UCSC engineers collaborate with Western Digital to accelerate genome sequencing

Benedict Paten
Benedict Paten directs the Computational Genomics Lab at UC Santa Cruz.

The UC Santa Cruz Genomics Institute and Baskin School of Engineering have entered into a multi-year, joint research and development agreement with Western Digital to accelerate genomics sequencing workflows using computational storage technology. Results from this research could ultimately lead to the acceleration of clinical genomic analysis and precision medicine diagnoses at scale.

"Baskin Engineering is pleased to partner with Western Digital on this important project," said Alexander Wolf, dean of the Baskin School of Engineering. "This initiative supports the campus's greater goals of building a vibrant, entrepreneurial culture that promotes the adoption of UC Santa Cruz inventions while delivering social and economic benefits to our local and global communities."

Currently, identification and treatment of cancers using genomic diagnostics is slowed by the time-consuming process of moving massive amounts of data to the computing resources. Researchers believe that moving computational capabilities closer to data storage will help speed the process of identification and treatment. Western Digital is researching a novel computational storage architecture to test this theory at scale.

“Our new architecture will distribute computation within a single computer system across multiple computational storage devices, each with its own storage and its own customizable computing resources,” said Robin O’Neill, head of emerging systems and software at Western Digital. “By moving the compute to the data, rather than the data to the compute, we expect to take advantage of significantly greater bandwidth access to the genomics data by the near-media compute, as well as the custom, parallel computing capabilities within each computational storage device.”

To take best advantage of this new computing architecture, the collaborating organizations are researching the optimal partitioning and placement of genomics data across the computational storage devices. They are also researching how to accelerate core functions within each device to accelerate performance and minimize host system requirements. This may also be an overall reduction in power consumption which translates to lower overall total cost of ownership.

“Genomic data is on a trajectory to grow faster than almost every other type of data in the world,” said Benedict Paten, assistant professor of biomolecular engineering and director of the Computational Genomics Lab at UC Santa Cruz. “Moving the compute to the data is a key strategy already being adopted at the software layer in several global genomics initiatives. With the support and close collaboration of Western Digital’s team, we’ll be able to take this all way down to the hardware layer.”

Heiner Litz, assistant professor of computer science and engineering at UC Santa Cruz, noted the interdisciplinary nature of the collaboration. “The structure of this project is a first for the UCSC Baskin School of Engineering, with the close collaboration of engineers at Western Digital at the hardware layer, researchers in computer engineering at the firmware and architecture layer, paired with researchers in genomics at the application layer,” he said.

Western Digital will supply funding to support the collaborative team of graduate students and investigators in genomics and computer engineering as well as an Ultrastar Data60 platform to be used by the UC Santa Cruz Genomics Institute to store data for this project.