Chapman_publishingweb_BOSC2009
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Chapman_publishingweb_BOSC2009 Chapman_publishingweb_BOSC2009 Presentation Transcript

  • Lowering barriers to publishing biological data on the web Brad Chapman Department of Molecular Biology Massachusetts General Hospital Boston, MA USA chapmanb@50mail.com http://friendfeed.com/chapmanb 27 June 2009
  • Motivation
  • Motivation Web accessible Interoperable in standard formats Displays for browsing Analyses Scale
  • Current state: Reusable libraries Parse file formats Run programs Build analysis pipelines Communities Python examples Biopython pygr bx-python PyCogent
  • Current state: Database schemas Represent biological data Expand analyses beyond flat files Interoperate with standards BioSQL Chado
  • Current state: Web applications
  • Faster and Bigger
  • Proposal Provide Reusable presentation components Quickly deployable frameworks Integrate Bioinformatics libraries Database schemas Web development frameworks
  • Proposal
  • http://biosqlweb.appspot.com/
  • Challenges: Design Reusable Components: avoid large framework Multi-language: javascript front end Accessible Automated data retrieval (REST) Standard formats (GFF, RDF) Available Creative Commons http://creativecommons.org/about/licenses Open Data Commons http://www.opendatacommons.org/licenses/
  • Challenges: Community questions How do we. . . provide plug-in components? leverage existing code? make reuse easier? communicate about these issues?