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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?

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Chapman_publishingweb_BOSC2009

  • 1. 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
  • 3. Motivation Web accessible Interoperable in standard formats Displays for browsing Analyses Scale
  • 4. Current state: Reusable libraries Parse file formats Run programs Build analysis pipelines Communities Python examples Biopython pygr bx-python PyCogent
  • 5. Current state: Database schemas Represent biological data Expand analyses beyond flat files Interoperate with standards BioSQL Chado
  • 6. Current state: Web applications
  • 8. Proposal Provide Reusable presentation components Quickly deployable frameworks Integrate Bioinformatics libraries Database schemas Web development frameworks
  • 11. 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/
  • 12. Challenges: Community questions How do we. . . provide plug-in components? leverage existing code? make reuse easier? communicate about these issues?