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

It is all about partnerships!

TAMULSU

UF

UNC, MCNC

UAHb

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