Fields, Christopher J | 2 Apr 03:57 2012

Re: Implementing Bioperl6 for GSoC 2012

Bart,

I think this is a good idea, but to address one concern up-front: I believe the time frame (possible start in
mid-July) will not be in your favor unless you can participate according to Google's schedule.  There is
some flexibility at the beginning, mainly during the community bonding period, but beyond that there
isn't much wiggle room; we're as constrained as you are.  The proposals to OBF over the last few years have
been highly competitive, and this year will prove even more so as a large number of major Perl-based FLOSS
orgs (primarily The Perl Foundation) were not accepted into GSoC.  

Now for Perl 6:

BioPerl6 is a project Philip Mabon and I have already started up on github:

   https://github.com/cjfields/bioperl6

The code is basically proof-of-concept stuff at this point, and I don't believe it's current to spec last I
checked or that it works on either the most current niecza or rakudo.  All this was enough of a moving target
to make it hard to maintain, but that seems to be settling somewhat now.  It's pretty wide open, though, as
far as I'm concerned.

If you are to pursue this as a proposal, you will need to focus on a specific task or set of classes to implement
along with docs and tests.  A straight port isn't the best option; you should take advantage of Perl 6's
strengths and possibly work on redesign where needed, keeping in mind that some aspects of bioperl might
be considered a bit over-designed and out-of-date w/ re: to modern perl dictums.  Also, learning a new
language is nice, but that isn't the main focus for any GSoC project.  At the end of the day, we should have
usable code for the community, and if it acts as a entry point for more people to get involved with Perl 6 the
better :)

(I see that Leon has also chimed in on this with similar comments as well)

(Continue reading)

Bart Wiegmans | 2 Apr 19:10 2012
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Re: Implementing Bioperl6 for GSoC 2012

Chris, Leon, others,

Thank you for your timely responses. So far as the timeframe is
concerned, I might be able to get student credits for participating in
this projects as it is related to my study. In that case I would have
more time free. At any rate, I understand it is suboptimal to start
working in july, so I will do my best to make as much time free as
possible.

I've already checked out the bioper-6 projects as well as the biome
project from github. I am not quite sure what scope of project to
choose and I was hoping for your advice. File format import / export
and database connectivity would come to mind, as these are subjects I
am most familiar with. In such a scenario, aside from a set of modules
/ classes, the end goal would be a script that could search for and
import a sequence from a number of popular databases, and save it on
the users' hard disk. I am very much open to suggestions, however.

Anyway, thank you for your time.
Kind regards,
Bart Wiegmans

2012/4/2 Fields, Christopher J <cjfields <at> illinois.edu>:
> Bart,
>
> I think this is a good idea, but to address one concern up-front: I believe the time frame (possible start in
mid-July) will not be in your favor unless you can participate according to Google's schedule.  There is
some flexibility at the beginning, mainly during the community bonding period, but beyond that there
isn't much wiggle room; we're as constrained as you are.  The proposals to OBF over the last few years have
been highly competitive, and this year will prove even more so as a large number of major Perl-based FLOSS
(Continue reading)


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