Dedicated hardware pushes speed limits

BOSTON (11/24/2003) - The emerging trend to use dedicated hardware to speed informatics research just got a boost from storage appliance supplier Netezza Corp. and accelerator board maker TimeLogic Corp. (acquired by Active Motif Inc. last summer), as both announced major product introductions.

Netezza introduced the Netezza Performance Server (NPS) data warehouse for bioinformatics. TimeLogic announced plans to offer a slimmed down, less expensive version of its powerful DeCypher accelerators.

The Netezza system lets companies build a so-called "biologically aware" data warehouse that integrates sequence searches and comparisons within the actual database storage system. To accomplish this, Netezza has integrated BLAST and defined genomic data types (e.g., large nucleotide and protein text types) that can be directly searched by any SQL query that supports the National Center for Biotechnology Information (NCBI) BLAST.

The result is a system that can store terabyte-sized genomic databases in dedicated hardware and speed SQL queries of such databases.

Netezza says the NPS architecture eliminates common bottlenecks in searches of large databases and provides the ease of management and reduced costs associated with appliances. (For a more detailed description of the NPS architecture, see the online article

Netezza has managed to coax at least one early adopter to go on record. "The NPS system dramatically decreases the time and cost to produce gene profiles and sequence comparison results," said Marshall Peterson, chief technical officer of the J. Craig Venter Science Foundation, in a released statement.

Industry analysts, too, think the dedicated appliance approach has merit. "Data analysis has traditionally been carried out using IT architectures that combine numerous software, server, and storage technologies," says Dan Vesset, research manager of IDC's analytics and data warehousing group. He suggests that an appliance that integrates components to optimize query performance would have great appeal in many data warehousing applications.

The NPS is designed to fit into existing life science infrastructures. Users can load it with data and continue using other database and analytical applications without having to modify them. This is possible because the NPS supports common application programming interfaces that allow queries to be submitted via SQL, ODBC, and JDBC.

NPS is available now, and pricing starts at US$622,000. Versions of the NPS line include models that support from 4.5 terabytes to 81 terabytes of total storage capacity.

TimeLogic and Active Motif are taking aim at the other end of the discovery process by integrating informatics analysis with lab-based data collection.

At first glance, the company looks odd. Time-Logic's forte is high-end hardware accelerators. Its DeCypher products are used in mainframes and large servers. Active Motif sells reagents and assays that allow companies to do basic cell and molecular biology research.

Now, Active Motif hopes to sell affordable versions of TimeLogic hardware to its customer base.

"Using just wet-lab (techniques), it will take several lifetimes to understand the function of cells," says Chris Wasden, an Active Motif spokesman. He notes that there is obviously a role for in silico work to complement the wet-lab work, and vice versa. "If you see something interesting in the lab, you might do computations, and if you see something interesting from an in silico (run), you will jump back to the lab," he says.

TimeLogic is modularizing the DeCypher product line to handle specific tasks such as BLAST computations. Slimming down the product for focused tasks cuts the price and eases implementation. "We're at the departmental approval level and down to the individual grant level," says Chris Hoover, TimeLogic's director of marketing.

This is a significant departure for TimeLogic products, which traditionally run in big systems such as Sun Microsystems Inc.'s SunFire 12K or 15K and require purchase approval from senior management.

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