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     * do not only rely on [DebPkg:ClustalW]] but alternatively also on other alignment tools of Debian      * do not only rely on [[DebPkg:ClustalW]] but alternatively also on other alignment tools of Debian
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     * extend usability as suggested [[GENtle|here]].
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  * '''Aims:''' Strategically, this project reminds ourselves that Debian is more than the packaging of readily available software. It is also about gluing components together or to prepare for it. The most tangible result is the time saving for all the molecular biologists out there using GENtle, PerlPrimer and friends. The tutorial introducing to these tools will attract more to our distribution and be of high educational value.   * '''Aims:''' Strategically, this project reminds ourselves that Debian is more than the packaging of readily available software. It is also about gluing components together or to prepare for it. The most tangible result is the time saving for all the molecular biologists out there using GENtle, [[DebPkg:PerlPrimer]] and friends. The tutorial introducing to these tools will attract more to our distribution and be of high educational value.

The main page is at SummerOfCode2011. This page contains ideas and proposals and information for applying.

Proposals

Example If you want to add your idea proposal, create a new page as a sub-page of SummerOfCode2011 by accessing its intended URL directly, select the "?SummerOfCode/ProposalTemplate" template and link to that page from here.

Debian installer

Hardware porting

Infrastructure

APT/dpkg

Bug tracking

linux-2.6 Packaging

packages.debian.org

Packaging and upgrades

Science

Streamline the preparation of BOINC projects

  • Mentor: SteffenMoeller

  • Summary: Further develop the boinc-server-maker package, complete the turorial and apply it all for virtual drug screening

  • Required skills:

    • good reading and writing skills
    • strong interest in scientific computing
  • Description: BOINC stands for the Open Infrastructure for Network Computing. Debian offers a readily usable package for the BOINC client since several years. Co-maintained with Ubuntu developers the package directly reaches tens of thousands registered installations and as such represents as considerable contribution to the volunteer computing community. The recent Google Code-In project seeded an effort to also help a larger adoption of the server side of BOINC for the distribution [1,2]. A thus reduced setup time for BOINC projects shall then foster the adoption of the technology for smaller environments and smaller problems. And a clearly paved technology shall further help to allow grant writers to focus more on the application side, which will this way also help the larger projects.

    • Challenges:

      • Show and document that the boinc-server-maker package of Debian is fully compatible with the VMware setup that BOINC provides itself.
      • Address the problem of MySQL schema changes between versions by using the tools BOINC provides.
      • Prepare a template package (e.g. from the examples) for application specific boinc-server packages. The boinc-server-maker package shall be a build dependency for that package.
      • Get as far as you can in preparing one or multiple Debian packages for in silico screening of molecular compounds with autodock [4].
    • Aims: This GSoC project shall take all the tears and fears from preparing novel BOINC projects. This shall take half of the time and determines the interim report. Then be as good as you can for the application on molecular docking. This may literally safe lives.

    • References:

      1. http://wiki.debian.org/BOINC/Server

      2. http://packages.debian.org/experimental/boinc-server-maker

      3. http://boinc.berkeley.edu/trac/wiki/QuickStart

      4. http://autodock.scripps.edu

  • Applications:

Genetic Cloning with Debian

  • Mentor: SteffenMoeller

  • Summary: Improve the interplay of several tools for preclinical research and write respective tutorials

  • Required skills:

    • good reading and writing skills
    • strong interest in computational biology and genetics
    • Perl
    • wxWindows
  • Description: Several routine tasks in preclinical research are a continuous nuisance with Open Source tools on any OS. Debian has an edge since it offers a series of applications that address most of those routine issues. This availability the upstream developers had not anticipated by the developers of those contributing tools. Also, some tools need a bit of maintenance to update their URLs.

    • Challenges:

      • Update URLs e.g. for Ensembl for PerlPrimer

      • Write a tutorial for cloning with GENtle

      • Improve GENtle

        • do not only rely on ClustalW but alternatively also on other alignment tools of Debian

        • prepare for some eye candy, e.g.use of svg icons, the use of standard icon collections and their extension by own work
        • allow GENtle to run PerlPrimer

        • extend usability as suggested here.

      • Improve PerlPrimer

        • Find way to integrate newer technologies, especially for quantitative PCR
        • again, better eye candy and usability
    • Aims: Strategically, this project reminds ourselves that Debian is more than the packaging of readily available software. It is also about gluing components together or to prepare for it. The most tangible result is the time saving for all the molecular biologists out there using GENtle, PerlPrimer and friends. The tutorial introducing to these tools will attract more to our distribution and be of high educational value.

  • Applications:

DebianPureBlends