Use of fortran in bioinformatics
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4.1 years ago
Bioaln ▴ 350

Hello. This is not really a question, more an open discussion regarding the use of Fortran in bioinformatics. I wonder, are there any courageous souls, who do not deal with MD, yet still use Fortran for algorithm development?

Thank you.

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Fortran is probably used only by those who were practicing bioinformatics when it was not formally called that. It is likely more widely used in structural bioinformatics.

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Nice one, why would that be the reason?

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There dwindling interest from students in perl (locally), let alone fortran. Python seems to be the preferred language now. That said fortran would likely be used in some embedded form as illustrated nicely by @Pierre and @Jean-Karim.

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4.1 years ago

yes, R is full of fortran:

$ wget -q -O - "https://pbil.univ-lyon1.fr/CRAN/src/base/R-3/R-3.4.1.tar.gz" | tar tfz - | grep '\.f$' 

R-3.4.1/src/modules/lapack/cmplx.f
R-3.4.1/src/modules/lapack/dlamch.f
R-3.4.1/src/modules/lapack/dlapack.f
R-3.4.1/src/modules/lapack/vecLibg95f.f
R-3.4.1/src/main/xxxpr.f
R-3.4.1/src/library/stats/src/bsplvd.f
R-3.4.1/src/library/stats/src/bvalue.f
R-3.4.1/src/library/stats/src/bvalus.f
R-3.4.1/src/library/stats/src/eureka.f
(...)

or search pubmed https://www.ncbi.nlm.nih.gov/pubmed/?term=fortran+bioinformatics e.g : https://www.ncbi.nlm.nih.gov/pubmed/26370961

(2015) The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins.

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Interesting, calling it from higher level languages is definitely a common phenomenon indeed.

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Of course. A lot of numerical libraries were and still are written in Fortran. See here.

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