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GE Teams with Harvard on Image-Analysis Software

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GE Healthcare has enlisted the help of a Harvard bioinformatics team to expand the capabilities of its IN Cell Analyzer cellular imaging system, and hopefully gain an edge over its competitors in the cell-based assay market at a time when high-content screening is gaining a greater foothold in pharmaceutical R&D and academic labs.

Under the terms of collaboration, the Harvard Center for Neurodegeneration and Repair’s Center for Bioinformatics will develop image-analysis software to extend the range of assays that can run on the IN Cell Analyzer platform. GE Healthcare will have the right of first refusal to commercialize any software developed in the open-ended project, but the company does not yet have any definite plans to do so.

“We’ll evaluate what comes out of [the collaboration], and if it’s commercially viable, then of course we’ll take it up and develop the application and the software,” says John Burczak, vice president of R&D at GE Healthcare. Burczak adds that GE’s own software for the platform is “modular,” so if the Harvard developers create an application with limited commercial appeal, “it might be something that we pass on, but we want to ensure that the links are there, that the application can run.”

Rich Fisler, director of biotech consulting firm Beachhead Consulting, says that GE Healthcare stands to benefit competitively from the collaboration even if it doesn’t commercialize the software that comes out of it. “It shows the industry that they’re pushing the envelope,” he says. “They’re not just sitting back on their heels and saying, ‘Let’s wait for someone else to do it.’ They’re saying, ‘Let’s really drive the development of applications in very pharmaceutically relevant areas like neurodegenerative disease.’”

— Bernadette Toner

 

The California Institute for Quantitative Biomedical Research and Lawrence Berkeley National Laboratory have partnered to create a joint Biological Data Management Core Facility.

 

The three primary public repositories for DNA and RNA sequence data — GenBank, the EMBL Nucleotide Sequence Database, and the DNA Data Bank of Japan — have surpassed the 100-gigabase mark, according to the National Library of Medicine.

 

The University of Pittsburgh and Carnegie Mellon University launched a joint doctoral program in computational biology to begin this fall with a first official class starting next year.

 

Bruker AXS expects to acquire privately held Socabim, a Paris-based software firm focused on X-ray analysis. The sale is expected to close in the first quarter of 2006.

 

The theoretical and computational biophysics group at the University of Illinois has released a new version of its Biological Collaborative Research Environment (BioCoRE) server software.

 

Invitrogen will market and distribute a number of products from Nonlinear Dynamics’ TotalLab and Progenesis lines. In related news, Ian Currie joined Nonlinear Dynamics as European sales manager.

 

Entelos announced that it is collaborating with Unilever to develop an in silico model for the study of skin allergy.

 

PATENT WATCH

US Patent 6,931,326. Methods for obtaining and using haplotype data. Inventors: Richard Judson, J. Claiborne Stephens, Andreas Windemuth. Assignee: Genaissance Pharmaceuticals. Issued: August 16, 2005.

This invention provides methods, computer programs, and databases to analyze and make use of gene haplotype information. The techniques and systems described facilitate the discovery and measurement of haplotype frequency in the general population, the correlation between individual haplotypes or genotypes and a clinical outcome, the prediction of haplotype from genotype for a gene, and the prediction of individual clinical response to a treatment based on genotype or haplotype.

 

US Patent 6,931,401. Methods and apparatus for high-speed approximate sub-string searches. Inventors: Michael Gibson, Richard Messenger, Marc Rieffel, Zheng Zhang. Assignee: Paracel. Issued: August 16, 2005.

The present invention relates to string searching and, more specifically, to computer-implemented string searching of databases. It utilizes a combined hardware/software system to implement an improved Blast algorithm that is two to three orders of magnitude faster than previous algorithms executed by single desktop processors. The invention can be applied to sequences of biological information such as DNA and peptides or to string searches of any kind.

 

Datapoint

600,180

The HapMap Data Coordination Center at Cold Spring Harbor Laboratory has made the first release of data from HapMap Phase II available for download. A total of 600,180 new genotype sets are available in the release, covering 54,016,200 genotypes.

 

The Scan

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