Version 7 (modified by ngoto, 17 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/ ... in progress
    • (future work) 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 ... in progress
    • (future work) tar.gz should move to ???
    • (future work) www.bioruby.org and bioruby.org should point bioruby.open-bio.org/wiki/Main_Page (redirection?)

BioMoby client in Ruby

BioSQL on BioRuby

  • rewritten by using ActiveRecord

Bio::Sequence improvements for round trip

Input (creation of Bio::Sequence object)

  • Bio::Sequence#read(str or file?~) ... Done
    • (or Bio::Sequence#input(str or file?) ???)
    • Bio::*#to_biosequence is automatically called ... Done
  • Bio::*#to_biosequence implementation
    • Bio::EMBL ... Done (jan)
    • Bio::GenBank? ... Done (ngoto)

Output (formatting)

  • Bio::Sequence#output(format = anything)
    • using ERB templates
      • Bio::Sequence#output(format = :embl) ... in progress (jan)
      • Bio::Sequence#output(format = :genbank) ... in progress (ngoto)

Easy access to Bio::Sequence inside BioRuby

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

Internal structure of Bio::Sequence

  • (future work?) generated from / compatible with XML Schema

NEXML parser in BioRuby

  • (future work) generate parser code from XML schema

Which XML library is better in Ruby for BioRuby?

  • REXML
  • XML parser
  • ...