[BioRuby] Bringing the fun back to programming! (The first BioRuby IRC conference on Dec 19th)

Pjotr Prins pjotr.public14 at thebird.nl
Tue Dec 14 07:32:28 UTC 2010

On Mon, Dec 13, 2010 at 08:31:52PM -0600, Chris Fields wrote:
> At some point the choice of a language will not matter as much, as
> long as it is implemented in a VM (something Perl 5 cannot claim at
> the moment, but Perl 6 does with the Parrot VM).

In my opinion, multiple VMs will only serve the diaspora in
bioinformatics. One VM would be optimal to make effective use of
shared competencies. It is pretty clear (to me) that Perl is going
it alone... Like the Erlang VM - it becomes a handicap, rather than an

> No idea.  The problem with lack of C-based bindings is a bit of a
> worry (Peter mentioned this in a previous post in this thread).

It is no real problem to bind C to the JVM, using SWIG (for example).
No worse than binding to Perl5. I am planning as much, since I don't
want to drop the C projects from the equation. Nice point is that, a
C/C++/FORTRAN lib once bound against the JVM, will work for all JVM

So, if, for example, the BioPython would resolve their math C
bindings, and make Jython work, it would naturally translate to Java,
Ruby, Scala, Clojure (which btw may be an R replacement), Groovy, and
any future language on the JVM. Now, *that*, my friends, would be a
major step forward in bioinformatics. Not only can we build on each
others work, but also, each of us can work in a language of choice.


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