Big Data Repository for Structural Biology:

Challenges and Opportunities

Piotr Sliz, PhD sliz@hkl.hms.harvard.edu

!SBGrid: http://sbgrid.org

SBGrid Data Bank: http://data.sbgrid.org Twitter: @SBGrid

YouTube: SBGridTV

SBGrid Consortium

Support Center at Harvard Medical School 300 Research Groups 13 Countries Long Term Sustainability: Membership Fee

Harvard Medical!School

SBGrid supports compilation, installation and upgrades of ~300 scientific applications

Several Software Categories (EM, NMR, Xrays, Comp Chem, etc.) Multiple versions of most applications OS X (10.6-10.10) and Linux support (CentOS 5-7) No additional, end-user configuration required

Software always works = more time for research

Core Mission:

Grid Computing (Open Science Grid VO + Grid Portal) General Research Infrastructure (Boston Area) Training (workshops, software cataloguing, webtales)

Webinars at youtube.com/SBGridTV Developer Resources Advocating for Open Source Software

Morin et al. Shining Light into Black Boxes. Science, 2012.

Other Activities:

Additional!Publications

Primary Citation:

Other Citations:

New Opportunity: Data

anonymous SBGrid member 1: “we cannot find the original frames for many of our structures (move from X to Y), including recent high impact projects. What do you recommend that we do?”

anonymous SBGrid member 2: “I was able to locate the data directory but I must have done a good job cleaning up the disk space before I left: usually there are only two .img files left in the data directory, the 1st and the last image of a full run.”

Lack of Storage Support for Diffraction Images

derive reproduce improve correct

• Stokes-Rees, I., Levesque, I., Murphy, F.V., Yang, W., Deacon, A., and Sliz, P. (2012). Adapting federated cyberinfrastructure for shared data collection facilities in structural biology. J Synchrotron Radiat 19, 462–467.

• Terwilliger, T.C., and Bricogne, G. (2014). Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data. Acta Crystallogr. D Biol. Crystallogr. 70, 2533–2543.

• Terwilliger, T.C. (2014). Archiving raw crystallographic data. Acta Crystallogr D Biol Crystallogr. • Guss, J.M., and McMahon (2014). How to make deposition of images a reality. Acta Crystallogr. D Biol. Crystallogr. 70,

2520–2532

Focus on Primary Data

SBGrid Data Bank. Pilot: May 1st, Production: June 1st, 2015

EZID

Dataset Lock BIODBCORE-­‐000683

re3data.org

Data Mining and

Annotation

Web Interface

Related!Datasets

Depositors:

URL: data.sbgrid.org

Dataset Landing Page

DataCite!Schema CC0 License

DownloadDataset URL

Current Statistics

Publication Workflow:

Data Access Alliance:

Make Data easily accessible for reprocessing Minimize Project Cost Increase Redundancy

ChallengesDataset Size (APIs, Data Access Alliance) Journal + Data Automation

automated embargo release cross-referencing coordination/communication with journals Data vs Journal Citations

Metrics: Dataset Deposition Rates Data Use: DAA Membership vs. direct downloads Dataset Quality (Level 0-2) Data Citations

Master Format OME-TIFF vs DataCite vs DataVerse schema

Transition to a Research Data Management Software ORCID integration and adoption

Opportunities

Better support to ~300 structural biology laboratories: Compliance Reproducibility Integration with PDB and other repositories Other data types in addition to X-ray diffraction

Thank you

Piotr Sliz, PhD sliz@hkl.hms.harvard.edu

!SBGrid: http://sbgrid.org

SBGrid Data Bank: http://data.sbgrid.org !

Twitter: @SBGrid YouTube: SBGridTV

Stephanie Socias

Pete Meyer

Merce Crosas