[BioRuby] GSoC question (regarding SDI algorithm)
Christian M Zmasek
czmasek at burnham.org
Mon Apr 5 23:24:17 UTC 2010
Thank you for you interest in this proposal.
Please remember that student applications are due by April 9, 19:00 UTC
-- so, you have not much time left.
I think your lack of experience in Biology is not a problem.
The idea is to implement the algorithm with the BioRuby toolkit
Some more advice:
If you plan to apply, you need to write a very detailed plan on how you
intend to accomplish this project.
For each step you should list:
3. Time estimation
4. Anticipated problems & possible alternative approaches
A. Prior to coding (from ... to .... )
1. Familiarize myself with BioRuby, set up git hub repository
3. 1 week
4. Not familiar with git, might need to...
B. Week 1 (from ... to .... )
1. Develop unit tests
2. Using manually created gene and species trees, I plan to...
3. 1 week
4. No problem anticipated
Basically you also need to write a short CV, similar to a job application.
Hope this helps,
Monika Machunik wrote:
> 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
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
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