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

[Chris Fields]

On Dec 14, 2010, at 1:32 AM, Pjotr Prins wrote:

> 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
> asset.

Much of this is due to the complexities involved in parsing the language.  It's long been said that only perl can parse perl, but that's changing with perl 6.

>> 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
> languages.
> 
> 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.
> 
> Pj.

The same exists for Parrot (the NCI interface) and likely must exist for any successful VM.  The preliminary DBI for Perl 6 uses it.

chris