[Biopython-dev] GSOC 2010 Tiny-PDB project

[Eric Talevich]

On Sun, Mar 21, 2010 at 12:29 AM, Konstantin Okonechnikov <
k.okonechnikov at gmail.com> wrote:

> Dear BioPython developers,
> my name is Konstantin. I am first-year master's student at Novosibirsk
> State
> University, Russia.
> The subject of my bachelor diploma work was development of  3D biological
> macromolecular structure visualization tool for open-source bioinformatics
> project called UGENE <http://ugene.unipro.ru/>. This work was successfully
> finished <http://ugene.unipro.ru/plugin_biostruct3d_view.html> about a
> year
> ago.
> The task included a lot of work with PDB format: parsing, correctness
> testing etc. For testing purposes even whole PDB database was downloaded
> and
> tested for simple assertions. Such stress testing revealed a lot of
> problems
> and helped to improve code significantly. So, one may say, I have some
> experience with PDB format :)
> I used BioPython when I was studying bioinformatics basics and really liked
> it. I would like to contribute to the project by improving Bio.PDB module
> and implementing a set of convenient tools to work with PDB files.
> Best regards,
>             Konstantin
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>


Hi Konstantin,

That's really cool. You might also be interested in a project based on this
idea from another GSoC organization, NESCent:
https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2010#Visualization_of_Protein_3D_Structure_Evolution

(It's OK to apply to more than one GSoC mentoring organization as a
student.)

I sent an e-mail earlier today describing some possible refinements to the
PDB-Tidy project; did any of those interest you?

While we're at it, here's a good place to start improving Bio.PDB before
Summer of Code begins:
http://bugzilla.open-bio.org/buglist.cgi?product=Biopython&bug_status=NEW&bug_status=REOPENED

Feel free to e-mail or gchat me with any questions you have.

Thanks,
Eric