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

Amr AL-HOSSARY amr_alhossary at hotmail.com
Thu Feb 6 09:56:03 UTC 2014

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


Best Regards, 

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

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:

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

Eric & Raoul
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