North Carolina Bioinformatics Grid Thom H. Dunning, Jr. HPCC Division, MCNC Chemistry, University of North Carolina

Genomics A Compute- & Data-Intensive Science * from TimeLogic

Data Explosion Rapid Growth of GenBank No. Gbases Growth of GenBank  Number of base pairs increasing dramatically (exponentially)  Growth in 2002 due to additions in just 21 days!

Data Explosion Number and Diversity of Databases Nucleic Acids Research, 2002, Vol. 30, No. 1 Table 1. Molecular Biology Database Collection Major Public Sequence Repositories DNA Data Bank of Japan (DDBJ) known nucleotide and protein sequences … Varied Biomedical Content … VirOligohttp://viroligo.okstate.eduVirus-specific oligonucleotides for PCR and … 333 Databases

Computing Explosion Assembly and Analysis of Genomic Data Celera Genomics–Assembling the Genome Compaq Alpha Clusters Number of processors: ~ 750 Peak performance: 1 teraops NuTech Sciences–Mining the Genome IBM p640 System Number of processors: ~ 5,000 Peak performance: 7½ teraops Total memory: 2½ terabytes Total disk storage: 50 terabytes

Genomics Meeting the Information Challenge Grid Middleware Data Storage Computers Network

North Carolina Supercomputing Center

North Carolina Research and Education Network Greensboro Charlotte Pembroke Winston Salem NCSU Centennial Campus NCCU Duke UNC-CH Wilmington Elizabeth City Asheville Cullowhee Fayetteville Greenville RTP MCNC Boone Morehead City Rocky Mount Qwest RTP RPoP NCREN3 Increased bandwidth Increased reliability Increased resiliency

Grid Technologies Major New Computing Technology Under development since mid-1990s Distinguishing Characteristics “Middleware” to support efficient resource sharing in a distributed, heterogeneous computing and data storage environment Focus on use of large-scale computing and data storage Some Major Grid Efforts NASA IPG—Testbed linking selected NASA centers DataGrid—International Grid being developed for high- energy physics (CERN)

Grid Technologies ( cont’d ) Some Major Grid Efforts (cont’d) GriPhyN—Research in Grid technologies for physics applications (Argonne, Florida) e-Science Grid—Major effort in UK to develop a Grid infrastructure for science and engineering research BIRN—Data Grid focused on neuroimaging data (UCSD, SDSC)

North Carolina Genomics and Bioinformatics Consortium Goal Provide a venue for Consortium members to share information and resources, plan strategic initiatives, and form alliances Distributed Across North Carolina Concentration in Research Triangle, but extends across all of North Carolina Diverse Goals and Expertise Human health, including animal models; agriculture and forestry; evolutionary biology basic research; tool development

Overall NC BioGrid Architecture Computing and Data Resources Network Grid Middleware BioApp #1 BioApp #2 BioApp #3 … Globus, Legion, … Grid-aware, -enabled bioinformatics applications NCREN3 NCSC plus Member’s Computing Centers

NC BioGrid Project Two Phases Testbed Phase—test existing middleware, resolve issues, prepare detailed plan (12-18 months) Production Phase—create and operate NC BioGrid Funding for Testbed from MCNC Project Manager Phil Emer, MCNC, Chief Architect/NC BioGrid Project Oversight MCNC Board of Directors HPCC Advisory Board NC BioGrid Technical Advisory Group