Stories by Bio-IT World staff

Apple makes HPC bioinformatics easy

Many vendors have cobbled together high-performance computing clusters aimed at life scientists. Some have even bundled-in open-source informatics applications. But Apple Computer Inc. has taken things further. Its Apple Workgroup Cluster for Bioinformatics is a preconfigured Xserve G5 cluster designed to be easy to manage and use.

Serving up simplification

The Netezza Performance Server (NPS) enables companies with terabytes of dynamic, detailed data to simplify complex business intelligence initiatives. The design of the NPS enterprise-class data warehouse combines off-the-shelf components and a Linux-based architecture that does not require customers to restructure data, tools, or applications, according to Netezza. The company says the NPS data warehouse incorporates several features specific to the bioinformatics field, including integrated BLAST and defined genomic data types. The system optimizes ad hoc and complex queries, Netezza says.

HP blade packs more muscle into clusters

Hewlett-Packard Co. (HP) has announced a new dual-processor blade server, the HP ProLiant BL30p, for scientific computing and other high-performance applications.

LION at the Oracle gate

LION bioscience AG has introduced the SRS Gateway for Oracle, a software module for SRS's informatics database integration platform. Using the gateway, a researcher running Oracle can access more than 900 public, flat-file informatics databases and integrate those data into their existing database system. Basically, this software module makes it easier to work with relational and flat-file databases simultaneously.

Blast away

DNAStar Inc.'s new StarBlast program gives scientists the tools they need to set up and then search their own DNA and protein sequence databases. A solo investigator could use StarBlast to store sequence files into an easily accessible database, then compare a newly discovered sequence to those already in the database. A team of investigators might want to store all their vectors in a database, so they can later locate a specific vector by keyword or by similarity.

Landing Lander

Eric Lander has joined the faculty of Harvard Medical School's fledgling Systems Biology Department. Landing Lander is a major boost for the department. As of last January, it had just four faculty members, none of whom "represented the center of systems biology," according to its founder, Marc Kirchner. With Lander on board, recruiting top talent for the 20 or so full-time positions still open should become easier. Lander is the quintessential "quantitative" biologist, having trained in mathematics and using that training during the international effort to sequence the human genome. Lander remains the director of the Broad Institute and a professor at MIT.

National lab victor(y)

Victor Markowitz has accepted the newly created position of chief informatics officer for U.S. Department of Energy Joint Genome Institute (JGI). He returns to the national laboratory after a six-year stint in industry, most recently as CIO of Gene Logic. He also serves as the head of the recently established Biological Data Management and Technology Center (BDMTC), within the Computational Research Division at Lawrence Berkeley National Laboratory.

Think small

Charles River Proteomic Services Inc. (CRPS) has purchased Advion Biosciences Inc.'s Nanomate 100 System technology to beef up CRPS's portfolio of research services. The company says its analytical technology now includes the world's only automated chip-based nanoelectrospray system (NanoMate 100 with ESI Chip). The technology is said to improve peptide mass fingerprinting and provide new capabilities in the areas of biomarkers and protein-protein interactions. "We are exploring the advantages this new technology provides with respect to biomarker validation/discovery, post-translational modifications of proteins, and increased de novo sequencing capabilities," says John Pirro, general manager of CRPS.

Incyte exit

FRAMINGHAM (03/23/2004) - Incyte Corp., a genomics pioneer, is closing its Palo Alto, Calif. headquarters next month, resulting in 257 redundancies. CEO Paul Friedman said the closure "reflects the difficult realities of the genomic information marketplace and our belief that Incyte's most promising, value-creating activities are taking place in drug discovery and development." Incyte retains about 180 employees in Wilmington, Delaware, and 35 employees at its Proteome subsidiary in Beverly, Mass. The company lost US$166.5 million last year.

Indiana sprout

FRAMINGHAM (03/22/2004) - Eli Lilly and Co. is collaborating with Indiana academic, industry, and governmental organizations to establish the Indiana Center for Applied Protein Sciences (INCAPS). According to Lilly, INCAPS comprises multiple components that will provide technology validation, protein analysis services, instrumentation, and technical support for both academic and industry investigators in Indiana. Lilly has pledged US$3,200,000 in participation fees, executive support, instrument training, and prepayment for services to be provided by the Center to Lilly over the next two years. A $2,000,000 support grant has also been approved by the 21st Century Research and Technology Fund Board, established by the Indiana General Assembly in 1999.

Going to Genego

FRAMINGHAM (03/22/2004) - Known for his work in the areas of in vitro and computational ADME and toxicity, Sean Ekins has joined GeneGo Inc. as the vice president of computational biology. Prior to GeneGo, Ekins was associate director of computational drug discovery at Concurrent Pharmaceuticals, and has also held various research positions at Eli Lilly & Co. and Pfizer Inc.

Double header

FRAMINGHAM (03/22/2004) - Invitrogen Corp. has named Michael Stapleton general manager and vice president of its bioinformatics business, and Vivien Bonazzi director of research and development for bioinformatics. Stapleton, a veteran software executive, was most recently executive vice president and chief operating officer at Accelrys Inc. Bonazzi comes from Celera Genomics, where she served as director of product development and scientific management.

Casciato out, Gill in as chief of Signet

FRAMINGHAM (03/22/2004) - Signet Laboratories Inc. founder Ronald J. Casciato has relinquished his role as president and CEO to Richard D. Gill, formerly president and CEO of AnVil Inc. Casciato remains at Signet as executive chairman.

Epigene expert

FRAMINGHAM (03/22/2004) - Susan Gasser has been named director of Novartis AG's Friedrich Miescher Institute (FMI) in Basel. A professor of molecular biology at the University of Geneva, Gasser has led a group at the Swiss Institute for Experimental Cancer Research in Lausanne for the past 15 years, as well as serving on various prestigious foundations and councils. FMI is one of the three Novartis corporate research institutes engaged in basic science research. It focuses on epigenetics, growth control, and neurobiology. "Epigenetics is the memory of the cell," Gasser says, speaking of one of her own areas of specialty. "Processes like this make it clear we will never understand the genome just from sequencing it."