Human Genetic Variation Alters Anthrax Toxin Sensitivity
Martchenko, Candille et al., PNAS
Researchers at Stanford University School of Medicine show that genetic variation affecting capillary morphogenesis gene 2, or CMG2, dramatically alters toxin sensitivity in humans. In its analysis, the team reports on "a CMG2 single-nucleotide polymorphism occurring frequently in African and European populations [that they found] independently altered toxin uptake." The group goes on to suggest "testing of genomically characterized human cell populations may offer a broadly useful strategy for elucidating effects of genetic variation on infectious disease susceptibility."
FPGAs Speedup Dot Plot
November 10, 2009
Buried beneath all the hype of Cloud Computing, multicore processing, and GPUs, FPGAs have not had much lip-service as of late, at least as far as life sciences applications go. But the folks over at Pico Computing have just announced a 5,000X speedup of a DNA sequence analysis and dot plot algorithm using an FPGA cluster consisting of 112 commodity cards. While not exactly evident in the press release, Mark Hur, director of sales & marketing kindly informed me that this is a 5,000x speedup over an Intelcore2Duo 2.66 GHz processor. The dot plot algorithm was written in C and ported to the FPGA using a C-to-FPGA tool provided by Impulse Accelerated Technologies. Here is a link to the white paper.
This is particularly
This is particularly impressive given that the port was done by a C-to-FPGA tool, not by an expensive hardware guy. The need for an FPGA guru is what has kept reconfigurable computing down for so long. How much does one of these Pico cards cost?