[Bioperl-l] Implementing Bioperl6 for GSoC 2012

Bart Wiegmans bartwiegmans at gmail.com
Mon Apr 2 13:10:47 EDT 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 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)
>
> I will be on and off #bioperl this week (pyrimidine).  IRC is also logged in case I need to backlog (provided by one Moritz Lenz):
>
>   http://irclog.perlgeek.de/bioperl/today
>
> chris
>
> On Apr 1, 2012, at 6:55 AM, Bart Wiegmans wrote:
>
>> Hello all BioPerl-ers,
>>
>> This is my first e-mail to the list and thus my introduction. My name
>> is Bart Wiegmans, I study biology at the University of Groningen, the
>> netherlands. It is my goal to implement bioperl6 this summer as part
>> of the GSoC program.
>>
>> Why would I want such a thing? For a start, I'd like to learn more
>> about bioinformatics. As I told you I study biology, so this has an
>> obvious advantage for me. Also, I'd like to learn perl6 well, and this
>> is only possible when one writes a significant program in it.
>> Moreover, I think perl6 is awesome, and having a real-world toolkit
>> like bioperl out there might just be enough to develop a significant
>> community using it. As a third, I think perl5's object support is
>> crufty, and difficult to learn for many people. These people include
>> biologists who might not be inclined to learn it, and rather use some
>> other tools instead.
>>
>> As to who I am, I already told you my name. I am 24 years old, and
>> study biology at an undergraduate level. (For those interested, yes
>> this means I haven't exactly been flying through my courses :-)). I
>> have been programming computers ever since I was 16 years old, and
>> earlier if you count BASIC. Starting out with C, most of that has been
>> websites (in PHP), scripts (in Perl), and other smallish programs (in
>> Java / Perl). For example, I implemented a parser and decoder for the
>> dirac video specification as part of GSoC 2008, and a script which
>> reads the NIH bookshelf website and translates this into ePub e-books.
>> Read quite a few of them that way.
>>
>> Aside from my motivation and capabilities, two other factors somewhat
>> complicate my involvement with GSoC. The first is that the academic
>> year ends halfway in July in the netherlands, not in may as in the USA
>> and in many other countries. This means that I am not 'free' in a real
>> sense before that time. Also, I have a day job as a PHP programmer for
>> a local online students' magazine, which also takes some time. Which
>> is unfortunate, because I'd rather spend my time writing useful
>> programs; hence, if you would accept me as a student I plan to take
>> leave from this job during the period of GSoC.
>>
>> Anyway, I realize this has been enough information for any interested
>> reader. If there is any interest on your side, I frequent freenode
>> under the nickname brrt. Other than that and this e-mail address, I
>> don't have much of an online presence.
>>
>> Kind regards,
>> Bart Wiegmans
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>



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