[GSoC] Feedback of application

[Peter Cock]

Hi Lluís,

Asking for feedback is a good idea - although in case you
were unaware I will remind everyone that this is a public
mailing list where anyone can read the archives (just
like most open source project discussion lists):
http://lists.open-bio.org/pipermail/gsoc/2014/000375.html

In brief, your proposal was very short, and didn't give
the impression you had really looked at the different
relevant modules in Biopython. Also the timeline and
goals were very vague. Did you look at any full GSoC
proposals from previous years for comparison/reference?

One factor which was outside your control was catching
the interest of a suitable mentor - that was always going
to be tough, with only a handful of potential Biopython
mentors coming up with project ideas on our wiki page:
http://biopython.org/wiki/GSOC

If you are eligible next year (and even if you are not),
I would encourage you to try to contribute to Biopython
(or any open source project) before then. This kind of
activity is a big plus - being able to include links to your
own code/contributions shows what you are capable of
(and can also look good on a CV or job application too).

I hope that was useful.

Regards,

Peter

On Mon, Apr 28, 2014 at 6:58 PM, Lluís Revilla <lluis.revilla at gmail.com> wrote:
> Dear all,
>
> I would like to have more feedback about my proposal. Mainly because
> depending if I get other internships or not I will be able to collaborate.
> And I don't know if it was just that there weren't more slots or that the
> idea was not well focused or how can I improve my overall proposal.
>
> My proposal was increasing the parsers included in Biopython.
>
> Thanks,
>
> Lluís Revilla
>
> PS: The proposal:
>
> On the Contributing page there is a statement about the parser, they need
> to be checked if they still work with each new version of the software
> they  parse.
>
> I found the a parser for BLAST and PSI-BLAST, Python Sequence Analysis
> Tools consists of modules to parse and iterate through various flat file
> databases (EMBL, GENBANK, SWISSPROT, PDBFINDER, ENZYME etc.) and does a few
> other things. This should be checked as it is said in the contribution
> page<http://biopython.org/wiki/Contributing>
> :
>
> "*For example, the GenBank parser needs to be checked to make sure it
> handles each new dump of GenBank*."
>
> It seems that it can be improved and better documented according to the SeqIO
> dev page. <http://biopython.org/wiki/SeqIO_dev> Where it states that other
> parsers could be
> integrated<http://biopython.org/wiki/SeqIO_dev#Possible_additional_formats>.
>
>
> As an active project there is also a parser of GFF under
> development<http://biopython.org/wiki/Active_projects#GFF_parser>.
> Which I could work on it.
>
> My proposal is to integrate this parsers into SeqIO and add the new
> HMMER <http://hmmer.janelia.org> website parser (as suggested in one
> contributor's blog <http://bow.web.id/blog/2013/02/state-of-biosearchio/>).
>
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