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Bioperl 1.0 Release

Posted by michael on from the frankenstein's-monster dept.

President Chimp Toe writes "The landmark 1.0 release of bioperl has just been announced. Bioperl is an open-source collection of perl modules designed for the life-sciences community, offering a comprehensive range of modules for DNA and protein sequence manipulation and analysis. More broadly speaking, bioperl is a beautiful example of the virtues of open-source programming and code re-use. Assembled over the last few years by a diverse group of individuals from academia and the private sector, bioperl has made life easier for countless bioinformatics and computational biologists. It allows us to cut out the crappy part of programming (dealing with biological data formats, for instance), and concentrate on the fun part - answering biological questions. Thanks all those involved - keep up the good work!"

8 comments

  1. More to biology than genomics! by RevAaron · · Score: 4, Insightful

    There are biologists out here that program, and we all aren't doing genomics or genetics! I use Squeak to do all sorts of ecological data analysis and visualization. The bio* projects should get another name, they don't encompass any of us. Perhaps genetiperl?

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    1. Re:More to biology than genomics! by monkeyserver.com · · Score: 2, Interesting

      Perhaps you should voice that concern to the bioperl community. I am sure they would love to have a more robust/full-featured package that is useful for all sorts of biologists.

      I bet they just don't have any ppl using perl for that means, or at least no one has contacted them with such code... you could be the first.
      I'm just happy to see perl making itself more and more useful

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    2. Re:More to biology than genomics! by jdiggans · · Score: 4, Informative
      they don't encompass any of us

      The content of Bioperl is driven far more by the interests of the bioperl community than by some malfeasant desire to exclude ecologists. What started out as a codebase dealing mostly with parsing sequence files and results from sequence-analysis applications is slowly branching out to include code for analysis of phylogenetic trees, etc.

      If bioperl doesn't meet your needs the community as a whole needs to hear from you! Let the mailing list know what interests you or, even better, start contributing code!

      The Bio* namespace can help address your problems only if you share them with the community! :)

      -j

  2. More about the story by jeneag · · Score: 3, Informative

    * Project page on freshmeat (sources, cvs, mailing lists, etc.)
    * Bioperl Documentation
    * Bioperl's Gene Object in UML (very nice diagram)
    * Beowulf & Bioperl discussion

    And related stuff that may interest you...
    * BioPython
    * BioCORBA
    * BioXML
    * BioJava
    * BioRuby
    * BioExchange Software tools (other tools for working with bio*, interesting.)

  3. Anyone that can point out some.. by linzeal · · Score: 1

    Geomorphology software? I have an interest in it as of late and even the most simple fluvial mechanics alone are over taxing my comprehension of fluid dynamics.

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