[BioRuby] GSoC question (regarding SDI algorithm)

Christian M Zmasek czmasek at burnham.org
Mon Apr 5 23:24:17 UTC 2010

Hi, Monika:

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:
1. Goal/deliverable
2. Approach
3. Time estimation
4. Anticipated problems & possible alternative approaches

Like so:

A. Prior to coding (from ... to .... )
     1. Familiarize myself with BioRuby, set up git hub repository
     2. ...
     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:
> Hello
> 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
> here..).
> 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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