Called a workflow, this technology automates many redundant processes used in analyzing biological problems, such as launching a group of applications and moving data among applications to achieve a scientific goal. Workflows aim to take the “busy work” out of science. Instead of reentering data in countless different formats to accomplish different steps in problem solving, the scientist simply loads the data into the front end of the workflow and lets the underlying infrastructure handle the busy work.

The first workflow offered through the Bioportal is called Gene2Life, developed through collaboration with the Center for Bioinformatics at the University of North Carolina at Chapel Hill. The Gene2Life workflow uses as input either a DNA or a protein sequence and compares that sequence to current databases of known sequences to determine its closest relatives. The workflow generates a “tree,” which depicts the relationships among the user input sequence and homologous sequences retrieved from the sequence databases. Gene2Life could be a useful first step for researchers examining either the function or the evolutionary origin of a sequence of interest.

“Workflows are all about letting the scientist concentrate on science and delegating the computational work to an underlying infrastructure,” said RENCI Director Dan Reed. “In talking to biologists, we’ve found that many of them are frustrated by the time they spend at repetitive tasks like reformatting data for every step in an analysis. Using the Bioportal and the workflows we are integrating into it, we aim to give them more time to concentrate on what they do best.”

The Gene2Life workflow, which is an automated system designed for a particular type of analysis, is the first of several targeted workflows in development. Over the next six months, RENCI researchers will develop a Bioportal infrastructure that will allow users to create and deploy their own customized workflows.

The awards were announced today at the GridWorld conference in Washington, D.C. RENCI received the following honor from GRIDtoday publisher Tom Tabor:

• Reader’s Choice Award: Research organization demonstrating the Most Innovative Grid Implementation in life sciences

“We appreciate the recognition from GRIDtoday,” said RENCI Director Dan Reed. “The RENCI Bioportal team has worked hard to develop a tool that makes conducting research on a grid more intuitive and more productive. The exciting thing is that the Bioportal is continuing to evolve and improve with the addition of workflows and new capabilities.”

The Bioportal (www.ncbioportal.org or www.tgbioportal.org ) is a shared, extensible portal environment that brings together more than 140 computational tools and applications and many standard biological data sets. RENCI began developing the portal as the North Carolina Bioportal in 2004 with seed funding from the University of North Carolina’s Office of the President. Funding from the TeraGrid Science Gateways program allowed RENCI to deploy the TeraGrid Bioportal, which allows TeraGrid researchers to use the portal and gives Bioportal users access to the high-performance computing resources of the TeraGrid. RENCI also receives support from the National Institutes of Health for work integrating evolutionary biology and biomedical tools into the Bioportal.

The GRIDtoday Readers’ and Editors’ Choice Awards were determined by a survey of thousands of GRIDtoday readers, and will be a permanent annual feature of the publication.  GRIDtoday has two categories of awards: (1) Readers’ Choice, where winners have been determined by a random poll of GRIDtoday readers, and (2) Editors’ Choice, where winners have been determined by votes of an advisory group of recognized luminaries, contributors and editors influential in Grid and Service-Oriented IT.

Grids are used in a wide range of research and development efforts, including automotive and aerospace, bioinformatics, humanities research, security and defense, financial services, government, manufacturing, oil and gas, and pharmaceuticals.

“We are very excited about this opportunity to articulate the views and opinions of our readers to recognize the accomplishments that are being made in advancing the development and adoption of Grid, Service-Oriented IT and virtualization,” said Tabor.  “These industry recognition awards send a strong message to the recipients that the many global contributors working in or watching this important computing segment recognize their work, and consider their efforts meritorious. Our congratulations go out to all the winners.”

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.

About Teragrid
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.

Relevant URLs
TeraGrid Bioportal
Official TeraGrid Website
North Carolina Bioportal