Skip to main content
Premium Trial:

Request an Annual Quote

SGI Makes Bid for Bioinformatics Market With Linux Cluster Rival

NEW YORK, Oct. 9 - SGI released its Origin 300 server for technical mid-range applications on Tuesday in an attempt to rival the Linux cluster platform.

The Origin 300 borrows the NUMAflex modular approach to configurability that SGI developed for its high-end Origin 3000 series. Bioinformatics teams who may not need the same capabilities of the Origin 3000 can use the various modules to create a cost-effective “dedicated appliance,” said Dan Stevens, marketing manager for scientific applications at SGI.

Stevens said that SGI’s application engineers have written wrappers around a number of bioinformatics applications, including Blast, FastA, ClustalW, and Hmmer, so that they operate in a “high throughput” capacity on these systems. These applications are freely available to SGI customers.

SGI said that in a benchmark against its own Origin 3000, the Compaq Alpha, the HP 9000, the IBM pSeries and SP high node, and Sun Fire, the Origin 300 had the best performance at any price point up to $500,000 in both floating point performance and integer performance.

But according to Stevens, high-performance computing vendors are not the primary competition for SGI in the bioinformatics sector—Linux clusters are. While more and more HPC users are turning to Linux clusters as a low-cost option to meet their number-crunching needs, Stevens said many don’t consider the total cost of ownership involved in maintaining them.

Recognizing the threat posed by Linux clusters, SGI also ran a benchmark of a 12-CPU Origin against a 32-CPU Dell PowerEdge 2250 (1 GHz Pentium III) cluster. Each system ran 100,000 BlastX searches per day for 1,140 EST sequence queries against a database of more than 600,000 sequences. SGI calculated that the three-year total cost of ownership of the Origin 300 was $140,100 vs. $225,600 for the Linux cluster.

SGI is also launching its TP900 storage system this week, an entry-level disk array that can stand alone or serve as an expansion module for the Origin 300.

The release of Origin 300 comes nearly one year after SGI partnered with Incyte to install a Linux-based bioinformatics system at Bristol-Myers Squibb.

In November 2000, Bristol-Myers became the first customer to sign up for the Incyte-SGI system, which links Incyte's Linux cluster with an SGI Origin 2000 server. The pharmaceutical giant said it planned to use the system for gene- and protein-sequence analysis, transcriptional profiling, and proteomics.

The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.