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

[Peter]

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.

> 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.

Peter