Customer Success Story Delaware Biotechnology Institute—University of Delaware
On the Web www.sun.com/grid
“Sun has given us future flexibility as we continue to grow and expand. The products have been easy to deploy, and when we have questions or need help, we know exactly who to call.” – Dr. Karl Steiner, Associate Director, Delaware Biotechnology Institute and Professor of Electrical and Computer Engineering, University of Delaware
Organization
Delaware Biotechnology Institute — University of Delaware
Business
Biotechnology-based research, education, and economic development
Key Business Challenges
The Delaware Biotechnology Institute needed to increase its compute capacity and selected Grid Computing to enable researchers to expand the scope of their work, to establish a statewide network, to compete successfully for federal funding, and to form research and business partnerships with pharmaceutical and biotechnology firms.
Key Business Solutions
The Delaware Biotechnology Institute implemented a Sun™ Infrastructure Solution for Grid Computing that utilizes Sun™ Grid Engine Enterprise Edition and Sun™ Control Station software to manage a 128 dual-node grid comprised of Sun Fire™ V60x servers. Meanwhile, a Sun Fire 4800 server handles the institute's database functions.
A Solution to Support Leading-Edge Research
The Delaware Biotechnology Institute–University of Delaware is a partnership between government, academia, and industry to help establish the First State as a center of excellence in biotechnology and the life sciences. The institute’s mission is to build and facilitate an interdisciplinary, statewide biotechnology network to enhance existing research, catalyze cross-disciplinary education and collaboration, and create new economic opportunities. Research is conducted in human health, agriculture, engineering, marine ecosystems, and the environment.
Under a large NIH-NCRR grant, the Delaware Biotechnology Institute is leading the effort to build a statewide Biomedical Research Infrastructure Network (BRIN) comprised of the state’s institutions of higher education: University of Delaware, Delaware State University, Delaware Technical & Community College, Wesley College, and the state’s largest hospital system— Christiana Care Health System. Research at the institute is supported by state-of-the-art core instrumentation centers, including mass spectroscopy, DNA and protein sequencing, structural biology, bioimaging, and common laboratories. The Delaware Biotechnology Institute’s Bioinformatics (BioIT) Center provides computing resources to researchers within the network, fostering a truly collaborative and interdisciplinary environment. Delaware Biotechnology Institute leadership believes that Delaware can be a major center for biotechnology, capable of competing on a national and international level. This requires top-notch scientists and researchers with access to state-of-the-art instrumentation and a flexible and expandable computing solution with the capacity to support leading-edge research.
Sun assessed the existing environment in the BioIT Center and proposed a Sun™ Infrastructure Solution for Grid Computing to provide for their current and future resource demands. Sun Architecture and Implementation Service for Grid Computing helped the BioIT Center create and implement “Biowolf,” the institute’s new Grid Computing infrastructure. A separate Sun Fire™ database server organizes and collects the massive influx of biological data.
The Delaware Biotechnology Institute Plans for Growth
For the past two years, the BioIT Center employed a 12-processor Sun Fire 4800 with 1.3 TB of storage as both a computational and a database server. But it quickly became clear that to realize the goal of becoming a first-rate research facility for the state, the BioIT Center had to dramatically increase its computational capacity.
“As we began to plan for the expansion of the BioIT infrastructure, we looked at a variety of different computational models, and decided that the most logical architecture would be a grid,” says Dr. Karl V. Steiner, associate director of the Delaware Biotechnology Institute and professor of Electrical and Computer Engineering. “A grid would give us all the flexibility, expandability, and power we need, but would be comparatively cheap to deploy. Of course, that led to the question of which grid system to install.”
In reviewing its needs, the BioIT team compiled several specific guidelines:
Upon review of the proposals, the Delaware Biotechnology Institute decided that the best solution was provided by Sun.
Sun’s Grid Solution for the Delaware Biotechnology Institute
The University of Delaware and the Delaware Biotechnology Institute were well acquainted with Sun prior to the selection of its grid solution. Sun has provided computing solutions for the University of Delaware and cultivated an excellent relationship with the university.
In 2001, the Delaware Biotechnology Institute was named a Sun Microsystems Center of Excellence in High-Performance Computational Biology. “We were pleased to be recognized by Sun as a COE. Not only did we benefit from working directly with Sun to further our biotechnology research, but it has also linked us with a rich network of first-rate research institutions,” says Dr. Guang R. Gao, professor of Electrical and Computer Engineering and director of the BioIT Center.
“Sun’s price/performance ratio was the best among all proposals,” states Dr.
Douglas O’Neal, manager, BioIT Center. “We briefly considered a custom-built system, but these systems usually require high maintenance. We wanted our researchers and graduate students focusing on life science research— not computer maintenance.”
To gauge performance, the Delaware Biotechnology Institute asked the four top candidates for two nodes and then ran some in-house research code for benchmarking. In these tests, the Sun Fire V60x Compute Grid rack system performed the fastest. But Sun offered more than fast computers. “Other vendors offered their own solutions, but we were very impressed with Sun’s end-to-end solution,” continues O’Neal.
Sun’s Grid Computing Solutions greatly reduce management time while increasing research availability.
With Sun Infrastructure Solution for Grid Computing, hardware, software, and services are implemented as a complete grid infrastructure.
This fall, the Delaware Biotechnology Institute installed “Biowolf” in the BioIT Center, a Sun Fire V60x Compute Grid rack system with 128 dual nodes for computing tasks. The Delaware Biotechnology Institute’s existing Sun Fire 4800 server is now dedicated to database functions, ferrying data back and forth from the StorEdge™ T3 and 3510 RAID arrays. Funding for the Biowolf Grid was provided by the National Center for Research Resources (NCRR) at NIH under the BRIN and a Center of Biomedical Research Excellence (COBRE) program.
For system management, the BioIT Center employs Sun™ Grid Engine Enterprise Edition and Sun™ Control Station. With Sun Grid Engine Enterprise Edition, policy-based resource allocation distributes needed compute power to each research group or project without any project dominating the system.
“With so many researchers in our network, this feature is critical to provide everyone with the resources they need to accomplish their work,” O’Neal comments.
Sun Control Station handles all of the grid’s service provisioning, health and performance monitoring, update/patch-level control, custom software payloads, volume deployment, and distribution of software packages.
Steiner says that Sun has continually focused on giving the BioIT Center a complete solution, rather than simply providing fast machines. Once the solution was deployed, the grid infrastructure rapidly became the Delaware Biotechnology Institute’s computational workhorse. “Most people don’t even think about it being there, while it is flawlessly meeting the needs of faculty, researchers, and students.”
Sun’s Grid Solution at Work
Sun’s Grid Solution allows researchers from different disciplines to collaborate and share relevant data, enabling them to discover new knowledge from the Delaware Biotechnology Institute databases. Since computing resources are both readily available and equitably allocated, the institute fosters a truly collaborative environment. “No one is currently competing for computer time, and that helps keep my phone quiet,” O’Neal says.
In a list distributed at the Supercomputing 2003 Conference, the Delaware Biotechnology Institute Biowolf Grid was ranked among the top 30 most powerful supercomputers among U.S. academic institutions. “When we told researchers about this ranking, they were ecstatic,” Steiner observes. “I could sense them already thinking in new dimensions— conceiving new research projects that would take advantage of this significant computational resource.”
With Sun’s Grid Solution, researchers can perform tasks that require significant amounts of computing power. Researchers can expand the scope of their work and compete successfully for federally funded research programs.
The grid also makes the developing statewide network an attractive partner for the large number of commercial pharmaceutical and biotechnology firms that are located in the northeastern Boston-Washington, D.C., corridor.
In the five years since the institute was established, researchers have taken full advantage of the significant infrastructure put in place. Among other success stories, Delaware has been able to triple its amount of federal research funding. “In some cases, individual faculty grants have grown from $50K-100K each to collaborative grants of $500K-$1M,” Steiner notes.
“With these funds,” he continues, “ our researchers are able to conduct more ambitious studies in fields such as protein folding, oncologene expression, and full-genome comparison.”
Dr. Yong Duan, assistant professor at the University’s Biochemistry Department, uses Biowolf to conduct ab initio calculations to study the way proteins fold and how proteins interact with one another. These types of calculations require huge amounts of computing power because of the complexity of proteins. Knowledge gained from these studies can help researchers interpret genetic information. While the actual process of protein folding may take only nanoseconds in nature, simulating this process is highly complex and requires significant computing resources. As a direct benefit of the installation of the Sun Biowolf cluster, more and more molecule models can be added to the study. With the grid, calculations that used to take a week can now be performed in a single day.
Dr. Guang R. Gao, BioIT Center director, has been conducting research in applying high-performance computing technology to challenging problems in computational biology and bioinformatics. “We are in the process of porting several computational biology and bioinformatics algorithms to the Sun Biowolf Grid,” Gao says. These algorithms include new methods for aligning multiple genomic sequences, the comparison of entire genomes, and protein classification algorithms. “In the future, we plan to use the grid for parallel medical imaging algorithms and for biological systems modeling,” Gao continues. “We have no doubt that these projects will encourage and foster interesting and important thesis research topics that would not be possible without the new Sun Grid system.”
Sun Helps Position the Delaware Biotechnology Institute for the Future
For now, the Sun Infrastructure Solution for Grid Computing provides the Delaware Biotechnology Institute with the computing muscle to attract top talent into the statewide biotechnology network. "By giving researchers the resources they need to conduct outstanding science, we feel that Delaware is in an excellent position to compete successfully in the life science environment,” says Steiner.
However, the Delaware Biotechnology Institute’s growing success requires continuous improvement, and the institute recently had to double its StorEdge T3 capacity from 1.3 TB to 2.6 TB with a Sun StorEdge 3510. When the time comes to expand the Biowolf Grid, Steiner is confident that the Sun Infrastructure Solution for Grid Computing will be ready.
Customer Success Story Delaware Biotechnology Institute—University of Delaware On the Web www.sun.com/grid
