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The Microsoft development team is asking the scientific community to submit research scenarios that will help the company develop new capabilities for version 2.0 of its MBF toolkit, scheduled for release next summer.

"It might not necessarily be an in vitro diagnostic that's going to hit the market," a Merck researcher said of the company's mass spec-based biomarker assays, "but it can certainly help us make decisions as we move a drug to market."

The technique could be used to diagnose diseases such as mental retardation, where copy number variation is a key characteristic, and as a screening tool to look for cancer biomarkers and assess drug effectiveness, the researchers said.

A Microsoft official said that bioinformatics vendors should not see the software giant's entry in the market as a threat, but an opportunity to focus on their "specialized functionality for the science" and "let Microsoft focus on the infrastructure."

The Microsoft Biology Foundation includes parsers for common bioinformatics file formats; various algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to key bioinformatics web services such as the National Center for Biotechnology Information's Blast.

The new employees will be critical for a contract Ceiba recently signed with Merck that made it the sole provider of software maintenance and support for Rosetta Biosoftware products. The company also plans to develop its own bioinformatics products in the area of translational research.

The Bangalore software firm will partner with the Microsoft biomedical information technology alliance.

By year's end, NuGen plans to launch an RNA-seq sample-preparation kit that allows users to start with less material, and plans to add "many more products for NGS in the near future."

Paired Ends: Oct 13, 2009

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Christopher Raymond, Dennis Ausiello, David Baltimore, Eli Broad, Drew Gilpin Faust, Jeffrey Flier, Susan Hockfield, Seth Klarman, Eric Lander, William Lee, Arthur Levinson, Phillip Sharp, Patty Stonesifer, Ratan Tata, Diana Chapman Walsh

IP Roundup: Oct 6, 2009

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Nanogen, Universitat Konstanz, the University of Chicago, PerkinElmer, Microsoft, Yeda Research and Development

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The US National Institutes of Health's All of Us project awarded $4.6 million to the company Color to develop a genetic counseling resource for the program.

The Times of India reports on a pilot study that used genomic testing to determine whether patients had drug-resistant tuberculosis.

New guidelines say that more women may benefit from genetic testing for hereditary breast or ovarian cancer, according to the Los Angeles Times.

In Cell this week: small proteins identified among human microbiome, role for tumor microbes in pancreatic cancer survival, and more.