Seattle, WA (PRWEB) January 11, 2013
Pico Computing will be sponsoring the Plant & Animal Genome conference (PAG XXI) which will be held on January 12-15, 2013 in San Diego, CA (booth #208). During the conference, the Pico Bioinformatics Accelerated Suite (PicoBASe) will be on display. Designed for accelerating short read alignment software packages typically run on CPUs, the PicoBASe has achieved a significant speedup for BWA (48X) and BFAST (1040X).
As science begins to understand more about the human genome, the computational workload required to process new incoming data has dramatically increased. Using commodity CPUs has become increasingly less attractive due to the lengthy processing cycles and high levels of power consumption. Often times, these processing cycles can take upwards of a day to complete while requiring over 3600 watt hours to operate. The PicoBASe system eliminates these run time inefficiencies and reduces the high power consumption by offloading the computational workload onto FPGAs in the PicoBASe system.
The PicoBASe accelerates the short read mapping process by parallelizing index lookups used in BWA and BFAST by replicating and partitioning large data structures across multiple memory banks. For example, the parallelization of BFAST resulted in the decrease in total runtime by up to 1040X while drawing only a fraction of the power (27 watt hours per module) required by a commodity CPU.
“Due to the embarrassingly parallel nature of BWA and BFAST, the PicoBASe is the ideal solution for scientists doing research in the field of genomics. With the BWA and BFAST software fully integrated, the integration of the PicoBASe system with existing workflows will be quick and seamless,” said Paul Draghicescu, Software Engineer at Pico Computing.
For more information please stop by Pico’s booth #208 during the conference or contact Pico at contact(at)picocomputing(dot)com.
About Pico Computing
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 http://www.picocomputing.com.