A web-based work environment developed at the Renaissance Computing Institute (RENCI) will give users of the National Science Foundation’s TeraGrid easy access to a wide range of bioinformatics and biomedical applications and databases and will allow the national biology research community to access computing, data, and other resources offered through the TeraGrid.
The TeraGrid Bioportal is a shared, extensible portal environment that brings together more than 100 applications and many standard biological data sets. It provides access to high-end computing resources, including a dedicated cluster and TeraGrid systems across the U.S. Through the Bioportal, biological researchers, students and educators are able to seamlessly access data, resources and applications, compare biological data stored in different formats and remotely collaborate with colleagues.
The portal builds on the success of the North Carolina Bioportal, which was developed by RENCI for use by researchers and educators in North Carolina with seed funding from the University of North Carolina’s Office of the President. Development of the portal for TeraGrid users was supported by the TeraGrid Science Gateways program. RENCI also receives support from the National Institutes of Health for work integrating evolutionary biology and biomedical tools into the Bioportal.
“By incorporating the Bioportal into the TeraGrid infrastructure we are giving a large community of researchers in genomics, proteomics, molecular biology and other fields access to a nationwide network of high-end resources,” said Dan Reed, director of RENCI and principal investigator on the Bioportal TeraGrid Science Gateway project. “These are researchers whose work will have far-reaching impacts. They are uncovering relationships between genetics and human diseases, developing new treatments and even finding cures.”
The Bioportal is an open source framework that builds on emerging grid technologies from the National Science Foundation Middleware Initiative (NMI) and the Open Grid Computing Environment (OGCE) tool suite. Its grid middleware layer is based on Globus, the fundamental open source software for sharing resources and tools across distributed sites, and MyProxy, the grid credential management system. Bioportal resources support a number of common research activities, including database searching, alignment and phylogeny, pattern searching, DNA/RNA analysis and protein analysis. In addition to offering access to TeraGrid resources, the TeraGrid version of Bioportal offers a number of new features, including:
- new versions of widely used open source bioinformatics applications
- automated file format conversion
- enhancements to security policies to align with campus policies.
“The Bioportal project is an excellent example of the how the TeraGrid Science Gateway projects are extending the capabilities of the TeraGrid and providing access to this national cyberinfrastructure facility for a wider community of users,” said TeraGrid Director Charlie Catlett of Argonne National Laboratory and the University of Chicago.
Before the end of the year, RENCI will incorporate a workflow system into the Bioportal that will allow users to chain applications together for multifaceted analyses. Workshops for researchers, educators and students also are planned.
RENCI…Catalyst for Innovation
The Renaissance Computing Institute (RENCI) is a catalyst for innovation in science, engineering, the arts, humanities, and commerce. It fosters multidisciplinary collaborations by leveraging and applying leading edge compute, network, and data information technology resources and capabilities. RENCI is a joint institute of the University of North Carolina at Chapel Hill, Duke University, and North Carolina State University that combines the strengths of these three institutions with the social, business and research opportunities of the Research Triangle Park and the state of North Carolina. For more, see www.renci.org.
The TeraGrid, sponsored by the National Science Foundation Office of Cyberinfrastructure, is a partnership of people and comprehensive resources that enables discovery in U.S. science and engineering research. Through high-performance network connections, the TeraGrid integrates a distributed set of high capability computational, data management and visualization resources to make U.S. research more productive. With Science Gateway collaborations and education and mentoring programs, the TeraGrid also connects and broadens scientific communities.