[BioRuby] Beautiful code for Bioinformatics

[Pjotr Prins]

On Fri, Feb 17, 2012 at 10:32:38AM +0300, George Githinji wrote:
> Tango development might not have stopped and tango has now been ported
> to D2 see this announcement
> http://forum.dlang.org/thread/jgagrl$1ta5$1@digitalmars.com

Indeed. Even if Tango had been dropped, it would not be a good reason
to say D has 'issues'. Saying that software libraries are not
maintained is rubbish - how many Ruby modules do you think are not
maintained?

Much about the D1 schism is FUD. As I wrote in my blog

''Finally some things that keep cropping up when I bring up D. First,
the licensing issues. D, for historical reasons was closed source.
That is changing now, with D2 compilers getting part of Fedora and
Debian to follow.  Second the schism and negativism of D1 users caused
by an the move to D2. That you'll find on the Internet. D2 is not
compatible with D1, and that has caused grief. D2 was reinvented as
the language designers progressed their ideas.''

  http://blog.thebird.nl/?p=93 :

I realise this is is not an appropriate mailing list to really vent
opinions about programming languages. Clojure, Groovy, and many more,
are fine languages. If anyone suggests that a language is superior
over another, I would like to point out that there must be a lot of
dumb people out there :). Every language has its pros and cons, and
there is only one way to find out - that is by trying them yourself.

So let us refrain from a flaming discussion on this ML. This list is
about Ruby. We are using other languages to bind against Ruby, and the
mechanisms for binding are universal. You can select pretty much any
computer language, and try that with Ruby (or not). This means we can
all gain, as long as the system can be deployed. With all languages
mentioned here, that is possible. It is a good thing to experiment.

I believe multi-language programming is necessary for big data
analysis. The reason is parallel computing and efficient data
structures. You may want to read our book chapter on language
bindings in

  Sharing programming resources between Bio* projects through remote
  procedure call and native call stack strategies

  by Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter
  Willis, Christopher Fields and Toshiaki Katayama

  chapter 21 in Evolutionary Genomics: statistical and computational
  methods, ed. Anisimova M. within Meth. Mol.  Biol. Series of
  Humana-Springer 2012 

coming out in a month from now :). Notice the authors are from Perl, Python,
Java and Ruby communities.

Pj.