[Biopython-dev] [GSoC] Further info about Codon alignment idea

[Peter Cock]

On Wed, Mar 27, 2013 at 2:09 PM, Lara Vignotto <lara.vignotto at gmail.com> wrote:
> Hello,
> I'm a student from Italy. I'm attending the first year of Biotechnology at
> the University of Udine, and I'm interested about the Codon alignment and
> analysis project proposed fot the Google Summer of Code 2013.
> Since I would like to know if I have got the skills required to contribute,
> can you tell me more about the project?
>
> Regards,
> Lara Vignotto

Hi Lara,

Welcome and thank you for your interest in taking part in GSoC 2013.

The background discussion to the outline idea on the wiki was here:
http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010449.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010471.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010474.html
http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010475.html
(I think that was all the posts - check the archive to be sure).

The text of the wiki is hopefully enough to spark your interest - what
we're really like to see is a student intrigued by the idea and driven
to expand the topic into a full project proposal. If for example your
current course work included some phylogenetics that might help
give you perspective about what is useful and worth adding to
Biopython. You should probably also have a look at the NESCent
GSoC project ideas if it is the phylogenetic side that really interest
you - in previous years Biopython has mentored GSoC students
with NESCent:
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2013

You would also need to be competent with Python - although if you
also know and love Perl or Ruby (etc) there might be a mentor
willing to supervise a related project with BioPerl or BioRuby -
that's good too from the wider OBF and Bio* perspective.

For tree traversal some back ground reading on things like
breadth first search and other algorithms for 'walking' the
tree would be a good idea (see also the Python os.path
module for 'walking' a file system tree).

I'm sure there will be other technical things to learn about and use,
depending on where a GSoC project based on this idea went.

Did that help? Is there something more specific I can try to
answer?

Regards,

Peter