[BioRuby] GSoC project

Fri Apr 9 05:26:31 UTC 2010

Hi Christian,

Thanks for your comments!
I agree that my plan is very rough, but elaborating detailed plan requires
lots of work with existing codebase, tests and new Ruby issues. So it looks
like almost impossible for me to write today a plan like 1) writing XXX
tests for YYY method of ZZZ class (2 days). 2) fixing XXX issue from Ruby
changelog in classes ZZZ (3 days).

So I have a time for writing detailed testing and porting plans in the
overall project plan.

By 'some tool' I mentioned that I currently can't say which one will be the
most suitable.. I'm not a big guy in Ruby language and tools (but not for a
long time, I hope).

Thanks,
Kostya.

On Fri, Apr 9, 2010 at 4:43 AM, Christian M Zmasek <czmasek at burnham.org>wrote:

> 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
>>
>
>