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LLNL to Install World’s Fastest Linux Cluster (For Now)

Just months after Pacific Northwest National Laboratory announced plans to install an 8.3-teraflop Hewlett-Packard Linux-based supercomputer to support its biological research projects, Lawrence Livermore National Lab said last week that it plans to top its DOE sibling with a 9.2-teraflop Evolocity cluster from Linux Networx.

The Salt Lake City-based company said it plans to have the supercomputer, which will be the largest and most powerful Linux cluster and among the five fastest supercomputers of any type in the world, by the fall. The cluster will use 1,920 Intel Xeon processors at 2.4 GHz.

To illustrate the speed of the system, Linux Networx noted in its announcement that the new cluster could assemble the human genome in 21 days, compared to the 150 days it took Celera Genomics on a Compaq Alpha cluster.

An LLNL spokesman said 27 projects are slated to run on the new cluster. Five of these are biology-based projects, including research in cellular modeling, molecular dynamics, and bioterrorism.


Spotfire, ABI Integrate Proteomics Software

Adding to its portfolio of proteomics partners, Spotfire signed an agreement last week with Applied Biosystems to integrate the ABI/MDS Sciex Pro ICAT software with Spotfire’s DecisionSite for Functional Genomics.

Spotfire has similar integration deals with Micromass and Thermo LabSystems.

The integrated Pro ICAT product is expected to improve the analytical workflow for protein expression analysis using ICAT reagents, including the Vision workstation for preparative multidimensional liquid chromatography, the API QSTAR Pulsar Hybrid LC/MS/MS system, and ICAT reagent kits.

The companies will collaborate to develop a unified interface for their products to allow researchers to access and analyze protein expression data.


UK’s MRC Picks DeCypher Accelerator

TimeLogic said last week that the UK’s Medical Research Council Laboratory of Molecular Biology would use its DeCypher accelerator system for hidden-Markov model analysis related to the Superfamily protein structure database (

“We already have conventional computing resources,” said the LMB’s Julian Gough in a statement, “but have installed DeCypher rather than expanding existing systems because we believe it is the best solution for dedicated HMM-based computing.”

The Superfamily database includes over 7,000 hidden-Markov models to assign structure to protein sequences. LMB will use a pair of Dell-based DeCypher servers to speed analysis of the Superfamily database using existing HMM techniques as well as new techniques under development.


Wipro Acquires GE Med Systems IT Group

Pleased with the early success of its Healthcare and Life Sciences unit, Bangalore, India-based Wipro Limited said last week that it plans to acquire GE Medical Systems Information Technologies Private Limited and its subsidiary Healthcare Information Systems Intellectual Properties. Upon completion of the transaction, the company will be named Wipro Healthcare IT Limited.

In a statement, D. A. Prasanna, CEO of Wipro Healthcare and Life Science, said that the progress of the business unit — launched in April — “is in line with our plan” and that the acquisition of GE Medical Systems IT will help Wipro achieve its goal of becoming “a leading global player in life science and healthcare IT services.”

For the quarter ended June 30, 2002, Wipro Healthcare and Life Sciences recorded revenue of $2 million with a loss of $500,000. The company estimated that for the quarter ending September 2002, the unit would increase its revenues to $3 million.

Wipro is not the only Indian IT player to move into the bioinformatics market. In the last year, Tata Consultancy Services and Satyam Computer Services also announced plans to tap into the life sciences.


AnVil Enters Clinical Market in HealthSouth Collaboration

Burlington, Mass.-based AnVil said last week that it will apply its data mining technology to patient treatment records in a collaboration with healthcare services firm HealthSouth.

In the first phase of the project, AnVil will study aggregated patient data collected by HealthSouth to analyze the effectiveness and efficacy of various cardiac medications on stroke populations. The company will also examine data from orthopedic treatments to assess the effectiveness of prescribed analgesics and anti-infectives.

AnVil said it would sell findings from its analysis to pharmaceutical, biotechnology, and clinical research organizations.


A Bioscience Center Grows in Ottawa

The University of Ottawa broke ground last week on a Can$59 million (US $38 million) teaching and research biosciences complex totaling 18,000 square meters (194,000 square feet).

The three-phase project will include over 30 laboratories and several greenhouses with space for 1,500 students, professors, and researchers in biology, biochemistry, bioinformatics, genomics, biopharmaceutical sciences, biomedical sciences, and environmental sciences.

The first phase of the project, expected to be completed by August 2003, will be construction of a new 5,364 square meter (58,000 square foot) research lab that will include 17 individual research labs as well as three large shared labs for bioinformatics, molecular biology, and extraction/analysis.

The second and third phases of the center are slated for completion in August 2004 and August 2005, respectively.


Investor Conference Could Launch Three Lucky Startups

Who says VC funding has dried up for bioinformatics? Investors at the 2002 Tech Coast Life Science Innovation Conference will be looking for a few good biotech companies this September 10 at the Hyatt Regency Hotel in Irvine, Calif., and have singled out bioinformatics as a target domain area for startup funding.

Venture Point Tech Coast Small Business Development Center will host the conference, where three entrepreneurs will have the opportunity to pitch their business plans to a panel of venture capitalists and life science investors.

Life science entrepreneurs in therapeutics, diagnostics, medical devices, and bioinformatics platforms are encouraged to submit an executive summary and PowerPoint presentation by July 29 to enter the selection process.

The complete application and schedule information is available at

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The Scan

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A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.