Making Beyond the PDF Current Practice<br />Phil Bourne<br />pbourne@ucsd.edu<br />
A Reminder of my Perspective …<br />Computational biologist<br />Co-direct the Protein Data Bank<br />EIC PLoS Computation...
What Has Happened for Me Post PDF Workshop?<br />Good news: Seen small shifts in the reward system<br />Bad news: See the ...
The Data Journal Posting<br />Response to the lack of innovation from HHMI/Wellcome/MP<br />A reward enough for publishing...
The Data Journal Response<br />Don’t reinvent the wheel<br />We have a technical solution!<br />Can we/should we review it...
Finally Getting onto Workflows!<br />Presented the TB druggome as the BtPDF challenge<br />Subsequently been working with ...
Status<br />Its hard and embarrassing<br />We have a working prototype using Wings<br />I can feel the potential productiv...
Yes Its Real<br />
Workflow – Tentative Plan<br />Have a new fellow who will use it to compute the T brucei(causative agent of sleeping sickn...
What Do I Want Out of This?<br />A clear way to contribute:<br />Start or work with an existing data journal?<br />Engage ...
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Dagstuhl Workshop 15-18 Aug 2011

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Dagstuhl Workshop - The Future of Research Communications

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Dagstuhl Workshop 15-18 Aug 2011

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