[BioRuby] Beautiful code for Bioinformatics

[Raoul Bonnal]

I'm studing D  because of Pjotr :-), next will be Scala.
Actually I tried Scala 2 year ago but my feeling was not so good with that
language, maybe it's me. I feel comfortable reading D book, and I find the
language a bit natural to me.
Pjotr is right, we as bioinformaticians should know both and try others.

What now is impossible with Ruby and Python is writing parallel
applications. I'm looking for the best way to write parallel code and use
the resources efficiently without forgetting easiness.
Obviously there are other techniques like Hadoop for processing "big data",
so ... Nothing is decided and we should discuss more.

I'm here and I want to hear about your experience/opinion/approach.


PS: Scala and D, both have binding to OpenCL

On 13/02/12 08.09, "Pjotr Prins" <pjotr.public14 at thebird.nl> wrote:

> I have written about D and Scala in 'Ruby is a pony, Scala is a
> thoroughbred, D is a dragon'.
> 
>   http://blog.thebird.nl/?p=93
> 
> There is more on Scala examples on that site too. I may add D stuff in
> the future. We all need to write more about software and programming.
> 
> Over the last year I prefer to program in Ruby and D - they are at
> both ends at the convenience vs.  performance spectrum ;). D natively
> links against C libraries, something I like a lot (saves a lot of data
> copying). There will be biogem examples of bindings soon. Also the
> LLVM version of D2 is doing well, D will become part of Fedora and
> Debian based systems.
> 
> If the JVM complex 'ecosystem' is no big issue, JRuby and Scala are
> also a brilliant match. You can check out my BioScala code and
> documents on github.  JRuby is a great performer, so that may come
> naturally to you. Ruby gems work really well on the JVM, even when
> written in C.  The JRuby developers have done a remarkable job.
> 
> Personally, I think it boils down to background and experience. C/C++
> programmers I see taking to D like a fish to water. People with a Java
> background may well prefer the JVM. Even after the balanced choice for
> D, I really miss some of the niceties of Scala. I guess, if I were
> programming Scala, I would do less in Ruby.
> 
> I would strongly suggest to buy and read both Andrei's D book and
> Martin's Scala book. They are both classics in their own right - and
> see what appeals to you most.
> 
> D and Scala are both next generation (strongly typed) languages
> designed by geniuses. They both work well with Ruby.
> 
> Pj.
> 
> On Sun, Feb 12, 2012 at 04:02:26PM -0800, Russell Whitaker wrote:
>> On Sun, Feb 12, 2012 at 3:35 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
>>> [SNIP]
>>> PS: I'm studing D :-)
>>> 
>> 
>> Do tell: what do you like about D? For that matter, have you evaluated Scala?
>> I've been curious about both...
>> 
>> -- 
>> Russell Whitaker
>> http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/
>> http://www.linkedin.com/pub/russell-whitaker/0/b86/329
>>