Does NEURON accept fortran programs?

Anything that doesn't fit elsewhere.
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sonyadave

Does NEURON accept fortran programs?

Post by sonyadave » Mon Jul 28, 2014 9:22 am

I know some versions of neuron can accept a python program. How about fortran? I request a model of cardiac action potentials from another author, and it is written in, of all languages, fortran! I want to incoporate some of it into my existing neuron model.
If not, i can get some CS-oriented person to convert it from fortran to python...

Thanks,
Sonya

ted
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Re: Does NEURON accept fortran programs?

Post by ted » Mon Jul 28, 2014 11:42 am

Don't waste any more time on those thoughts--such an approach is doomed to fail, if you're lucky, and if you're not lucky, after "investing" a lot of time and effort you'll end up with code that runs but produces garbage results--and you may not recognize that they're garbage until some reviewer reads your manuscript and tells you so.

What you need to do is extract, from the paper(s) that describe the model and the fortran that implements it, the equations that are of interest to you, and the parameters used in those equations. Then you have to incorporate those equations into your own conceptual model, and figure out how to express them in your existing NEURON model. This is not a mechanical process that can be delegated to a programmer or "CS-oriented person" who lacks specific knowledge of cardiac or neuronal anatomy and biophysical properties. It requires domain-specific knowledge and judgement.

sonyadave

Re: Does NEURON accept fortran programs?

Post by sonyadave » Mon Jul 28, 2014 4:00 pm

Thanks for the input and advice. I suppose I'll look at the model in fortran for now, and decide how useful it will be. And, then, I'll go from there.

Sonya

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