Press Release

Assembling the human genome in less than an hour

November 12th, 2012

Salt Lake City, UT Stillwater Supercomputing, Inc., Pico Computing, Inc., and the Systemix Institute will be unveiling a new class of bioinformatics appliances designed for de novo assembly of the human genome in less than an hour. The first application of this technology will be on display at Supercomputing ’12 in Salt Lake City, November 12-15. The Bioinformatics appliance is based on the SC5 SuperCluster platform developed by Pico Computing, Inc.

The appliance is running a state-of-the-art genome assembler developed by Dr. Manoj Samanta, principal at the Systemix Institute. The goal of building appliances that can assemble human-sized genomes in less then an hour is driven by the new field of metagenomics. Metagenomics is a new scientific field that involves the analysis of genomic DNA sequences obtained directly from the environment, enabling studies of novel microbial systems. Metagenomics is made possible through high-throughput sequencing technologies. The analysis of the resulting sequencing data sets requires sophisticated computational analyses and data mining. In clinical settings, a fundamental goal of metagenomics is to help people diagnose and cure disease in clinical settings.

The new assembler developed by the Systemix Institute is taking an integrated approach. The architecture is based on a collection of parallel algorithms for bioinformatic operators, such as k-mer counting, filtering, and alignment. The goal of the new software is to research and refine algorithms required to solve the metagenomics big data problems. The new assembly algorithm leverages the Knowledge Processing Platform developed by Stillwater Supercomputing, Inc.

The Stillwater Knowledge Processing Platform solves the problem of hardware independence for high performance applications. As these types of bioinformatics applications may need to run on multi-core, many-core, GPUs, and FPGAs, the desire is to decouple the assembler algorithm from the underlying hardware. The Stillwater Knowledge Processing Platform provides this decoupling and enables the application to run across this wide spectrum of hardware without modifications. Furthermore, the Stillwater Platform can take advantage of multiple FPGA chips to create scalable supercomputing systems to match any required throughput for medium to large scale genome centers.

Pico Computing will demonstrate the technology in its booth at Supercomputing ’12 in Salt Lake City. On display will be a Pico board-based Bioinformatics Appliance executing the genome assembler, jointly created by Pico Computing, Dr. Manoj Samantha, principal at Systemix Institute of Seattle and Dr. Theodore Omtzigt, principal at Stillwater, who will all be available to answer any of your questions at Supercomputing ’12.



About Stillwater Supercomputing, Inc.

Stillwater Supercomputing, Inc. was founded in 2006 and Incorporated in 2007 to develop the next generation platform for computational science and engineering. Focused on improving the efficiency of execution, the Stillwater Knowledge Processing framework is facilitating the creation of best-in-class intelligent systems for high-performance embedded and autonomous systems, to large-scale cloud-based systems for bioinformatics, science, and engineering. For more information about Stillwater products and services, visit www.stillwater-sc.com, or contact info@stillwater-sc.com.

About Systemix Institute

Based in Redmond, Washington, Systemix Institute Inc. specialized in developing bioinformatics applications and providing services. Systemix solutions are highly scalable to properly address big-data problems inherent in next-generation sequencing technologies. For more information about Systemix products and services, visit www.systemix.org, or contact info@systemix.org.

About Pico Computing, Inc.

Based in Seattle, Washington, Pico Computing specializes in highly integrated development and deployment platforms based on Field Programmable Gate Array (FPGA) technologies. Applications for Pico Computing technologies include cryptography, networking, signal processing, bioinformatics, and scientific computing. Pico Computing products are used in embedded systems as well as in military, national security, and high performance computing applications. For more information about Pico products and services, visit www.picocomputing.com.