High-performance bioinformatics for everyone
Wednesday, 25 April, 2007
CLC bio has released the CLC Bioinformatics Cell, which enables users to transform their ordinary Intel- or AMD-based workstation computers to super-computing units.
Tasks previously taking two hours can now be computed in one minute without any hassles, the company says.
"A very important research area of molecular biology today concerns the use of small interfering RNA (siRNAs)," senior scientific officer at CLC bio, Dr. Jannick Bendtsen, said.
"The design of siRNA relies on database matching to ensure that strong cross-hybridisation to non-target genes does not occur. However, due to the small size of siRNA molecules, potential cross-matches can be missed by heuristic algorithms like BLAST.
"With the speed of the Bioinformatics Cell we are now making it possible to abandon heuristics, and to weed out cross-matching siRNAs, by using Smith-Waterman - the most accurate matching algorithm that exists."
It is commonly accepted that the amount of data which needs to be computed is growing faster than the increase in processor speed. The CLC Bioinformatics Cell aims to solve this by accelerating bioinformatics algorithms, such as Smith-Waterman and ClustalW, up to 110 times faster than what a fast desktop computer can handle today.
The speed-up is achieved through innovative use of single instruction, multiple data (SIMD) technology.
A scientist can buy a single unit for a laptop computer - a lab can share a couple among their desktop computers - or it can be plugged into each computer in a computer cluster.
The CLC Bioinformatics Cell works with a simple hassle-free plug 'n play concept through CLC bio's workbench platform.
The device is simply plugged in to the USB port of any Intel- or AMD-based computer, be it Mac OS X, Windows or Linux.
Command-line execution is also an option, giving the option of integrating the Bioinformatics Cell with existing bioinformatics workflow of scripts and in-house programs.
Genesearch
Tel: 07 5594 0299
Email: info@genesearch.com.au
www.genesearch.com.au
AI-designed DNA switches flip genes on and off
The work creates the opportunity to turn the expression of a gene up or down in just one tissue...
Drug delays tumour growth in models of children's liver cancer
A new drug has been shown to delay the growth of tumours and improve survival in hepatoblastoma,...
Ancient DNA rewrites the stories of those preserved at Pompeii
Researchers have used ancient DNA to challenge long-held assumptions about the inhabitants of...
