[BioRuby] GSoC project

[Konstantin Stepanyuk]

Hi Pjotr and folks,

here is my proposal written according to the scheme published on OBF
GSoC page. It is quite compact since I have not buried into the
codebase and tests deeply. So I will appreciate any help or
suggestions, and I'm looking forward to contribute to your project
during the GSoC.

Thanks!
Kostya.

1.Contact information

Full Name: Konstantin Stepanyuk

Address:
Pirogova str. 20/1, app. 800,
Novosibirsk,
Zip code: 630090
Russian Federation.

E-mail: konstantin.s.stepanyuk at gmail.com
Phone: +7 923 247 2424
ICQ: 427601980


2. Motivation and goals.
Bioinformatics is one of my primary fields of interests. I already
have a solid background in bioinformatics since I have been
participating in Unipro UGENE (http://ugene.unipro.ru) open-source
bioinformatics project for two years. My existing research area in
university includes local sequence alignment and genome assembly.

I highly appreciate Ruby programming language and I was very glad to
get to know that there is an open-source ruby-based open-source
bioinformatics project.
I believe that cross-version of BioRuby is an important issue for the
project, since the project is quite modern and perspective. The one of
the main tasks in porting BioRuby to version 1.9.2 is improving test
coverage, since currently project has quite little unit tests. It will
make us more certain about introducing compatibility & conformance
fixes.


3. My skills summary and work experience
 Programming languages: C++ (3 years), Java, Ruby, Python.
 Projects:
 * Unipro UGENE - free and open-source Integrated Bioinformatic Tools
(http://ugene.unipro.ru).
   - Role: C++ and Qt developer for two years (Unipro LLC).
   - Implemented and tested several algorithms, such as Smith-Waterman
local sequence alignment (and its SSE, CUDA and ATI Stream versions).
 * Apache Harmony - clean-room implementation of J2SE platform
(http://harmony.apache.org).
   - Role: Intern in Intel corporation
   - Implemented tool for aggregating and reporting perfomance and
statistical counters.


4. A project plan.
I propose to divide the total work into two big milestones,
accordingly to Google schedule.

1) Improving test coverage of the project. 23 May - 16 July (total 8 weeks)

2) Porting the project codebase to be compatible with Ruby 1.9.2. 16
July - 20 August (total 5 weeks).

Each of this chunks of work is divided into several subparts:

1)
 - Evaluate test coverage (1 week). Consider integration of some tool
to build process to automate test coverage reporting.
   Create concrete test plan which will be targeted to improve test
coverage up to 90-100%
 - Write unit-tests according to the plan. Consider creating the
stress-test suite. (6-7 weeks)

2)
 - Elaborate the list of incompatibilities with new version of Ruby (1 week)
 - Port the codebase (4 weeks)

5. My plans for the summer
I plan that GSoC project will be my primary occupation during the
summer. But I'm going to a have a 1 week vacation in July.

On 4/7/10, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Hi Konstantin,
>
> Not much time left. Leave us enough time to help comment.
>
> Pj.
>
> On Wed, Apr 07, 2010 at 01:02:07PM +0800, Konstantin Stepanyuk wrote:
>> Hi All,
>>
>> My name is Kostya Stepanyuk, I'm an undergraduate student from
>> Novosibirsk State University in Russia and I'm a looking forward to
>> participate in 'Ruby 1.9.2 support of BioRuby' GSoC project.
>>
>> I already have a background in bioinformatics since I have been
>> participating in Unipro UGENE (http://ugene.unipro.ru) open-source
>> bioinformatics project for a long time. Also, I highly appreciate Ruby
>> programming language and I was very glad to get to know that there is
>> an open-source ruby-based open-source bioinformatics project.
>>
>> My motivation in participating in this project is to improve my
>> knowledge of Ruby, to familiarize myself with your great project and
>> to help BioRuby become more qualitative and popular. I'm looking
>> forward to contribute to your promising project!
>>
>> I'm going to send the full application as soon as possible.
>>
>> Thanks,
>> Kostya.
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>