Chapman_publishingweb_BOSC2009

  • 380 views
Uploaded on

 

  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
380
On Slideshare
0
From Embeds
0
Number of Embeds
0

Actions

Shares
Downloads
1
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 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
  • 2. Motivation
  • 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
  • 7. Faster and Bigger
  • 8. Proposal Provide Reusable presentation components Quickly deployable frameworks Integrate Bioinformatics libraries Database schemas Web development frameworks
  • 9. Proposal
  • 10. http://biosqlweb.appspot.com/
  • 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?