Sun Center of Excellence for Visual Genomics at the University of Calgary

Three-Dimensional Visualization Environment for Genetics Research Based on Full Sun Solution

The Sun Center of Excellence for Visual Genomics at the University of Calgary is a non-profit organization that is advancing technology for computational biology based on Sun solutions. It helps researchers in many ways, including identifying specific gene sequences and their functions, and by creating an advanced three-dimensional visual model of the human body that can be studied.

Customer Challenges

Provide a reliable, flexible, scalable and efficient solution for data-intensive processing needs
Deliver broad, secure access to innovative applications
Implement an efficient, cost-effective storage architecture to enable data storage in perpetuity

Solution

Through tight collaboration with Sun, this organization is using Sun servers and storage systems, Sun virtual desktop solutions, the Solaris 10 Operating System and Java technology to offer innovative new applications in a scalable, stable and cost-efficient environment.

Business Results

Used Java to ensure broad access to resources and to provide ground-breaking visualization capabilities
Leveraged Sun Ray technology for secure, high-performance access to visualization solutions
Provided genetics analysis in a matter of hours as compared to weeks for alternative solutions
Implemented a Sun SAN infrastructure to store tens of millions of files in a four-tier architecture

Products and Services

Story Details

Dr. Christoph Sensen, head of the Sun Center of Excellence at the University of Calgary, has been advancing the field of genetics research for the past 14 years with the help of Sun technology.

One key initiative for the center is a Java 3D-enabled CAVE, a recursive acronym which stands for CAVE Automated Virtual Environment. As the first bioinformatics visualization tool of its kind, this CAVE implementation enables 3D genetics data to be explored visually in an immersive chamber that can also simulate the passage of time. In May 2007, this center completed “CAVEman,” a 3D model of the human body. By applying specialized data sets, CAVEman can be used to study effects on the human body, such as drug reactions over time.

" Our applications need to push the edge of bioinformatics research while we address practical concerns like performance, data availability and a limited IT staff. Sun technology has been extremely stable and very flexible, which makes our job of advancing scientific research much easier. "

— Dr. Christoph Sensen, Director, Sun Center of Excellence for Visual Genomics of the University of Calgary

These applications are extremely data-intensive, requiring a highly stable, secure and powerful computing platform. In addition, a robust and cost-efficient storage technology is essential for the tens of millions of files that must be stored in perpetuity and served quickly.

The center initially chose a Sun Fire 6800 server as its computing platform due to its high throughput. The server has been upgraded over time so that it is now equivalent to a Sun Fire 6900 server with a total of 24 UltraSPARC processors and 96 GB of memory. A range of additional UltraSPARC-based servers further extend compute power and infrastructure services. These servers, equipped with FPGA processors and Sun clustering technology, assist in high-throughput database searches that identify gene sequences in raw data. By using Sun technology, the center has shortened each search process from weeks to hours.

Java and the Java 3D API were chosen as the development platform for the visualization software due to their portability and readily accessible base of programming skills. The custom Java-based visualization software runs on Sun Fire V440 and Sun Fire V880z servers with the Sun Shared Visualization software to enable 3D viewing. The output from this software can be viewed either in the fully immersive visualization CAVE designed by Fakespace Systems or with a Sun Ray solution.

The center leverages the stability and binary compatibility of the Solaris 10 Operating System to run its applications, including applications developed 14 years ago. With Solaris Containers, the center can easily create virtual servers that isolate test environments. It also uses ZFS to store backup images of the operating system.

For added flexibility, the staff uses Sun Ray virtual desktops for secure access to the center’s computing resources and Microsoft Windows applications. With Sun Secure Global Desktop software, the staff and researchers working remotely can log into the center’s resources from anywhere in the world.

The storage solution includes Sun StorageTek Storage Archive Manager with the Quick File System (SAM-QFS) software in a 229 terabyte four-tier architecture that provides policy-based data serving from a range of Sun StorageTek disk and tape hardware solutions. Sun Honeycomb technology is part of this infrastructure, since it is well-suited to low-cost intelligent storage of annotated genetics information. For added protection, all data is replicated to a remote Sun StorageTek L700e tape library.

This comprehensive Sun platform boosts productivity. Today, 2 system administrators proactively manage an operation that includes many domains on more than 100 computing systems, over 500,000 Web site hits monthly and 28 databases.

Always looking to the future, Dr. Sensen is working with Sun to accelerate the rate at which new genetic information is recorded, from 1,000 genomes over the past 14 years to 1,000 genomes per week going forward. They are also considering commercializing some of the many advances that have come out of this center.