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Microsoft Offers Updates from BioIT Alliance

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At the recent the Bio-IT World Conference & Expo, Rudy Potenzone, Microsoft's industry technology strategist for pharmaceuticals, presented a panel of diverse collaborations underway through the BioIT Alliance, an organization Microsoft formed in 2006 to link vendors in the life sciences space to "explore new ways" of data sharing and to better leverage IT to foster personalized medicine.

One of the new collaborations is with the Pistoia Alliance, a cross-pharma collaborative venture that seeks to "streamline non-competitive elements" of drug-discovery workflow. Named after the Tuscany town in which the first meeting took place last year, it was founded by discovery informatics researchers from Astra-Zeneca, GlaxoSmithKline, Novartis, and Pfizer, and launched publicly in February.

Another project is in the realm of chemistry and authoring. A division called Microsoft External Research that supports projects with firms, industry, and governments, has supported the development of chemistry-related authoring and rendering in Word 2007 documents through a partnership with chemist Peter Murray-Rust from Cambridge University's Unilever Centre for Molecular Science Informatics.

At the BioIT Alliance session, Murray-Rust demonstrated Chem4Word for the first time in public and said it will be released in the early summer. Murray--Rust, an open-source and open-data advocate, created Chemical Markup Language, CML, which is an XML-language for chemical information used for representing molecules, spectra, reactions, and computational chemistry.

Another venture in the BioIT Alliance portfolio is an open source life science Web registry project called BioCatalogue, described in Nature Proceedings, spearheaded by Carol Goble and colleagues from the University of Manchester's School of Computer Science and colleagues at the EMBL European Bioinformatics Institute.

It began as a collaboration between EMBL-EBI and the myGrid project at the University of Manchester.

— Vivien Marx

Datapoint

100 thousand
The number of volunteer genome sequences that will be stored on Isilon hardware purchased by the Personal Genome Project

Bioinformatics notes

InforSense says that Celera is using the firm's platform to integrate internal and public data to identify biomarkers. InforSense's Translational Research Solution will allow Celera scientists to browse enzyme-linked immunoassay, SNP, and other data.

Compendia Bioscience is partnering with MDS Pharma Services to create OncoPredictor, a platform to improve cancer drug development. The platform combines MDS's OncoPanel with Compendia's Oncomine so drug developers can see which patients are likely to respond to a new therapy.

Data mining firm DecisionQ and Thomas Jefferson University's Kimmel Cancer Center are using predictive analytic and machine learning to mine the university's cancer registries and tailor patient treatment.

Funded grants

$311,442/FY 2009
Continual Development of Protein Docking Algorithms
Grantee: Zhiping Weng, University of Massachusetts Medical School, Worcester
Began: May 1, 2009; Ends: Apr. 30, 2013

This funding will be applied to the development of -computational methods, algorithms, and software to facilitate three-dimensional protein-protein structure predication. Weng and his lab have recently developed a new energy function, IFACE, which improves the performance of ZDOCK, a protein docking algorithm.

$407,935/FY 2009
Bioinformatics Tools for the Analysis of the Spatiotemporal Organization of Protein Expression in Neural Functional Units
Grantee: Eduardo Macagno, University of California, San Diego
Began: Apr. 15, 2009; Ends: Mar. 31, 2010

This grant will go toward funding the development of computational tools to support the study of the development and repair of the nervous system at the molecular level. The researchers plan to design new tools to analyze data obtained via mass spectrometry imaging.

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