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

Pjotr Prins pjotr.public14 at thebird.nl
Thu Dec 16 13:26:58 UTC 2010

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


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.


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