Building an Information Infrastructure to Support Genetic Sciences
1. “ Building an Information Infrastructure to Support Genetic Sciences " Invited Talk Celebrating a Decade of Genome Sequencing UCSD La Jolla, CA December 6, 2005 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technology; Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD
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3. Genomic Data Is Growing Rapidly, But Metagenomics Will Vastly Increase The Scale… GenBank Protein Data Bank www.rcsb.org/pdb/holdings.html www.ncbi.nlm.nih.gov/Genbank 100 Billion Bases! Total Data < 1TB 35,000 Structures
4. Metagenomics Will Couple to Earth Observations Which Add Several TBs/Day Source: Glenn Iona, EOSDIS Element Evolution Technical Working Group January 6-7, 2005
5. Challenge: Average Throughput of NASA Data Products to End User is < 50 Mbps Tested October 2005 http://ensight.eos.nasa.gov/Missions/icesat/index.shtml Internet2 Backbone is 10,000 Mbps! Throughput is < 0.5% to End User
6. Why Optical Networks Will Become the 21 st Century Driver Scientific American, January 2001 Number of Years 0 1 2 3 4 5 Performance per Dollar Spent Data Storage (bits per square inch) (Doubling time 12 Months) Optical Fiber (bits per second) (Doubling time 9 Months) Silicon Computer Chips (Number of Transistors) (Doubling time 18 Months)
7. Solution: Individual 1 or 10Gbps Lightpaths -- “Lambdas on Demand” ( WDM) Source: Steve Wallach, Chiaro Networks “ Lambdas”
8. National Lambda Rail (NLR) and TeraGrid Provides Cyberinfrastructure Backbone for U.S. Researchers San Francisco Pittsburgh Cleveland San Diego Los Angeles Portland Seattle Pensacola Baton Rouge Houston San Antonio Las Cruces / El Paso Phoenix New York City Washington, DC Raleigh Jacksonville Dallas Tulsa Atlanta Kansas City Denver Ogden/ Salt Lake City Boise Albuquerque UC-TeraGrid UIC/NW-Starlight Chicago International Collaborators NLR 4 x 10Gb Lambdas Initially Capable of 40 x 10Gb wavelengths at Buildout NSF’s TeraGrid Has 4 x 10Gb Lambda Backbone Links Two Dozen State and Regional Optical Networks DOE, NSF, & NASA Using NLR
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10. Prototyping Cabled Ocean Observatories Enabling High Definition Video Exploration of Deep Sea Vents Source John Delaney & Deborah Kelley, UWash Canadian-U.S. Collaboration
11. A Near Future Metagenomics Fiber Optic Cable Observatory Source John Delaney, UWash
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13. Driving Cyberinfrastructure with Environmental Metagenomics Samples Collected by Sorcerer II Approved Yesterday!
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15. Metagenomics “Extreme Assembly” Requires Large Amount of Pixel Real Estate Source: Karin Remington J. Craig Venter Institute Prochlorococcus Microbacterium Burkholderia Rhodobacter SAR-86 unknown unknown
16. Metagenomics Requires a Global View of Data and the Ability to Zoom Into Detail Interactively Overlay of Metagenomics Data onto Sequenced Reference Genomes (This Image: Prochloroccocus marinus MED4) Source: Karin Remington J. Craig Venter Institute
17. The OptIPuter – Creating High Resolution Portals Over Dedicated Optical Channels to Global Science Data Green: Purkinje Cells Red: Glial Cells Light Blue: Nuclear DNA Source: Mark Ellisman, David Lee, Jason Leigh 300 MPixel Image! Calit2 (UCSD, UCI) and UIC Lead Campuses—Larry Smarr PI Partners: SDSC, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST
18. Scalable Displays Allow Both Global Content and Fine Detail Source: Mark Ellisman, David Lee, Jason Leigh 30 MPixel SunScreen Display Driven by a 20-node Sun Opteron Visualization Cluster
19. Allows for Interactive Zooming from Cerebellum to Individual Neurons Source: Mark Ellisman, David Lee, Jason Leigh
20. Calit2 Intends to Jump Beyond Traditional Web-Accessible Databases Data Backend (DB, Files) W E B PORTAL (pre-filtered, queries metadata) Response Request + many others Source: Phil Papadopoulos, SDSC, Calit2 BIRN PDB NCBI Genbank
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23. The OptIPuter Enabled Collaboratory: Remote Researchers Jointly Exploring Complex Data New Home of SDSC/Calit2 Synthesis Center Calit2/EVL/NCMIR Tiled Displays with HD Video Source: Chaitan Baru, SDSC Source: Mark Ellisman, NCMIR
24. Eliminating Distance to Unify Remote Laboratories SIO/UCSD NASA Goddard www.calit2.net/articles/article.php?id=660 August 8, 2005 HDTV Over Lambda OptIPuter Visualized Data 25 Miles Venter Institute
25. Looking Back Nearly 4 Billion Years In the Evolution of Microbe Genomics Science Falkowski and Vargas 304 (5667): 58