[BioRuby] GSoC question (regarding SDI algorithm)

Monika Machunik monika.machunik at gmail.com
Mon Apr 5 18:41:36 UTC 2010


My name is Monika Machunik and I am planing to apply in this year's Summer
of Code. I have read your idea description about "Implementation of
algorithm to infer gene duplications in BioRuby", and, although my
background does not include any biology, I got quite interested in this
project (I could not find mentors' email addresses, so I'm posting it

I would like to shortly introduce myself to get your opinion if I would be
suitable for this project.

I have about a year of work experience in Java programming, including some
internships and last year's GSoC. Besides Java I know C++, some C, Php,
HTML, etc. I am not experienced in Ruby programming (at least have seen Ruby
code;)), but I learn fast. Currently I am doing my Master degree in Computer
Science, so I have some knowlegde about algorithms and data structures. I
have never worked at the intersection of biology and CS, but this
conjunction has always been intriguing to me.

And now my thoughts about possible content of the workload.

I have read the abstract of the article and, despite of my lack of
biological knowledge, I managed to comprehend it;). I think I also should
have no problem with understanding the algorithm itself. Apart from
implementing the algorithm, the project would involve getting familiar with
BioRuby, understanding phyloXML in such extent to be able to write an
algorithm operating on its ready structures.

I am not sure if the algorithm should be implemented inside some exisitng
software, or will it be a kind of standalone algorithm? If it should be
accomodated inside some application, the project would probably involve
doing that too...

...let it be all for now. Let me know if I have any chances in this project

Best regards
Monika Machunik

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