NEURON + Python + Genetic Algorithms

Using the Multiple Run Fitter, praxis, etc..
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slarson
Posts: 2
Joined: Wed Jul 07, 2010 8:34 am

NEURON + Python + Genetic Algorithms

Post by slarson » Fri Dec 09, 2011 1:55 am

Hi,

I wonder if others have experience combining the Python build of NEURON with external software to do optimization, like say with custom Genetic Algorithm code. I imagine that NeuroFitter does something like this, but not via Python.

I'm looking for a high-level software strategy of how this could be accomplished. If you have any suggestions it would be most appreciated.

Thanks,
Stephen

hines
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Joined: Wed May 18, 2005 3:32 pm

Re: NEURON + Python + Genetic Algorithms

Post by hines » Fri Dec 16, 2011 9:32 am

This may not be analogous to what you desire but an example of adding the Scipy bfgs optimizer as an alternative to praxis in the MultipleRunFitter is in the bfgswrap.py
file of the bfilt repository. i.e.
http://www.neuron.yale.edu/hg/z/bfilt/f ... fgswrap.py

hines
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Posts: 1580
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON + Python + Genetic Algorithms

Post by hines » Fri Dec 16, 2011 9:42 am

To run the file I mentioned in the last post, one needs to load the multiple run fitter first. e.g.

nrngui -c 'load_file("mulfit.hoc")' bfgswrap.py

If one NEURONMainMenu/Tools/Fitting/MultipleRunFitter
then the Parameters/SelectOptimizer menu will have a BFGS item.

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