[Biojava-l] accepted GSoC projects

[Mark Chapman]

Hi all,

Thank you to Google, Open Bioinformatics Foundation, BioJava, and my mentors for 
this opportunity.  As a short introduction, I am Mark Chapman, a graduate 
student in Computer Sciences at the University of Wisconsin - Madison.  My focus 
is in artificial intelligence and bioinformatics.  This summer, I will add a 
Multiple Sequence Alignment module to BioJava.

My first task will be to update the alignment module to BioJava3 and to design 
the interface for MSA.  My second goal is to implement a progressive MSA styled 
after clustalw.  After that, I will add alternative routines for each step.

Any ideas for the MSA project as well as more sources of programming wisdom are 
quite welcome.  For example, Andreas suggested a series about Java parallelism 
and lazy execution 
(http://apocalisp.wordpress.com/2008/06/18/parallel-strategies-and-the-callable-monad/). 
  I also noted a useful tip for iterative development 
(http://en.flossmanuals.net/GSoCMentoring/Workflow).

Thanks again,
Mark


On 4/27/2010 12:33 AM, Andreas Prlic wrote:
> Dear all,
>
> Google has released the results for GSoC: Congratulations to Mark
> Chapman and Jianjiong Gao for having been accepted to work on the MSA
> and PTM projects for BioJava! Let's start the "community bonding"
> process ( http://en.flossmanuals.net/GSoCMentoring/MindtheGap )  and we
> all are looking forward to work with you on this during the summer. The
> Mentors and co-mentors will be Peter Rose for the PTM and Scooter Willis
> and Kyle Ellrott for the MSA project (and me).
>
> I want to thank all of of you who submitted proposals or showed interest
> in other ways for the Google Summer of Code. We hope you are not too
> disappointed if your application did not get accepted this time. We had
> a  large number (52) applications and the the overall quality of the
> submissions was very high. We would like to stay in touch with you and
> we hope that you are interested in BioJava also beyond the scope of
> GSoC. There are a number of different ways how to contribute:  We are
> always looking for people who provide code and patches to further
> improve our library, help out with the documentation on the Wiki page,
> or answer questions on the mailing lists.
>
> Let's all give Mark and Jianjiong  a warm welcome to the BioJava
> community.  For those of you who are interested in following the
> progress of the projects, as usually, the development related
> discussions are going to be on the biojava-dev list.
>
> Happy coding!
>
> Andreas
>
>