[BioRuby] Bringing the fun back to programming! (The first BioRuby IRC conference on Dec 19th)
cjfields at illinois.edu
Tue Dec 14 13:05:31 UTC 2010
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
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
> 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.
The same exists for Parrot (the NCI interface) and likely must exist for any successful VM. The preliminary DBI for Perl 6 uses it.
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