By Matthew Dublin
Thanks to renewed funding from the National Science Foundation, the Virginia Bioinformatics Institute at Virginia Tech is continuing its collaboration with hybrid-core hardware maker Convey Computer.
The $1M project, funded through the NSF's Strategic Technologies for Cyberinfrastructure (STCI) program, centers on Convey's FPGA designs and will allow developers to track efficiency and usage patterns, and develop tools that will be available on the web for researchers to download.
The program will also fund a two-week summer program for undergraduates aimed at giving students some hands-on experience with developing for hybrid HPC architectures.
VBI was an early adopter of Convey solutions, its hybrid-core system Shadowfax features Convey's HC-1 system and is used on a range of bioinformatics projects including everything from gene annotation to sequencing analysis. Shadowfax is a 212 core Intel 64-bit cluster, with 16 GPUs, three 64-bit Xeon processors, three Convey HC-1s with 12 Xilinx FPGAs.
"This partnership will usher in a paradigm shift in the way bioinformatics researchers process data by using Convey's hybrid-core platform and relevant technologies," said Harold Garner, VBI executive director. "Researchers are literally drowning in data," said Garner. "This grant allows us to leverage the most cutting-edge HPC technology to extract meaningful information from such a data-rich environment and move toward applications of lasting value for developers, bioinformaticians, and clinicians."
In May, Convey announced that its software GraphConstructor accelerates de novo genome assembly up to 8.4 fold on its hybrid-core architecture.