Question: Bioinformatics Tutorials Utilizing The Go ( Of Google Fame ) Programming Language
4
gravatar for Delinquentme
8.7 years ago by
Delinquentme200
Delinquentme200 wrote:

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.

parallel • 5.0k views
ADD COMMENTlink modified 5.6 years ago by Samuel Lampa1.2k • written 8.7 years ago by Delinquentme200
7

Predecessor? Perhaps you mean 'successor' :)

ADD REPLYlink written 8.7 years ago by Daniel Swan13k
5

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.

ADD REPLYlink written 8.7 years ago by Damian Kao15k
4

GO is about as search-engine friendly as R.

ADD REPLYlink written 8.7 years ago by Neilfws48k
1

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

ADD REPLYlink written 7.5 years ago by ed.liaw90
1

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

ADD REPLYlink written 8.7 years ago by Steve Moss2.3k

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

ADD REPLYlink written 8.7 years ago by Delinquentme200

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.

ADD REPLYlink written 8.7 years ago by Burlappsack660

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?

ADD REPLYlink written 8.7 years ago by Delinquentme200
6
gravatar for Steve Moss
8.7 years ago by
Steve Moss2.3k
United Kingdom
Steve Moss2.3k wrote:

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!

ADD COMMENTlink written 8.7 years ago by Steve Moss2.3k
1

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

ADD REPLYlink written 8.7 years ago by Delinquentme200
3
gravatar for brentp
5.6 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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

ADD COMMENTlink written 5.6 years ago by brentp23k
2
gravatar for Steve Lianoglou
8.7 years ago by
Steve Lianoglou5.0k
US
Steve Lianoglou5.0k wrote:

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.

ADD COMMENTlink written 8.7 years ago by Steve Lianoglou5.0k
2
gravatar for Samuel Lampa
5.6 years ago by
Samuel Lampa1.2k
Stockholm
Samuel Lampa1.2k wrote:

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.

ADD COMMENTlink modified 2.7 years ago • written 5.6 years ago by Samuel Lampa1.2k
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