Renaissance Computing Institute: An Overview Lavanya Ramakrishnan, John McGee, Alan Blatecky, Daniel A. Reed lavanya@renci.org Renaissance Computing Institute.
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Renaissance Computing Institute: An Overview
Lavanya Ramakrishnan, John McGee, Alan Blatecky, Daniel A. Reed
lavanya@renci.org
Renaissance Computing InstituteDuke University
North Carolina State University University of North Carolina - Chapel Hill
RENCI: A Catalyst for Innovation
• A multidisciplinary institute– Duke, UNC, NCState, …
• Economic development– helping companies and people
• Inter disciplinary research engagement – biology, humanities, atmospheric sciences, etc
• Education and outreach– providing hands on experiences– training the next generation work force
www.renci.org
Next Generation CyberInfrastructure
• Regional vision, national visibility– national and international coupling – standards-based tools and infrastructure
• Infrastructure to support the science– computing, communications and data
management, visualization
RENCI/UNC Health Sciences Library
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Research Project Focus Areas• Scalable Performance Tools
– adaptive resource management – real-time performance and fault indicating data – SvPablo, HAPI, Autopilot, etc.
• Data Access & Federation– data and metamodels – information visualization
• Bioinformatics and Biomedical– shared, extensible portal infrastructure– genetics, hapmap simulator, etc
• Disaster Response– storm surge modeling (SCOOP), – dynamic, adaptive workflows (LEAD)
Integrated Disaster Response
• SURA Coastal Ocean Observing Program– Integrated Ocean Observing System
(IOOS) – event drive storm surge modeling and
forecast system
• NSF ITR Linked Environments for Atmospheric Discovery (LEAD)– an integrated, scalable cyberinfrastructure – performance monitoring and adaptation – fault-tolerance, performability and recovery
BioScience Communities
• The Carolina Center for Exploratory Genetic Analysis– preliminary planning grant for a national center– develop a prototype informatics infrastructure
• BioScience Gateways– initial seed funding from UNC-OP – TeraGrid deployment– leverage state-wide investment in bioinformatics and grid– undergraduate education, graduate education, faculty research
More on the Bioportal/BioScience Gateway!
Current BioScience Applications• Applications
– ~140 distinct codes• Application Suites
– EMBOSS• European Molecular Biology
Open Software Suite– GLIMMER
• gene identification in microbial DNA
– HMMER• Hidden Markov Model program
for profile-based sequence analysis
– NCBI• diverse set of tools
– PHYLIP• PHYLogeny Inference Package
for inferring phylogenies • Others (incomplete list)
– ClustalW, FASTA
• Standard bioinformatics databases– NCBI Aggregate (95 GB)
• three formats: native, BLAST and WUBLAST
– GenBank (206 GB)– GenPept (3 GB)– PDB (6.3 GB)– Prints (72 MB)– RepBase (8.6 MB)– UniProt (12 GB)– PFam (8.7 GB)– ProSite (16 MB)– TransFac (36 MB)
• Database update mechanism– follows the schedule of the
distribution source– currently NCBI Aggregate is the
only one updated nightly
Leveraging the TeraGrid
• BioScience and Biomedical Gateway
• Adapt the portal to use TeraGrid Resources– Support the Community Account usage model– Enhanced logging and tracking– New Distributed Administration features– Resource Site prep: Pre-Reqs, App deployment, etc
• Further decoupling of the web application tier and back-end computing tier
Future Directions
• Comprehensive BioScience Discovery and Learning Environment
• Hosting environment for RENCI production and research software
• Outreach and training
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