[BioRuby] SciRuby (The first BioRuby IRC conference on Dec 19th)

[Pjotr Prins]

On Wed, Dec 15, 2010 at 05:02:27PM -0600, John Woods wrote:
> Working in a bioinformatics lab, my experience has been that most people go
> with Python over Ruby because of SciPy and NumPy (and matplotlib). At least
> for us, it's not because of speed at all. If I need something speedy, I code
> it in C++ and use Rice to build a Ruby adapter.

That is what I always did. Reason to switch to functional languages
are that they are stronger with parallelization abstractions (and
shared memory). C++ can do parallelization, but it is harder work and
more dangerous.

> Anyway, a couple of us (me, John Prince, Ara Howard, a few others) have been
> brainstorming a bit. We think the #1 thing Ruby is missing is SciRuby (and
> with it, good numerical support).

Great! Be good if it supports JRuby!

> To that end, we've been working a bit to put together a spec for how a
> SciRuby with plotting and numeric capabilities would work.

I did a GSL port to Ruby

  https://github.com/pjotrp/ascilib

using SWIG. It may not interest you, but it does support Perl too,
and probably soon the JVM. Using SWIG is not that hard, and the
advantage is a wider target.

> I'm not quite ready to say anything specific about it publicly just yet, but
> if you're interested in being involved, please write me back.

It is a good thing, thanks, looking forward to it.

Pj.