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Canada s NRC, Waban, DOE, DiaDexus, SGI, AnVil, Aventis


Canada’s NRC Launches Bioinformatics Consulting Service

The National Research Council of Canada last week launched the Canadian Bioinformatics Resource Industry Service, a one-year pilot project that will provide bioinformatics training and consulting to small-to-medium-sized biotechnology companies at a new Can$1.3 million (US$94 million) facility at the British Columbia Institute of Technology.

Western Economic Diversification Canada is contributing Can$190,000 in start-up and launch funding and the NRC has provided more than Can$1 million in resources, including mainframe computer equipment to support the effort.

Waban to Build Genomic LIMS for Partners Healthcare

Waban Software said last week that its laboratory information management system technology will be installed at the Harvard Medical School-Partners HealthCare Center for Genetics and Genomics (HPCGG).

The LIMS will support the clinical and operational needs of the HPCGG Laboratory for Molecular Medicine, where it will manage the development and delivery of tests for complex diseases, as well as traditional single-gene disorders.

DOE Seeks Microbe Sequencing Nominees

According to a notice in the Federal Register last week, the Department of Energy is seeking nominations for “candidate microbes, microbial consortia, and 100 Mb-or-less-sized organisms for draft genomic sequencing.”

In particular, the DOE is looking for microbes that will support research in climate change, bioremediation, carbon management, energy production, and environmental protection.

Selected organisms will be sequenced at a draft level (6-8x coverage) by the DOE Joint Genome Institute.

Nominations are due by June 26, 2003. Further information is available at

DiaDexus to use Linux Networx Cluster

Linux Networx said last week that DiaDexus will use its Evolocity II cluster computing system for genetic analysis.

The company said it expects the system to speed the rate of gene analysis for the development of future diagnostic products by more than 20 times compared to the multiprocessing RISC-based machine it used previously.

DiaDexus will run Blast, Blat, and Hmmer on the 32-processor Linux Networx system.

SGI Releases Altix Blast Benchmarks

SGI last week released preliminary performance results for its Linux-based Altix 3000 servers and superclusters running the new Intel Itanium 2 “Madison” processor.

SGI said it expects the Madison processor to deliver system performance over 50 percent faster than the current Altix 3000 system.

In preliminary tests on an SGI Altix system running four 1.5 GHz Madison processors against “the industry’s closest competitor” — an IBM eServer pSeries running four Power4 processors — NCBI Blast ran 57 percent, or 2.3 times, faster than the IBM system. In tests of HTC-Blast, SGI’s high-throughput driver program for Blast, the Altix performed more than 72 percent, or 3.5 times, faster than IBM, SGI said.

AnVil Adds SPSS Text Mining to Analysis Platform

Statistics firm SPSS said last week that its Clementine data mining, text mining, and statistical analytics software will be added to the Anvil Data Analysis Platform (ADAPT) from AnVil.

AnVil will also offer SPSS’ LexiQuest Mine, a linguistics-based text mining product, as part of the new partnership agreement.

Aventis Licenses Gene-IT’s Biofacet

Gene-IT said last week that Aventis has purchased its Biofacet comparative genomics software for in-house computational biology research.

Gene-IT also said it recently completed two comparative genomics projects for Aventis using the Biofacet technology. In one, an anti-infectives study, the software was used to determine the conserved protein sequences of a “diverse set” of bacterial genomes. In the second study, the software identified DNA fragments shared among several fungal species.

For the projects, Gene-IT said it annotated and curated the genome databases; performed a pair-wise comparison of the genomes; identified related gene and protein fragment-pairs across species; and used this information to create clusters of orthologous genes.

Filed under

The Scan

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Limited Rapid Testing

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Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.