Salon is running a book review on Glyn Moody’s “Digital Code of Life” with subheading ‘tells the story of the bioinformatic revolution: The merging of computers and molecular biology’: ‘…Moody’s last book was “Rebel Code: Linux and the Open Source Revolution,” one of the better books to be written about the free software movement. There are some very significant linkages between the free software movement and bioinformatics. Central to both has been the tension between those who want to share their information (or code) and those who want to keep it secret for proprietary commercial advantage. In the world of cutting-edge genetic research this is a hugely controversial issue…’

Linux Networx announced today that diaDexus, a developer of diagnostic and therapeutic products, is using a Linux Networx� Evolocity� II (E2) cluster computing system to expedite the development of diagnostic products for cancer and cardiovascular disease. The E2 system has helped speed the rate of gene analysis for the development of future diagnostic products from weeks to hours, or by more than 20x compared to the large, multiprocessing RISC-based machine diaDexus used previously.

Diagnostics help detect the presence of certain diseases so proper medical treatment can begin in the early stages of the disease. The Linux Networx system analyzes DNA and protein sequences to locate specific disease targets. The targets are then used to develop diagnostic products for diseases that are typically difficult to detect at an early stage, such as ovarian cancer.

Using applications such as BLAST�, BLAT and HMMER, the Linux Networx system allows diaDexus to evaluate public and private databases of gene data much faster than was ever possible before, allowing diaDexus to stay current with any new gene and genomic information.

�Obtaining up-to-date information is critical to our discovery and development. The Linux Networx cluster helps us reduce the information processing time from weeks to hours, saving diaDexus significant costs and speeding up our R&D timelines,� said Timothy Burcham, Ph.D., senior director of bioinformatics for diaDexus. �We knew we could trust Linux Networx to build a fast, reliable cluster solution because of their experience in the life sciences and demonstrated Linux cluster expertise.�

Linux clustering is a method of linking multiple computers together to form a unified and more powerful system. diaDexus� E2 system includes 32 Intel� Xeon� processors, and Clusterworx� and ICE Box� cluster management tools from Linux Networx. Linux Networx has built some of the world�s fastest supercomputers, and currently has a system that ranks as the world�s fastest Linux computer and also ranks the fifth fastest supercomputer ever built (www.top500.org).

About Linux Networx
Linux Networx (www.linuxnetworx.com) brings its powerful and easy-to-manage cluster technology to those demanding high performance computing and high availability systems. Linux Networx provides solutions for organizations involved in biotechnology research, oil and gas exploration, aeronautical and chemical modeling, graphics rendering and visual effects, and other technological research fields. Through its innovative Evolocity� hardware, ICE� cluster management tools and professional service and support, Linux Networx provides end-to-end clustering solutions. To date, the company has built some of the fastest cluster systems in the world, and boasts numerous Fortune 500 customers. In 2002, Linux Networx designed and delivered the world�s fastest Linux supercomputer.

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Linux Networx announced today the Centers for Disease Control and Prevention (CDC) is using a Linux NetworxTM EvolocityTM cluster supercomputer to study smallpox genomics in light of the threat of possible bioterror attacks. The cluster is designed to provide optimum performance for bioinformatics problems and will be used by the Biotechnology Core Facility Branch at CDC, the nation�s leading public health agency. Due to health problems caused by the current smallpox vaccine, CDC is using the extra computing power to study the disease and evaluate new vaccines.

SALT LAKE CITY, April 14, 2003 – Linux Networx announced today the Centers for Disease Control and Prevention (CDC) is using a Linux Networx Evolocity cluster supercomputer to study smallpox genomics in light of the threat of possible bioterror attacks. The cluster is designed to provide optimum performance for bioinformatics problems and will be used by the Biotechnology Core Facility Branch at CDC, the nation�s leading public health agency. Due to health problems caused by the current smallpox vaccine, CDC is using the extra computing power to study the disease and evaluate new vaccines.

The threat of potential biological weapons attacks prompted President Bush to order members of the U.S. military and first response medical personnel to receive the smallpox vaccination during 2003. Since the current smallpox vaccine can sicken recipients, and one to two out of every million recipients will die, CDC has been working to ensure public health concerning the vaccine. The Linux Networx computing system increases the agency�s capacity to study various aspects of smallpox genomics, and it has already been helpful in ascertaining the usefulness of new vaccines.

Linux clustering is a method of linking multiple computers together to form a unified and more powerful system. Linux Networx recently shipped an 11.2 teraFLOPS cluster, which currently ranks as the world’s fastest Linux supercomputer, and the fifth overall fastest supercomputer in the world (www.top500.org).

CDC is running multiple alignment programs on the Linux Networx cluster including ClustalW, Dialign and MGA, to study how the disease functions. The cluster has improved computing performance for the agency, running 45 pairwise genomics alignments in one day compared to two weeks with a previous computing solution. The cluster is also used to run BLAST� to quickly determine the function of newly discovered smallpox genes.

�Linux Networx offers life sciences customers a complete solution optimized to speed-up life sciences research,� said Eric Pitcher, Linux Networx Vice President, Product Marketing, Government, Industrial and Life Sciences. �We are honored that CDC has chosen a Linux Networx system to study smallpox and assess vaccines more quickly, potentially averting life-threatening consequences from bioterrorism.�

For more information on how a Linux Networx supercomputer is powering smallpox research, visit
http://www.lnxi.com/news/cdc_facts.php.

About Linux Networx
Linux Networx (www.linuxnetworx.com) brings its powerful and easy-to-manage cluster technology to those demanding high performance computing and high availability systems. Linux Networx provides solutions for organizations involved in biotechnology research, oil and gas exploration, aeronautical and chemical modeling, graphics rendering and visual effects, and other technological research fields. Through its innovative EvolocityTM hardware, ICE� cluster management tools and professional service and support, Linux Networx provides end-to-end clustering solutions. To date, the company has built some of the fastest cluster systems in the world, and boasts numerous Fortune 500 customers. In 2002, Linux Networx designed and delivered the world�s fastest Linux supercomputer.

Infoworld,reports in this article about two genome researchers views of open source expoused at the O’Reilly convention: ‘…two leading researchers involved with the sequencing of the human genome delivered presentations citing the benefits of open source both in the development of computer systems and in science.

“I don’t think you can have science without open source,”…

Thanks to Karsten Hilbert for this link. LinuxPlanet has an article on the use of a Beowulf cluster for defibrillator research: In a small server room on the campus of UAB sits a kitchen supply rack, with four big shelves, each of which holds four dual-processor Dell computers. These sixteen boxes are hooked together in a standard Beowulf cluster, so that all 32 CPUs are working on the same computations in concert, providing a level of computation, their administrator believes, that rivals the performance he could get out of a supercomputer and at a fraction of the cost.

Dr. Andy Pollard is a Biomedical Engineer who is very familiar with using supercomputers and mainframes. Throughout much of the last 15 years, he has used them to perform the billions of calculations needed to simulate the effects of electrical fields on human heart tissue in a deep effort to understand exactly what are the triggers for a fibrillation event…

Extreme Tech is reporting on a new committee which will create an XML-based standard for biometric information: ‘…”Existing biometric standards use binary encoding formats, which severely limit their use in XML systems and applications,” said Phillip Griffin, chair of the new committee. “XCBF will provide a standard way for biometric functions to be done using XML.”

Drug Discovery Online has an article on how Linux clusters are doing the heavy lifting in bioinformatics: ‘Linux clusters, which network multiple processors together to form a unified and more powerful computing system, are becoming a major technology in the bioinformatics industry. Universities, government labs and commercial entities now boast Linux clusters of dozens, if not hundreds of these processors or “nodes” for the explicit purpose of gene sequencing, proteomic research, or drug discovery and development…’

O’Reilly has a new book entitled ‘Beginning Perl for Bioinformatics’: ‘This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving a particular problem or class of problems, so you’ll finish the book with a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to tackle more advanced bioinformatics programming.
‘ Full description here.

O-Reilly is reporting on the debate over whether publicly funded research should result in open source code, with links to both sides of the argument. It also reports on the movement by some in the bioinformatics community at Openinformatics.org

The Milwaukee Journal Sentinel has a report on a particularly interesting Biotech company, Third Wave: ‘…Third Wave is one of dozens of companies searching for the holy grail of genetic research, to reach a point that by examining a person’s genetic profile, doctors can predict a predisposition to disease or an adverse reaction to a particular drug.

In the dawning era of so-called personalized medicine, drugs and treatments will be specifically tailored to the individual…’