[BioRuby] GSoC project

Thu Apr 8 11:48:51 UTC 2010

Hi Konstantin,

In the project, Ruby porgramming skill is very important.
Write more about your Ruby programming experiences.
In addition, can you show URL to Ruby scripts you wrote?

Please improve project plan more. For example:
 * Preparation. E.g. to subscribe to ruby-core mailing list
   to check current status of Ruby 1.9.2, installing Ruby
   1.9.2 and 1.8.7, etc.
   Note that Ruby 1.9.2 are now under feature freeze, and
   will be  released on July 30 ([ruby-core:28665]).
   You will need to compile Ruby 1.9.2 svn version at least
   several times. (Optionally, in every week or every day,
   and to contribute Ruby 1.9.2's bug fix).
 * About development environment and tools you will use.
 * About coverage check tool (rcov?).
 * Reading changes from Ruby 1.8.7 to 1.9.1 and from
   1.9.1 to 1.9.2, and brush up the plan.
    http://svn.ruby-lang.org/repos/ruby/tags/v1_9_1_0/NEWS
    http://svn.ruby-lang.org/repos/ruby/trunk/NEWS
 * Extracting bioruby-1.4.0.tar.gz, looking at lib/ and
   test/unit (andtest/functional), and checking existance
   of test files and directories corersponding to library
   main files. For example, you can find that
   lib/bio/db/genbank exists, but test/unit/bio/db/genbank
   does not exist. Of course, in some cases, test files
   exist but their contents are poor.
   Although it is very difficult, but if you can, it is
   good to estimate the needed efforts. It is also good 
   to prioritize classes/modules to write tests. I think
   Bio::GenBank and Bio::GenPept are high priority.
 * ...
(Not all will be needed, and not limited to the above.)

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Thu, 8 Apr 2010 16:55:25 +0800
Konstantin Stepanyuk <konstantin.s.stepanyuk at gmail.com> 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