MRF to explore parameter space

Using the Multiple Run Fitter, praxis, etc..
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menica
Posts: 45
Joined: Wed Sep 02, 2015 10:02 am

MRF to explore parameter space

Post by menica » Thu Apr 28, 2016 6:42 am

Hi,
I start using the Fitting tool of NEURON. I would like to explore the parameters space of my model, but I find out that this tool is more suitable for fitting the model outputs with experiments and then refine the model parameters.
I am wondering if there is a way to use this tool to perform a study on the model parameters without using experimental data. I want to see what happens to the model changing each parameter, having the AP shape fixed.
I read that would be possible find the optimal values for the mechanism (mod) parameters, but I didn't find any example that explain how to do it.
Any suggestion?

Thanks
Best
Menica

ted
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Re: MRF to explore parameter space

Post by ted » Thu Apr 28, 2016 12:02 pm

menica wrote:I start using the Fitting tool of NEURON. I would like to explore the parameters space of my model, but I find out that this tool is more suitable for fitting the model outputs with experiments and then refine the model parameters.
Yes, parameter optimization is the design goal that guided development of the MultipleRunFitter. It would not be useful for parameter space exploration. Parameter space exploration can be done with a few nested for loops, as in this simple example:

Code: Select all

// assumes single compartment model called soma that has hh
// $1 = how many runs to execute
// $2 = gnabar_hh increment
proc batrun() { local i, gsaved
  gsaved = soma.gnabar_hh
  for i = 0,$1-1 {
    soma.gnabar_hh = i*$2
    run()
    postprocess() // a procedure you wrote
      // that saves and/or analyzes simulation results
  soma.gnabar_hh = gsaved // restore original value
  }
}
I want to see what happens to the model changing each parameter, having the AP shape fixed.
I don't understand what the sentence means. Changing a parameter will change the shape of the action potential.
I read that would be possible find the optimal values for the mechanism (mod) parameters, but I didn't find any example that explain how to do it.
On the Courses page at http://www.neuron.yale.edu/ click on the link at the start of the sentence Here's an on-line version of the exercises from the 2008 summer course. You want to work through this exercise:
9. NMODL : Kinetic Scheme : potassium channel.
You might want to download the entire course archive from the link on the Courses page.

menica
Posts: 45
Joined: Wed Sep 02, 2015 10:02 am

Re: MRF to explore parameter space

Post by menica » Wed Sep 20, 2017 12:15 pm

Hi
I am having some problems when I am trying to use more parameters.
I want to run a simulation for every combination (in a range from 0 to 0.5) of the sodium and potassium conductances, for different values of the amplitude of the stimulating current.
I can do it only changing two parameters, the amplitude and one of the conductances.
I tried to use 3 nested for loop but it is not working.
any help is appreciated
best

menica
Posts: 45
Joined: Wed Sep 02, 2015 10:02 am

Re: MRF to explore parameter space

Post by menica » Thu Sep 28, 2017 12:16 pm

I solved my problem

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