KIEL, Germany & AARHUS, Denmark–Today, CLC bio and German high performance computing experts, SciEngines, announced a collaboration to completely integrate CLC bio’s server- and desktop-based sequence analysis software with SciEngines’ FPGA-based RIVYERA platform for massively parallel computing. Initially, the system will feature implementations of nucleotide-nucleotide BLAST (BLASTn), protein-protein BLAST (BLASTp), and Smith-Waterman. More algorithms will be added continuously.

Chief Software Architect at SciEngines, Jost Bissel, states “Preliminary BLASTp benchmarks using the tree species Populus trichocarpa, black cottonwood, have demonstrated a 188x increase in speed using a RIVYERA S3-5000 computer with 64 FPGA chips compared to a Xeon E5520 core. The benchmark ran BLASTp to align 920000 amino acids against a database of 1 billion amino acids. Similar acceleration has been achieved in early benchmark tests of the BLASTn version, and we expect both BLAST implementations to be accelerated even further before the final release.”

“Several of our big customers estimate that more than 80% of their computing resources are spent on doing BLAST searches and implementing this setup will dramatically increase the overall capacity of their data analysis pipelines,” continues CEO at CLC bio, Thomas Knudsen, and adds, “We think this is a very intriguing solution for the enterprise segment of our customers within the biotech, pharma, biofuel, and especially the agro sectors.”

The development of the algorithms is a joint project between SciEngines’ German engineers and CLC bio’s R&D department. The BLAST software for the RIVYERA hardware platform, in which up to 128 FPGAs can be set up in each compute unit, is currently still in development. An early version will be showcased at PAG XX, the International Plant & Animal Genome conference, January 14-18, 2012, in San Diego, California, USA. Both parties retain the rights to resell the combined products and are looking forward to provide efficient high-performance computing solutions to the scientific community.