the inconvenience.
by mart
Wed Mar 01, 2017 6:01 am
Forum: Adding new mechanisms and functions to NEURON
Topic: HCN channels modulation by cAMP
Replies: 3
Views: 6430

HCN channels modulation by cAMP

Dear modelers, I am very interested in having the (deterministic) HCN channels of my neruon modulated by [cAMP] however, I didn't find lots of information about this topic. To my knowledge, the only related post in this forum is this - https://www.neuron.yale.edu/phpBB/viewtopic.php?f=18&t=3025 -, a...
by mart
Fri Dec 05, 2014 9:51 am
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

I tried to start my Optimization process with MRF from different points in the parameter space. In many cases cases (6 out of 10) the optimization finished with a very similar trade-off, a set of values for my free parameters that minimized the error to something like 11... These set of values were ...
by mart
Mon Nov 24, 2014 10:59 am
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

Dear Michael L. Hines, Your last message was really helpful. Now I see that there is little to do when praxis takes a set of parameters as the ones putting the function in the local minimum. I tried to use as much exponential parameters as possible (my model has 4 free parameters, half of them are e...
by mart
Fri Nov 21, 2014 12:36 pm
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

Dear Michael L. Hines, First of all, thanks a lot for your quick reply. Let's see if I understood correctly yout questions. The minimum error reported by MultiRunFitter is "11", if I am not wrong, this value is the square difference between data and dependent variable treated as continuous curves. S...
by mart
Fri Nov 21, 2014 10:46 am
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

Thanks for the hints, I understand that by looking at the commented lines in "src/scoplib/praxis.c" you get the basics on "attr_praxis" as summarized in the programmatic analysis documentation of NEURON's website: http://neuron.yale.edu/neuron/static/new_doc/analysis/programmatic/optimization.html#a...
by mart
Fri Nov 21, 2014 7:47 am
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

Dear Michael L. Hines, I tried again the "QUITVAL" strategy and I didn't achieve what I wanted, this is to keep the optimization process running until the minimum error = QUITVAL or until I manually stop it, actually nothing changed after using such a strategy. Then I tried playing around with the f...
by mart
Wed Nov 05, 2014 2:23 am
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

Ok, understood. Now, what what about overcoming praxis' default stop criteria? As I explained before, instead of defining a fixed number of "quads before return" I would really like to keep the optimization process going through an infinite number of rounds until certain error is reached. If the err...
by mart
Tue Nov 04, 2014 11:56 am
Forum: Optimization
Topic: Initialization & MultiRunFitter
Replies: 1
Views: 6095

Re: Initialization & MultiRunFitter

Ok... I identified the problem. The initialization strategy is actually working but my I_Clamp electrodes go crazy when I use negative time values during my initialization and they do weird stuff. How can I modify the IClamp mechanism so that it understands negative times? I found some information a...
by mart
Tue Nov 04, 2014 4:37 am
Forum: Optimization
Topic: Initialization & MultiRunFitter
Replies: 1
Views: 6095

Initialization & MultiRunFitter

I need to initialize my model to steady state before every run of the optimization procedure. I proceeded in a considerably intuitive way taking as a starting point the MultiRunFitter tutorials & the section 8.4.2 of The Book of Neuron (Chapter 8: How to initialize simulations). I modified the proce...
by mart
Tue Nov 04, 2014 3:34 am
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

Has anybody tried to overcome the default criteria for praxis to stop an optimization procedure? Did anybody manage to keep the optimization endlessly running unless a user-defined amount of error is reached? I didn't... so far I can only manually click again in optimize when the procedure stops by ...
by mart
Mon May 19, 2014 12:39 pm
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Re: Programming Praxis' stop criteria

I am not qiute sure about what did I do wrong, but the "QUITVAL" strategy didn't work. My understanding of Brent's algorithm is pretty basic, having said "I am just guessing", I would claim that the stardard MRF's criteria imposes an end to the optimization process when it is established that the fr...
by mart
Wed May 07, 2014 4:05 am
Forum: Optimization
Topic: Programming Praxis' stop criteria
Replies: 16
Views: 15612

Programming Praxis' stop criteria

In order to restrict the amount of the error so that the Praxis stops the fitting when it reaches that amount of error, two strategies can be followed: (1) To modify the 4th argument that is to be fed into the function fit_praxis() (2) To modify the procedure after_quad() in the file "nrn/lib/hoc/mu...