SBGrid (Morin et al., 2013, eLIFE and www.sbgrid.org) is a Harvard based structural biology global computing consortium with a primary focus on the curation of research software. Dr. Sliz will discuss a recent SBGrid project that aims to establish a repository for experimental datasets from SBGrid laboratories. Issues of handling large data volumes, data validation and repository sustainability will be addressed in this talk.

1. 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

2. 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:

3. 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

4. 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

5. Web
Interface
Related!
Datasets
Depositors:
URL: data.sbgrid.org
Dataset Landing Page
DataCite!
Schema CC0 License
Download
Dataset URL

6. Current Statistics
Publication Workflow:

7. Data Access Alliance:
Make Data easily accessible for reprocessing
Minimize Project Cost
Increase Redundancy
Challenges
Dataset 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

8. 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