Dagstuhl Workshop 15-18 Aug 2011Presentation Transcript
Making Beyond the PDF Current Practice Phil Bourne firstname.lastname@example.org
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
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
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?
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
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
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
Yes Its Real
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
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?