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.
- University of North Carolina, Office of the President
- NSF TeraGrid Project
- State of North Carolina
- Judson Knott, Information Technology Services, UNC-Chapel Hill
- Hemant Kelkar – Center for Bioinformatics, UNC-Chapel Hill
- Sylvia Harrison, Wake Technical Community College
- Charles Schmitt, project manager
- John McGee
- Kevin Gamiel
- Mark Reed
- Ruth Marinshaw
- Michael Shoffner
- Timothy A. Chagnon, Wake Technical Community College
- David Fargo, Tom Randall, Center for Bioinformatics, UNC-Chapel Hill
- UNC Research Computing Group, UNC-Chapel Hill
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.
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.
Lavanya Ramakrishnan, “Building the Bioscience Gateway,” Global Grid Forum, June 2005.
- 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