Applied Biosystems

Sun Helps Genomics R & D Group in Leading Life Sciences Company Get Critical Research Tools to Market in Record Time

A business group of the Applera Corporation, Applied Biosystems (AB), headquartered in Foster City, California, serves the life science industry and research community by developing and marketing instrument-based systems, consumables, software and services. Customers use these tools to analyze nucleic acids (DNA and RNA), small molecules and proteins to make scientific discoveries, develop new pharmaceuticals and conduct standardized testing.

Customer Challenges

Develop genotyping assays as quickly as possible, in response to newly released data
Access required compute resources securely and cost-effectively

Solution

Through Sun Grid Compute Utility, AB was able to perform the compute-intensive data research to develop millions of new genomic assays in a matter of days rather than months. In addition, because the company only had to purchase the number of hours required, at a rate of $1 per CPU hour, it avoided an investment in infrastructure that would have cost the company hundreds of thousands of dollars.

Business Results

Sped time to market of predesigned genotyping assays by reducing computing time from three months to six days
Eliminated the need to purchase additional hardware, saving the company several hundred thousand dollars
Simplified data management and delivery of results

Products and Services

Sun Grid Compute Utility

Story Details

The research and testing that result from successful efforts to map the human genome isn't abstract, ivory-tower science. The causes—and cures for—devastating illnesses such as Alzheimer's, Type I diabetes, bipolar disorder and many forms of cancers, lay in part encoded in our DNA. As scientists begin to crack that code, treatments for many of the illnesses that plague us today will become more innovative and more effective.

Single nucleotide polymorphisms or SNPs (pronounced "snips") are variations in the DNA sequence that often do not cause disease but rather help researchers localize genes that increase the likelihood that someone will develop a particular disease. Applied Biosystems creates the tools, called assays, that researchers use to characterize (or "genotype") these variations.

In October, 2005, the National Institutes of Health (NIH) announced the completion of the first phase of an international project to validate millions of sequence variations (SNPs) and made the data publicly available. In response, AB needed to develop millions of new designs of their proprietary TaqMan® SNP genotyping assays as quickly as possible.

" Genetic discoveries are going to become more and more important in terms of finding cures and finding the genetics of a disease, so our goal is to make sure that our researchers and customers have access to the tools they need to accelerate the science. Sun Grid helped us achieve this goal. "

— Francisco M. De La Vega, Scientific Fellow and Senior Director of Computational Genetics, Applied Biosystems

To design that volume of assays requires a specialized database search to ensure assay specificity that is compute intensive and consumes considerable resources. It would have taken as long as three months on the company’s existing internal grid, a possible competitive disadvantage. Although the company commands some 80 percent of the genomics market, competitors are working hard to catch up.

To get to market quickly, the company had three choices: invest in architecture and have AB researchers perform the search internally; negotiate an outsourcing contract with a company to provide the compute power AB needed; or turn to Sun’s innovative new utility solution

The internal approach would cost hundreds of thousands of dollars, delay the project and divert the company’s attention from its core competency. Because outsourcing would involve negotiating a contract and provide limited access to compute power, AB rejected that option as well. Instead, based on Sun’s reputation for quality and reliability, AB chose to go the utility route with Sun Grid.

Through the Sun Grid, AB had access to affordable enterprise compute power through a convenient network portal. The AB system administrator submitted the input SNP data to the Sun Grid through a secure Web-based portal, and then uploaded the command script through the same portal. When the computations were complete, AB got its data and ended its project on the Sun Grid.

AB estimated some 35,000 CPU hours would be required to complete the database search, but thanks to the power of the Sun Grid, the entire process took only six days—or 26,000 CPU hours—from start to finish. Because Sun Grid charges companies only for the CPU hours they use, AB was able to save hundreds of thousands of dollars when compared with purchasing the equipment they would have needed to perform the research themselves, and because the company had budgeted for more than it needed, the surplus hours will be used for another project.

The convenience, reliability, security and cost-efficiency of using Sun Grid proved an ideal solution for AB. In addition, the ability to use a simple public utility solution allowed the company to focus on its core competencies: creating the advanced tools required to perform medical genetic research. As ongoing genomic research provides ever-greater volumes of data, AB anticipates using the Sun Grid again and again to help the company achieve its mission of providing the most complete and accurate collection of assays and biomedical tools available anywhere in the world.