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Bioinformatics Briefs: Feb 18, 2002


Affy Probe Sequences to Appear in Public Databases


BioInform’s sister publication, BioArray News, reported last week that Affymetrix plans to integrate the sequences of the oligonucleotide probes from its microarrays into the University of California, Santa Cruz “golden path” assembly of the human genome and the European Bioinformatics Institute’s upcoming ArrayExpress expression database.

Affy first made the sequences publicly available on its NetAffx website less than a month ago. That decision, in conjunction with the integration into the UCSC assembly and ArrayExpress, are in line with a new strategy that Affymetrix calls its “open access initiative.”


3rd Mill Wins SBIR Contract


Bioinformatics consulting firm 3rd Millennium has received a Phase I Small Business and Innovation and Research contract from the US Department of Defense to develop a bioinformatics system for the management and analysis of microarray data.

The system will integrate data generated from laboratory experiments with computational information in support of the DOD’s Defense Technology Area Plan in Infectious Diseases of Military Importance.

The platform will build on technology Cambridge, Mass.-based 3rd Millennium is developing through a $1.8 million Advanced Technology Program grant from the US Department of Commerce that was awarded in October 2000.

According to 3rd Millennium, the new system will combine a laboratory information management system with an analysis information management system in order to track computational processes and capture the biological context of the samples used in laboratory processes.

The contract “further validates one of the most critical issues in informatics: the integration of physical laboratory information with the downstream analysis,” said Richard Dweck, CEO of 3rd Millennium, in a statement.


York Wins Beowulf Grant


The University of York was recently awarded a £234,000 (US$330,500) grant for a new Linux cluster that has been earmarked for a number of applications, including biomolecular modeling research.

The UK’s Engineering and Physical Sciences Research Council awarded the grant for the 33-computer cluster of Pentium 4 Xeon processors, which will be linked through a high-bandwidth, low latency network.

Alan Real, a computing officer in the department of physics at the university, said that, among other initiatives, the new system would support molecular dynamics simulations to investigate interactions between DNA and polyamines.

Real said that the university’s current single-processor PC systems would require approximately two weeks to calculate one nanosecond’s worth of information for such a simulation, but “with the new facility, this one nanosecond will be completed over a single night of computation.”


Millennium Expands Spotfire Deal


Spotfire of Somerville, Mass., said last week that Millennium Pharmaceuticals expanded its license agreement for Spotfire’s DecisionSite software.

Millennium, a Spotfire customer since 1997, now has licenses for Spotfire DecisionSite, Spotfire DecisionSite for Lead Discovery, and Spotfire DecisionSite for Functional Genomics.


Digital Gene Picks up a Paracel GeneMatcher2


Pasadena, Calf.-based Paracel sold a GeneMatcher2 sequence similarity analysis supercomputer to Digital Gene Technologies for use in its gene discovery and functional genomics efforts.

DGT, based in La Jolla, Calif., also licensed Paracel’s Transcript-Assembler software for EST clustering and assembly.

Brian Hilbush, vice president of discovery biology for DGT, said the company would be using the GeneMatcher2 system to aid gene identification in conjunction with its own TOGA (total gene expression analysis) technology, which identifies genes through expression-based research.


ThinkGen to Build Singapore Bioinformatics Hub


The Financial Express of India reported on February 11 that ThinkGen, a Bangalore-based bioinformatics company, is collaborating with the Singapore government to set up a “bioinformatics hub” in Singapore.

Rama Subramaniam, managing director of ThinkGen, told the paper that “advanced talks” about the project were underway.

According to the Financial Express, ThinkGen plans similar projects in Dubai, Africa, Europe, and 21 additional locations, and plans to expand its facility by 35,000 square feet and augment its staff of 70 by an additional 200 employees over the coming year. The company is expecting revenues of $5 million during the current fiscal year, the paper reported.


Singapore Center to Provide GenoMax Access


InforMax of Bethesda, Md., has entered a strategic alliance with Sun Microsystems to provide its GenoMax enterprise bioinformatics system through Singapore’s Application Service Provider Center.

The ASP Center, a joint initiative of Singapore’s Infocomm Development Authority, Nanyang Technological University, and Sun, works with industry partners as an incubator for new ASP-based businesses.

An ASP spokeswoman was not available before press time to provide further details.


Genomics Collaborative Builds New Database


Genomics Collaborative is developing a new database, called Tantalus, that will integrate biological data with information extracted from the scientific literature, the company said last week.

As part of its development of the database, designed to mine the biomedical literature for specific genes involved in complex diseases, the company licensed Genetic-Xchange’s K1 data integration middleware platform.

“Using the K1 system significantly reduced the amount of resources required to build and maintain Tantalus. … [It] enhanced our ability to develop the system, access information from their source websites and databases, and to create production software integrated with the rest of our informatics architecture in a very short time,” said Brent Richter, director of bioinformatics at Genomics Collaborative, in a statement.


NSF Earmarks $8M Per Year for Bioinformatics


The Biological Databases and Informatics program of the US National Science Foundation is offering $8 million in grants for bioinformatics research.

In a program announcement released last week (NSF 02-058, available at, the NSF said it plans to award about 25 new grants for up to five years apiece that are worth between $50,000 to $500,000 a year.

The Biological Databases and Informatics program, a cross-disciplinary effort backed by the Directorate for Biological Sciences, is charged with aiding the design, development, and implementation of new information tools.


Compugen’s LEADS Platform Predicts Two Novel Proteins


Compugen, based in Tel Aviv, Israel, said last week that it had discovered two novel prostate-specific proteins using its LEADS computational biology platform. The company verified the predicted proteins in its wet lab.

A paper on the discovery, which the company said could have important applications in developing diagnostic tools for prostate cancer, appears in the current Journal of Biological Chemistry. The paper details the identification of unusual mRNA splice variants of the KLK2 and KLK3 genes and the novel proteins encoded by these transcripts, named prostate-specific antigen-linked molecule (PSA-LM) and hK2-linked molecule (K-LM).

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