[BioRuby] Google summer of code 2010 - Stathis Kamperis

[Christian M Zmasek]

Hi, Stathis:

Thank you for your interest in this proposal!

Stathis Kamperis wrote:
> Dear Dr. Zmasek,
> 
> my name is Stathis Kamperis and I'm interested in this year's Google
> Summer of Code project:
> "Implementation of algorithm to infer gene duplications in BioRuby".
> 
> I am a medicine graduate, physics undergraduate and computer
> enthusiast. I come from Greece and I am 26 years old.
> I have a long standing programming experience with a vast range of
> programming languages including, since recently, Ruby.
> I also have a decent molecular/biology background.
> 
> I successfully participated in last years Google Summer of Code
> working for the DragonFlyBSD[1] organisation. My work had to do with
> POSIX standard conformance audit, regression testing and quality
> assurance.
> 
> As I understand, the project is about implementing your algorithm to
> BioRuby. Is there any prototype implemented in any language/framework
> at the moment ?

Yes, there is:
See: 
http://forester-atv.cvs.sourceforge.net/viewvc/forester-atv/forester-atv/java/src/org/forester/sdi/

Especially, SDI.java and SDIR.java (for unrooted trees)


In your abstract you mention:
> "We show empirically, using 1750 gene trees constructed from the Pfam
> protein family database, that it appears to be a practical (and often
> superior) algorithm for analyzing real gene trees."
> So, I wonder, what does 'empirically' mean here or how did you conduct
> your tests ?

Essentially, my Java implementation was used to run this tests.

Hope this helps,

Christian