[BioRuby] GSoC project

[Christian M Zmasek]

Hi, Konstantin:

Your project plan is not detailed enough and partially vague (for 
example, what do you mean by "some tool"?)

Christian


Konstantin Stepanyuk wrote:
> 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
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby