Satellite meeting for BioRuby? development and documentation

Topics

Miscellaneous things about BioRuby? delvelopment and documentation.

Participants

• Naohisa Goto
• Raoul JP Bonnal
• Toshiaki Katayama
• Jan Aerts
• Mitsuteru Nakao

Targets

• Developer of BioRuby?
• End-users of BioRuby?

Date

• 2009/3/19 17:00-
• Any time via online :-)

Room

• 3F Chura Hall

Results

• Hack
  • New features
    • FASTQ format parser
  • Bug fixes
    • Bio::PubMed?.esearch bug -- fixed by Toshiaki
    • Bio::Fasta::Report problem -- in progress
  • Improvements
    • BioSQL -- Raoul
    • Tutorial -- Pjotrp (remote)
• Discussion
  • BioRuby? documentation
    • To add use-case documents quickly and efficiently, we decided to "translate" BioPerl?'s HOWTOs into BioRuby?.
    • In addition to the translation, we are going to add new HOWTOs.
    • Priority to translate (or to write from scratch) is assigned.
    •  http://bioruby.open-bio.org/wiki/HOWTOs
  • Discussion about next version release
    • Current version is 1.3.0.
    • 1.3.1: Bug fixes and some improvements
      • TogoWS as default data source
      • BioSQL
      • tutorial
    • 1.4.0: New features
      • New web services clients / servers?
      • Large data handling
        • manifest files?
      • Phyloinformatics
        • PhyloXML support -- maybe in GSoC
        • NeXML support -- hopefully to collaborate with MX project
  • BioRuby? publication plan

TODOs

• Writing documents
• hack, hack, hack