[Biojava-dev] [GSoC] Project Proposal

[Krzysztof Ropiak]

Hi,
It time for my proposal draft. I hope I've included all my thoughts 
about project.
And few more questions:
1) Do you mind adding some tests to short-coding-exercise? :)
2) Should I mention short-coding-exercise at all in proposal?

Proposal:

Project name :
     Amino acids physico-chemical properties calculation

Student:
     Krzysztof Ropiak (+contact information here)

Abstract:

The basic aim of this project is to develop new high-performance 
implementations of standard algorithms for a range of calculations 
within BioJava3.
Calculation examples:
    1. Molecular weight
    2. Extinction coefficient
    3. Instability index
    4. Aliphatic index
    5. Grand Average of Hydropathy
    6. Isoelectric point
    7. Number of amino acids in the protein (His, Met, Cys)


About me:

I am second year student at Gdansk University of Technology (Poland). If 
accepted, it would be my first time to work in an open source project - 
however I really like OS idea and I'm hoping for first experiences in 
that regard. I am Java technology enthusiast and high-quality code fan. 
Another thing is that I feel really comfortable with algorithms. I have 
participated in number of algorithmic contests - as an example, I have 
achieved Second Round of last year's Google Code Jam (-- is link needed 
here? :) --). I've got also knowledge about multithreaded processing. I 
know more that few design patterns and I'm ready to recognize situations 
where they are needed. I am familiar with modern Java frameworks - ex. 
Sprint, Hibernate - I've read that BJ3 should be easy to work with them. 
Each day, I am doing my best to write clean code.

Weak points:

I can see two of them:
  - Time of my participating in GSOC would be limited in first two weeks 
as academic year in Poland is not yet finished. Fortunately, I am not 
kind of student, who has problems with studying and I am sure I can work 
before my studies finishes. I will not be able to work in the last week 
of GSOC, because of travelling.
  - I am computer science student, not biology (and others). My 
knowledge is not really big here. Still, I strongly believe I can 
contribute without it.


Project basic plan:

Before GSOC start:
     Getting in touch with BioJava
     Looking for all knowledge needed to calculate properties mentioned 
above
     Looking for best (usually faster) methods to calculate properties.

Coding part :

May 24 - June 10
     Molecular weight
June 11 - June 20
     Extinction coefficient
June 20 - June 30
     Instability index
July 1 - July 10
     Aliphatic index
July 11 - July 20
     Grand Average of Hydropathy
July 21 - July 31
     Isoelectric point
August 1 - August 10
     Number of amino acids in the protein (His, Met, Cys)

August 11 - till the end of GSOC:
     Finishing documentation & all other things to polish whole work 
done and make it as much valuable for BJ as possible


** This is just a basic plan. Order of calculations can be changed due 
to mentor's ideas. In this plan I reserved more that two weeks for first 
calculation, due to my limited time at start. All other calculations are 
supposed basically to implemented up to 10 days. I think there is a 
possibility of me doing more that just these calculations and I strongly 
hope I can finish these calculations much quicker that planned and spend 
some time on polishing work done previously or some other mentor's ideas.

** I would like to use test-driven-development approach, which would 
make sure code is tested properly. Implementing particular calculations 
would be finished with providing javadoc and other documentation.

Hope you enjoyed reading :)

Krzysztof Ropiak