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North Carolina Bioportal

Overview
The North Carolina Bioportal is a shared, extensible bioinformatics portal for use by students, educators, teachers and bioinformatics researchers in North Carolina. It provides access to many tools and databases commonly used in bioinformatics research and is a tool for distributing and publishing new bioinformatics services and tools.  In 2006, the NC Bioportal was offered to the users of the National Science Foundation’s TeraGrid as the TeraGrid Bioportal, one of the TeraGrid Science Gateway efforts.

The project leverages several concurrent developments in North Carolina:

  • a substantial state commitment to bioinformatics and genomics,
  • the emergence of the Renaissance Computing Institute, a multidisciplinary institute which spans UNC-Chapel Hill, Duke and NC State universities,
  • continued support for bioinformatics research at UNC-Chapel Hill through the Center for Bioinformatics,
  • collaborative contributions by the high performance computing department at Wake Technical Community College.

The project builds on experience operating a bioinformatics portal for statewide use and on toolkits and standards for the use of portals, clusters and computational grids. The Bioportal infrastructure provides access to more than 100 diverse bioinformatics tools, 300 GB of data, distributed resources, and a web-based collaborative environment. The Bioportal framework builds on emerging grid technologies from the NSF Middleware Initiative (NMI). The portal is based on the Open Grid Computing Environment (OGCE) tool suite and the grid infrastructure is based on Globus and MyProxy. The bioinformatics user interfaces are based on PISE, an XML tool that has descriptions for each application's interface and the logic to process these applications. This integrated framework provides an infrastructure which allows researchers to work more efficiently and effectively. Bioportal is also an educational tool, which introduces students to the basics of bioinformatics research using the same tools as academic research teams.

The RENCI Contribution
RENCI continues to lead the Bioportal development effort and now focuses on integrating new bioinformatics research tools developed at RENCI into the Bioportal infrastructure. These tools include workflows that automate and simplify many biological research processes and tools developed through the Carolina Center for Exploratory Genetic Analysis.

Funding
University of North Carolina, Office of the President
NSF TeraGrid Project
State of North Carolina

Principal Investigators
Judson Knott, Information Technology Services, UNC-Chapel Hill
Hemant Kelkar – Center for Bioinformatics, UNC-Chapel Hill
Sylvia Harrison, Wake Technical Community College

RENCI team members
Charles Schmitt, project manager
John McGee
Kevin Gamiel
Mark Reed
Ruth Marinshaw

Other collaborators
Timothy A. Chagnon, Wake Technical Community College
David Fargo, Tom Randall, Center for Bioinformatics, UNC-Chapel Hill
UNC Research Computing Group, UNC-Chapel Hill

Publications
Lavanya Ramakrishnan, Mark S.C Reed, Jeffrey L. Tilson, Daniel A. Reed, Grid Portals for Bioinformatics, Second International Workshop on Grid Computing Environments (GCE), Workshop at SC|06, November 2006, Tampa, Florida
Daniel A. Reed, et.al. "Building the Bioscience Gateway," Global Grid Forum Technical Paper, June 2005.

Presentations
Daniel A. Reed, "North Carolina Bioportal," Global Grid Forum, June 8, 2005.
Daniel A. Reed, "Bioinformatics and the Bioportal," North Carolina HPC Advisory Committee Meeting, August 15, 2005.   ncbioportal/NC_HPC_Meeting_081505.pdf
Lavanya Ramakrishnan, "Building the Bioscience Gateway," Global Grid Forum, June 2005.

Partners
Information Technology Services, UNC-Chapel Hill
Center for Bioinformatics, UNC-Chapel Hill
GridNexus Project, University of North Carolina at Wilmington
High Performance Computing Department, Wake Technical Community College
RENCI

Links
NC Bioportal Home Page
TeraGrid Science Gateway

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