Bioinformatics Tutorials Utilizing The Go ( Of Google Fame ) Programming Language

Question

[Delinquentme]

So I've heard many novel things about GO

one resounding claim was something along the lines of: " Go is the spiritual predecessor of C++ "

I'm interested to know if anyone knows any implementations of GO specifically in bioinformatics

GO has a reputation for being the bees knees when it comes to parallelization so I'd guess it would be ideal.

[User 59]

Predecessor? Perhaps you mean 'successor' :)

[Damian Kao]

I've been keeping an eye on GO since it started. It looks cool. But I am always fearful of Google's product because they like to introduce a cool product and then shut it down.

[Neilfws]

GO is about as search-engine friendly as R.

[ed.liaw]

Use golang as the search term, I've found.

[Steve Moss]

Yeah, lots of gene ontology stuff in the results, lol :-S

[Delinquentme]

Hmm I know what you're saying... but correct me if I'm wrong but most of the stuff they've shut down has been apps / platforms? I think GO might be a little deeper

[Burlappsack]

I have been asking myself similar questions on the "next best" language for bioinformatics. Recently I have taken an interest in clojure, with lisp syntax(write efficient code), full java interlope (use existing libraries) and a software transactional memory(great concurrency support) I think it might be worth taking a look at.

[Delinquentme]

burlappsack this sounds like no other implementation I've ever heard of ... I have no idea how clojure or lisp are implemented but after a search someone said " find any way to sneak it in ". What does this stack look like? are you using particular functions in lisp which are called in java? Or?

Answer 1

[Steve Moss]

I've been interested in GoLang for sometime, but had never considered it for bioinformatics development previously! I had a quick Google for "golang bioinformatics" and came across the BioGo library on GitHub

https://github.com/kortschak/BioGo

Any good for you? Seems to have some decent functionality so far!

[Delinquentme]

"golang" this is a slightly useful search term... Checkmark!

Answer 2

[brentp]

I just released a small bioinformatics library in go: https://github.com/brentp/irelate

Answer 3

[Steve Lianoglou]

Tangential information for you related to your question: if its parallelization/concurrency you are after in the bioinformatics realm, perhaps you'd be interested in these series about new concurrency mojo in C++11.

It's not GO, but perhaps you know C++ already, or you can look at other C++ libraries used in bioinformatics and adapt with concurrency stuff you learn in these tutorials.

This is assuming you're just looking to learn for learning's sake ... if you really want to work in GO and only GO, then ... this won't help you so much.

Answer 4

[Samuel Lampa]

I'm developing a workflow library focused on bioinformatics, in Go: SciPipe.

It does not implement any actual bioinformatics algorithms, but lets you coordinate and combine both existing commandline bioinformatics software, as well as your own components written directly in Go.