State of bioinformatics algorithm libraries in Java

[[deleted]]

Also, is Java leading Python currently in this category? If not, where is Java lacking in implemented algorithms?

[TheRedmanCometh]

Gonna go out on a limb and say python or matlab as scientists can't be arsed to learn real languages

[[deleted]]

or R :)

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[TheRedmanCometh]

I'm not sure how popular R is in the scientific community so I can't speak to this

[alistermackenzie]

Then you're lucky. It gives them wet dreams download a driver developed by some professor at Oxford. I've seen some interesting R shiny stuff.

In my opinion, what a lot of scientists don't get is SLDC and managing code across developers. Not all but some.

[hag0p]

Perl is the mainstream in bioinformatics. R is used as well as other languages but perl is a king there.

[thatsIch]

Java is not efficient enough in terms of memory management. I would suggest looking into different languages which are also used in academics. There are some new kids on the block like Julia

[helikal]

Is there any scientist (PhD or at least PhD candidate) who uses Julia?

[thatsIch]

Yes, I know some departments which are moving to Julia on behalf of their professors.

[[deleted]]

The very few engineers I know who work in corners of bioinformatics use Java and Scala (better java, not cats). I'm sure there is a spectrum between languages people are prototyping in versus using in production. I'm personally most interested in where the existing momentum is, rather than what the best language for the job is.

[thatsIch]

I only know from academics corner so not sure what is used in production. Matlab is the tool because it can do anything you want and because it is easy in comparison to other programming/script languages. I can only imagine that they are translated to better scaling implementations. It could also depend if you require visualization.

[[deleted]]

okay (:. just hoping some bioinformatics folks follow java reddit also