[BioRuby] Bringing the fun back to programming! (The first BioRuby IRC conference on Dec 19th)

Raoul Bonnal bonnalraoul at ingm.it
Mon Dec 13 17:57:39 UTC 2010

Il giorno 13/dic/2010, alle ore 15.44, Peter ha scritto:

> On Mon, Dec 13, 2010 at 11:42 AM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
>> On Sun, Dec 12, 2010 at 08:43:15PM +0100, Francesco Strozzi wrote:
>>> The performance of many common tasks (e.g. parsing a large Blast
>>> report) are superior than with BioRuby libraries, for what I have
>>> seen.
>> Here you have a good point. BioRuby is lagging behind BioPython,
>> BioPerl and BioJava.
> 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.
This is the right approach.
Junior Programmers tend to load everything and/or create huge hashes, at the same time the old
 ruby interpreter had a bad garbage collector.
It's always a matter of coding if we are discussing about performances each language can have worst performances.

If scala can be used to easily express the concept or better help in parallel programming why not trying it?

>> My proposal is to use BioJava together with BioRuby. You can do
>> something similar with Jython (Python on the JVM), though I have the
>> impression Jython is not as active as JRuby, anymore. JRuby is
>> getting strong industry support, at this point.
> Just for reference, we do test Biopython on Jython (i.e. on the JVM)
> and most things work. There is a significant downside that you can't
> use compiled C code, in particular this means you can't use NumPy
> under Jython (the numerical python library, used in matplotlib and
> SciPy). Nevertheless, some people are using Biopython on Jython.

>From my point of view Python guys are doing a very good job on all fields.
Unfortunately I'm in love with ruby :-)


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