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

[John Woods]

I saw ruby-statsample, and it looks like one of many things we'd (ideally)
like to integrate.

I'm glad you brought up publishing to the web. We spent a not-insignificant
amount of time debating graphics platform, and ultimately we decided that
HTML5 canvas, and SVG-type graphics, were probably the ideal. For the
moment, we're looking at protovis. Interestingly, Claudio Bustos has been
working on a Ruby protovis port <http://rubyvis.rubyforge.org/> (he also
wrote ruby-statsample, I believe).

The other big piece is NArray. Masahiro Tanaka is apparently rewriting it
with a goal of getting it incorporated into Ruby core. John Prince has been
working on documentation for the existing NArray, in part to see if it's got
everything SciRuby would need. But ultimately, the NArray rewrite/core
integration is the key. It's years from being finished, supposedly -- but
perhaps if there are some eager volunteers we could speed that up. =)

So it seems like most of the pieces are present -- it's just a matter of
tying them together.

And I just said I wasn't going to get into detail -- but there, you just got
me going. =)

John

On Wed, Dec 15, 2010 at 6:29 PM, Raoul Bonnal <bonnalraoul at ingm.it> wrote:

> +1 for me.
> Did you take a look at http://ruby-statsample.rubyforge.org/ ? and there
> is also an optimized version.
>
> John, in the web era a way to easily publish plots on the web not just as
> static images would be great.
>
> Probably I could not attend the first meeting, work trip. Btw if someone is
> around these day I'll try to be in the channel.
>
> Il giorno 16/dic/2010, alle ore 00.02, John Woods ha scritto:
>
> > Hi everyone,
> >
> > I wanted to put in my two cents about this (not this specific email, but
> the
> > thread).
> >
> > I come from a CS background, and so when I began working in
> bioinformatics,
> > I shifted from C++ to Python, Perl, back to Python, and finally to Ruby
> (and
> > Rails!).
> >
> > 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.
> >
> > 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).
> >
> > 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'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.
> >
> > Best,
> > John O. Woods
> > NSF Fellow
> > The University of Texas at Austin
> >
> >
> > On Mon, Dec 13, 2010 at 3:48 PM, Chris Fields <cjfields at illinois.edu>
> wrote:
> >
> >> On Dec 13, 2010, at 12:16 PM, Pjotr Prins wrote:
> >>
> >>> On Mon, Dec 13, 2010 at 06:57:39PM +0100, Raoul Bonnal wrote:
> >>>>> Part of how we try to handle big data files in Biopython is using
> >>>>> Python iterators, whereby the file is loaded record by record (how
> >>>>> depends on the file format - for BLAST we do this query by query),
> >>>>> not all into memory in one go. I think BioPerl does something very
> >>>>> similar in their parsers, I'm not so familiar with BioJava.
> >>>
> >>> BioJava uses a visitor pattern. In effect an iterator.
> >>>
> >>> With all current implementations IO runs, then code, the IO, etc.
> >>> While we are IO constrained, we are actually doing worse.
> >>>
> >>> What I want is an IO thread going at maximum throughput. Every item
> >>> should get parcelled out for further parsing and processing, in
> >>> parallel to the IO thread.
> >>>
> >>> We should do better, and make it a generalization. I think we can do
> >>> it by using Scala and the standard BioJava iterators. With Scala it
> >>> can be turned in a parallelized iterator. That is a fun project.
> >>>
> >>>> From my point of view Python guys are doing a very good job on all
> >> fields.
> >>>> Unfortunately I'm in love with ruby :-)
> >>>
> >>> All you need is love :)
> >>>
> >>> Pj.
> >>
> >> 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).
> >>
> >> chris
> >> _______________________________________________
> >> BioRuby Project - http://www.bioruby.org/
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
>
>