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?