[Bioperl-l] Proposal of GSoC 2012 >> ACEtoSAM and SAMtoACE

afia hayati afia.hayati at gmail.com
Thu Apr 5 00:52:01 EDT 2012


Dear all,

I am afia, a PhD student in Bioinformatics.  I am so interested to
participate GSoC and would like to apply for project Bio::Assembly, Ace2Sam
and Sam2Ace converter. I have written a proposal based on the guidance for
prospective GSoC student. I paste my proposal in here.
If you have time, please give me suggestions.
Thank you very much.

Sincerely,
Afiahayati
[~Be Passion, Patient and Persistent~]


*Google Summer of Code 2012*

*Proposal*

*ACEtoSAM and SAMtoACE*




   1.

   *Contact information *
    1.

      Full name :Afiahayati
      2.

      Address : Hiyoshi International House (Room C301-1), 223-0061
      Yokohama-shi Kouhoku-ku, Hiyoshi 2-27 Kanagawa – Japan
      3.

      Email : afia.hayati at gmail.com
      4.

      Phone number : 818044637237
      5.

      IRC nick : afia

    2.

   *Motivation to join this project *

   I am a PhD student in bioinformatics. My research is in genome assembly,
   especially metagenome assembly. I have same idea that the converter from
   ACEtoSAM and vice versa is very useful. I am familiar with Perl and
   BioPerl, so there is no reason for not participating in this project

    3.

   *Programming experience and skills *
    1.

      Perl also BioPerl since January 2010
      2.

      R, since January 2008
      3.

      Oracle, since January 2008
      4.

      Biojava, since January 2007
      5.

      PHP , since January 2006
      6.

      C++, since January 2006
      7.

      Java, since January 2006
      8.

      MySQL, since January 2005
      9.

      C , since January 2005

    4.

   *Open source projects involved with *
    1.

      Metagenome Assembly, 2012 (with supervisor)

      Develop de novo assembler for metagenomic data from short sequence
      reads

      Using C, C++ and Perl
      2.

      Develop some interfaces in RCommander, 2010 (in team)
      3.

      Computer system of academic hospital, 2009 (in team)

      By modifying an open source hospital information system,
Care2x<http://www.care2x.org/>

      Using PHP, Java script and HTML
      4.

      Academic data warehouse and data mining, 2008 (in team)

      Using Pentaho Business Analytics and R programming language

    5.

   *Project Plan *

    1.

      *Before April 23 *
       1.

         Study the format of SAM and ACE more detail
         2.

         Study the biodesign related to module Bio::Assembly::IO especially
         Bio::Assembly::IO::ACE and Bio::Assembly::IO::SAM
         3.

         Study the documentation and the code of module
         Bio::Assembly::IO::ACE and Bio::Assembly::IO::SAM

          2.

      *April 23 - May 20 (before official coding period) *
       1.

         To do self coding for Bio::Assembly::IO::ACE and
         Bio::Assembly::IO::SAM to improve my understand.
         2.

         Keep contact with my mentor and the BioPerl community. I will
         active in mailing list and IRC to confirm my understanding about
         Bio::Assembly::IO::ACE and Bio::Assembly::IO::SAM and also discuss the
         operations (the methods) needed for a module ACEtoSAM and SAMtoACE
         converting.
         3.

         With the supervision from my mentor, try to determine the
         appropriate design of module ACEtoSAM and SAMtoACE converting.

          3.

      *May 21 - June 21 *
       1.

         Determine the final design of module ACEtoSAM and SAMtoACE
         converting.
         2.

         Code the module ACEtoSAM and SAMtoACE converting
         3.

         Test my code by myself
         4.

         Discuss with my mentor to design good test
         5.

         Test my code based on the test design

          4.

      *June 22 - July 8 *
       1.

         Discuss with my mentor about my code in order to publish in
         bioperl community
         2.

         Publish my code to the community and learn the feedback

          *JULY 9 MID TERM EVALUATION *

      5.

      *July 9 - August 5 *
       1.

         Improving the code (do iteration activities) :
          1.

            Keep contact with the community, learn the feedback
            2.

            Make changes in the code, with the supervision from my mentor
            3.

            Test the code and publish the code to the community
             2.

         Finalize the code
         3.

         Start writing the POD documentation

          6.

      *August 6 - August 13 *

      For final documentation

      *A buffer of a week for unpredicted delay *

      *AUGUST 20 FINAL EVALUATION*



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