SGI Releases Bioinformatics Benchmarks for Linux ‘Superclusters’
With last week’s launch of its new line of Linux-based Altix 3000 servers and “superclusters,” SGI has set out to combine the scalability and low price of commodity-based Beowulf clusters with the global shared memory and efficient load balancing of a traditional Unix-based supercomputer.
The new product line also shatters the eight-processor-per-node barrier that has limited the use of Linux clusters in high-performance computing — it can run up to 64 Intel Itanium 2 processors per node with up to 512 GB of memory. According to SGI, this architecture enables data to be transmitted up to 200 times faster than conventional clustering methods.
The Altix line is expected to be of great interest in the science and technical market, said Dan Stevens, life and chemical sciences market manager at SGI. In terms of pricing, the product line comes in a bit above clusters built with Dell or other commodity boxes, but it easily outperforms these systems, he said.
SGI’s engineers have optimized Blast, Fasta, Hmmer, and ClustalW to run on the Altix system, and have released some early benchmarks of the Altix machines vs. IBM systems. For the 1 GHz Altix 3000 using SGI’s Blast against the IBM 1.3 GHz pSeries 690 using NCBI Blast v2.2.1, the SGI system ran from 1.6 times faster on a single CPU, and up to 6 times faster on 16 CPUs. Using 64 processors, for which there was no data available on the IBM system, the Altix processed nearly 120,000 sequences per hour.
SGI will begin shipping the Altix 3000 systems later this quarter. The entry-level server starts at $70,176 for four processors with up to 32 GB of memory and scales to 12 processors and 96 GB of memory. A 64-processor SGI Altix 3000 system starts at $1,129,262. The supercluster model currently scales to hundreds of processors and over 1 TB of memory today, with future scalability to 2,048 processors and 16 TB of global shared memory.
Lion Makes the Prime Cut
Lion Bioscience said last week that its shares had been accepted into the German stock exchange’s Prime Standard segment — a new trading segment that the stock exchange has introduced for companies that meet higher transparency rules for their accounting.
As a member of Nasdaq since its IPO in August, 2000, Lion said it has consistently fulfilled Nasdaq accounting and reporting requirements, and was therefore eligible to apply to the Prime Standard segment, which requires quarterly reporting, international accounting standards (IAS or US GAAP), a corporate calendar, at least one analyst conference per year, and ad hoc disclosures in English. Companies that adhere only to German disclosure standards are assigned to the General Standard segment.
Amersham, GeneBio to Partner on Proteomics Software and Training
Amersham Biosciences and Geneva Bioinformatics said last week that they would partner to develop and distribute bioinformatics and training tools for proteomics research.
Through the partnership, Amersham will become the exclusive distributor of GeneBio’s Bioinformatics and Proteomics Training Program, which teaches researchers how best to use bioinformatics and data analysis tools.
It was not clear what — if any — new proteomics software would be developed under the collaboration.
ViaLogy Secures $3.9 M in Equity Financing
Vialogy, a Pasadena, Calif.-based developer of microarray analysis software, said last week that it has extended its first round of equity financing to $3.95 million. Lead investor BioProjects International, a London life sciences investment firm, increased its equity interest in ViaLogy.
In March 2002, BioProjects International invested $3 million in ViaLogy, which is collaborating with Intel on a biosignal processing technology to improve signal detection on microarrays.
Tripos Projects Q4 Profitability, Growth in 2003 Revenues
Tripos of St. Louis issued an update on its fourth-quarter and year-end 2002 last week, as well as initial projects for the 2003 fiscal year.
The company anticipates profitability for the fourth quarter, with revenues just below the anticipated $53 million to $58 million range. Company officials did not comment specifically on the exact level of profitability in the fourth quarter.
“Looking forward, we are anticipating double-digit revenue growth in 2003 accompanied by full-year profitability from operations,” said CEO John McAlister in a statement.
Tripos will report complete and audited 2002 fourth-quarter and year-end results on Feb. 13, 2003.