Dagstuhl Workshop 15-18 Aug 2011

Making Beyond the PDF Current Practice
Phil Bourne
pbourne@ucsd.edu

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?

Dagstuhl Workshop 15-18 Aug 2011

by Philip Bourne

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