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

Raoul Bonnal bonnalraoul at ingm.it
Thu Dec 16 00:29:44 UTC 2010

+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
>> _______________________________________________
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