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

Tue Dec 21 16:46:08 UTC 2010

Apotomo looks like it could be very useful. I think widgets are definitely
the way to go.

One thing I want to make clear is that although many of us are biologists,
SciRuby should be a standalone project. This is not simply intended as a
bioinformatics tool. It should be something general purpose, that any
scientist/statistician would feel comfortable using. With that said, I think
it's appropriate to write plugins that bridge BioRuby and SciRuby.

Can you be more specific with your question? I'm planning on taking a look
at what we already have later today and updating the spec. (Unfortunately,
our lab website is being upgraded, so I can't link you to the current spec
right now.)

Incidentally, I just set up a Google Group for SciRuby development. It's
public.
http://groups.google.com/group/sciruby-dev

Best,
John

On Tue, Dec 21, 2010 at 5:13 AM, Raoul Bonnal <bonnalraoul at ingm.it> wrote:

> Dear John,
> do you have an idea, plans on how to arrange all this stuffs ?
> During this holiday I'll work on the plugin system, code name bio-gem.
>
> Googling around I found this framework http://apotomo.de/ which seems to
> be very promising for building rich web applications.
> Why using widget ?
> Suppose to associate a widget to a biodata you can publish is immediately
> or interact with it easily, just an idea.
> I think there is another widget for rails but I can't remember the name.
>
> On 16/dic/2010, at 01.50, John Woods wrote:
>
> 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
>>
>>
>>
>
>