[Biojava-l] Google Summer of Code 2014 - Call for project ideas

[Amr AL-HOSSARY]

I think we can start thinking in redesigning the structure module, getting
rid of the current design, which is tightly coupled to PDB representation.

Some of the details would include:
- Separating I/O from the model (i.e. creating specialized I/O classes
PDBReadr/Writer, MOL2Reader/Writer, etc).
- redefining terms like group, molecule, bond, and model. As well as
redistributing attributes among them. (e.g. a model is an entity that has
properties, not just a list of chains. Also an atom has more properties like
partial charge. a carbon atom can be SP2 or SP3).


If the idea is accepted in principle, we can start discuss it here or
off-list.

Amr



Best Regards, 
Amr AL-HOSSARY 


Amr Ali AL-HOSSARY |   Ph.D. Student | International PhD program in
Computational Biology and Bioinformatics | School of Computer
Engineering |   Nanyang Technological University | Singapore (GMT+8)
|  Email:  aalhossary at pmail.ntu.edu.sg |  Mobile: +65-94572816 





-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org
[mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Eric Talevich
Sent: Monday, February 03, 2014 3:14 PM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Google Summer of Code 2014 - Call for project ideas

Hi everyone,

Google Summer of Code is on again for 2014, and the Open Bioinformatics
Foundation (OBF) is once again applying as a mentoring organization.
Participating in GSoC as an organization is very competitive, and we will
need your help in gathering a good set of ideas and potential mentors for
BioJava's role in GSoC this year.

If you have an idea for a Summer of Code project, please post your idea here
on the BioJava mailing list for discussion and start an outline on the wiki
page:
http://biojava.org/wiki/Google_Summer_of_Code

We also welcome ideas that fit with OBF's mission but are not part of a
single Bio* project, or span multiple projects -- these ideas can be posted
on the OBF wiki and discussed on the OBF mailing list:
http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas
http://lists.open-bio.org/mailman/listinfo/open-bio-l

Here's to another fun and productive Summer of Code!

Cheers,
Eric & Raoul
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