Version 2 (modified by ngoto, 10 years ago)

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BioRuby Topics

Migration of BioRuby web resources

  • rubyforge.org
    • gem (already available)
    • using BTS and Feature Requests in rubyforge.org ... Done
    • RDoc is moved to bioruby.rubyforge.org ... Done
    • Unused services should be disabled ... Done
  • open-bio.org
    • mailing list (already available)
    • preparation of MediaWiki? by OBF server administrators ... Done
    • moving contents from wiki.bioruby.org to bioruby.open-bio.org/wiki/
    • migration from CVS to SVN
  • bioruby.org
    • moving wiki to bioruby.open-bio.org/Wiki
    • moving RDoc to bioruby.rubyforge.org ... Done
    • moving toppage to Wiki
    • tar.gz should move to ???
    • www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?)

Bio::Sequence improvements for round trip

Output (formatting)

  • Bio::Sequence#output(format = anything)
    • ERB templates
      • Bio::Sequence#output(format = :embl)
      • Bio::Sequence#output(format = :genbank)

Input (creation of Bio::Sequence object)

  • Bio::Sequence#read(str or file?) or Bio::Sequence#input(str or file?)
    • Bio::*#to_biosequence is automatically called?
  • Bio::*#to_biosequence implementation?

Easy access to Bio::Sequence inside BioRuby

  • Bio::Sequence#embl, Bio::Sequence#gb
    • can access as if it is Bio::EMBL or Bio::GenBank? objects
    • delegates to Bio::Sequence objects (or translation/conversion may be needed)
    • Bio::EMBL changed to Bio::Sequence delegation objects?
      • delayed evaluation?

Internal structure of Bio::Sequence

  • generated from / compatible with XML Schema?