Dagstuhl Workshop 15-18 Aug 2011
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Dagstuhl Workshop 15-18 Aug 2011

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Dagstuhl Workshop - The Future of Research Communications

Dagstuhl Workshop - The Future of Research Communications

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Dagstuhl Workshop 15-18 Aug 2011 Presentation Transcript

  • 1. Making Beyond the PDF Current Practice
    Phil Bourne
    pbourne@ucsd.edu
  • 2. A Reminder of my Perspective …
    Computational biologist
    Co-direct the Protein Data Bank
    EIC PLoS Computational Biology
    Wanting to embrace what you are developing
    Willing to promote your developments in any way I can
    Co-hosted the Beyond the PDF workshop
  • 3. What Has Happened for Me Post PDF Workshop?
    Good news: Seen small shifts in the reward system
    Bad news: See the crisis in the research system thwarting innovation in scholarship
    Think maybe SciVerse is a game changer?
    Initially thought a data journal was a logical development
    Convinced myself that workflows are critical, but not sure yet whether they are practical
  • 4. The Data Journal Posting
    Response to the lack of innovation from HHMI/Wellcome/MP
    A reward enough for publishing data?
    A new paradigm in computation?
    Are Dryad, Dataciteetc enough?
    Are institutional repositories enough?
    Is it a good idea to have database developers as publishers?
  • 5. The Data Journal Response
    Don’t reinvent the wheel
    We have a technical solution!
    Can we/should we review it?
    Gels with the executable journal ideas of Anita/Tim/Dave/Carole/others
    Cf CKAN, github
    PLoS is trying Dryad
    F1000 trying a hybrid model
    NPG will be trying something
  • 6. Finally Getting onto Workflows!
    Presented the TB druggome as the BtPDF challenge
    Subsequently been working with Yolanda Gil (USC) and Daniel Garjiro (Elsevier Fellow) to build into a workflow
  • 7. Status
    Its hard and embarrassing
    We have a working prototype using Wings
    I can feel the potential productivity gains
    Its been a lot of fun and will enable us to improve our processes regardless of the workflow system itself
  • 8. Yes Its Real
  • 9. Workflow – Tentative Plan
    Have a new fellow who will use it to compute the T brucei(causative agent of sleeping sickness) druggome
    Publish a follow-up paper in the PLoS Comp Biol software section to the original TB druggome research article which is the workflow published by the journal
  • 10. What Do I Want Out of This?
    A clear way to contribute:
    Start or work with an existing data journal?
    Engage PLoS somehow?
    Use the Protein Data Bank (PDB) as an exemplar in some way
    Do something new and exciting science via workflows and data deposition?