1. Richard LeDuc, Ph.D. (Manager)
National Center for Genome Analysis Support Leverages XSEDE Resources to Support Life Scientists
William K. Barnett, Ph.D. (Director)
Richard LeDuc, Ph.D. (Manager)
National Center for Genome Analysis Support
XSEDE 2013, San Diego CA, 7/23/2013

2. Summary What is NCGAS? What do we do? How do we do it?
I will assume you know more about HPC than biology.
National Center for Genome Analysis Support:

3. Funded by National Science Foundation
Large memory clusters for assembly
Bioinformatics consulting for biologists
Optimized software for better efficiency
Collaboration across IU, TACC, SDSC, and PSC.
Open for business at:

4. Making it easier for Biologists
Common
Rare
Computational Skills
LOW
HIGH
Web interface to NCGAS resources
Supports many bioinformatics tools
Available for both research and instruction.

5. We Provide: Large RAM computational resources Appropriate storage
Data transport assistance
IT (help-desk-like) Support
Bioinformatic Consultation and support

6. The services announced today include:
Storage of up to 50 terabytes of research data on IU's Scientific Data Archive tape storage system.
Services for curation and long-term storage of data sets and final results from genome research in the IUScholarWorks…
• NCGAS will write letters of commitment for consulting, computation, and data storage resources to include with grant proposals …

7. Service Continuum
Focus

8. Staffing 3.7 FTE Direct Staff
I’m a biologist with 15 years software engineering experience
PhD Computer Scientist
Full-time Bioinformatic Analyst
50% of a PhD Genomicist
20% of people above me
But we have direct access to the rest of our partner supercomputing centers
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11/22/2018

9. NCGAS Cyberinfrastructure at IU
Rockhopper: 11 servers with 48 cores and 128 GB RAM.
Mason large memory cluster: 16 nodes with 32 cores each and 512 GB RAM per node.
Data Capacitor: 1 PB at 20 Gbps throughput.
SDA – 17(+) PB hierarchical tape archive
Additional resources through our XSEDE partners
XRAC allocation
National Center for Genome Analysis Support:

10. Rockhopper
Penguin Computing's Penguin-On-Demand (POD) supercomputing cloud appliance hosted by Indiana University.
A collaborative effort between Penguin Computing, IU, the University of Virginia, the University of California Berkeley, and the University of Michigan.
Provides supercomputing cloud services in a secure US facility.
Researchers at US institutions of higher education and Federally Funded Research and Development Centers (FFRDCs) can purchase computing time from Penguin Computing, and receive access via high-speed national research networks operated by IU.
National Center for Genome Analysis Support:

11. Standardized Trinity Analyses
National Center for Genome Analysis Support:

12. Who do we serve?

13. Zhao et al. BMC Bioinformatics 2011, 12(Suppl 14):S2
Haas, B., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P., Bowden, J., Couger, M., Eccles, D., Li, B., Lieber, M., MacManes, M., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C., Henschel, R., LeDuc, R., Friedman, N., and Regev, A. (2013) De novo transcript sequence reconstruction from RNA-Seq using the Trinity platform for reference generation and analysis, Nature Protocols, in press.

14. The Project
A project represents a single NSF grant, or similar for Server-on-Demand services.
Projects are inherent organic organizational structures used in biology.
Researchers know what projects they are on, who else is on the project, what the project is trying to accomplish etc.
Projects are frequently widely distributed.

15. Projects
“SUGAR”: Schaack lab Undergraduate Genome Analyses at Reed

16. Projects as of Early July 2013

17. How do we support Projects

18. Support varies by Project need
Most projects just need access to the resources, and some technical support.
Other projects require more staff interaction; up to and including intellectual contributions to the project.
Several projects have utilized “private” Galaxy instances.

20. GALAXY.NCGAS.ORG Model Quarry Mason
NCGAS establishes tools, hardens them, and moves them into production.
Virtual box hosting Galaxy.ncgas.org
The host for each tool is configured individually
Individual projects can get duplicate VMs.
Quarry
Mason
Each project can get 50 TB of archive space for raw data.
Policies guarantee that untouched data is removed with time.
Data Capacitor
Archive

21. Current System Globus On-line and other tools Lustre WAN File System
NCGAS Mason
(Free for
NSF users)
100 Gbps
Your Friendly
Neighborhood
Sequencing Center
Optimized Software
Lustre WAN File System
Globus On-line and other tools
IU POD
(12 cents
per core hour)
Data Capacitor
NO data storage Charges
Your Friendly
Neighborhood
Sequencing Center
Other NCGAS XSEDE Resources…
How this works at scale:
Biologists use Galaxy to execute workflows
Sequence data mounted via Lustre WAN or automatically transferred using Internet2
Data Capacitor flows data into Mason or other computational clusters
Data Capacitor mounts or mirrors reference data from NCBI or other sources
Results delivered through web interfaces and to visualization or other science tools
10 Gbps
Your Friendly
Neighborhood
Sequencing Center

22. Future Direction

23. NCGAS gives back to XSEDE
NCGAS is a Tier 2 XSEDE Partner.
XSEDE allocations are available on Mason (our large RAM cluster).
300,000 SU’s of 0.5 TB RAM nodes with NCGAS support software.

24. Thank You Questions? Bill Barnett Rich LeDuc Le-Shin Wu Carrie Ganote
Tom Doak