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Microsoft Research Connections Blog

The Microsoft Research Connections blog shares stories of collaborations with computer scientists at academic and scientific institutions to advance technical innovations in computing, as well as related events, scholarships, and fellowships.

  • Microsoft Research Connections Blog

    Microsoft Biology Foundation Available for Free Download


    On July 10, in Boston, the External Research division of Microsoft Research will introduce the Microsoft Biology Initiative, resources designed to help biological scientists and programmers conduct research more efficiently and affordably. These include the first post-beta release of the Microsoft Biology Foundation (MBF), a language-neutral bioinformatics tool kit built as an extension to the Microsoft .NET Framework. In addition to a new genome assembler, performance enhancements, and other improvements, MBF builds upon the vision and goals that drove the development of the beta versions. Those included a commitment to community involvement, extensibility, cross-platform and interoperable functionality, language neutrality, and support for best practices. While there are other libraries of biological functionality available, MBF supports universally accepted standards of the bioinformatics community and implements a range of unique functionality derived from original Microsoft research. The code for MBF and supporting documents is available on CodePlex[RK1].

    Like MBF itself, the audience during the 11th annual Bioinformatics Open Source Conference, held in conjunction with the 18th annual International Conference on Intelligent Systems for Molecular Biology, represents a powerful combination of technology and biology. To harness technology in support of biological discovery, MBF implements parsers for common bioinformatics file formats and algorithms used to manipulate DNA, RNA, and protein sequences. In addition, it provides a set of connectors to biologial Web services, such as the Basic Local Alignment Search Tool, as well as a utility that enables scientists to view their data within Excel easily and quickly.

    From its core technology to the free availability of the code on which it is built, MBF is the result of collaboration between Microsoft Research and industrial and academic partners, with the aim of building the tools scientists need to pursue biological research. With Microsoft .NET as its base, MBF makes it easier for developers to leverage current technologies, with thousands of functions and a common code base that can be accessed and used with great flexibility.

    One of the areas in which MBF is particularly valuable is the field of genomics, which has experienced tremendous advances since the human genome first was sequenced a decade ago. A full understanding of the human genome offers great potential for advances in health care. To reduce the computational complexity of reconstructing the the whole genome, MBF includes a new whole-genome-assembly algorithm, PaDeNA (Parallel de Novo Assembler). PaDeNA has the potential to reconstruct the DNA sequence of a patient rapidly from huge volumes of experimental data, the first step in using the genome in health care. While PaDeNA is provided freely as a part of MBF, it is designed to be modular and is fully documented, enabling experimental biologists and software developers to tweak the basic algorithm and add features to meet the needs of their research.

    Another example of MBF at work is the research undertaken by David Heckerman, senior director of the eScience group within Microsoft Research. Heckerman, an expert in machine learning, is working on the design of HIV vaccines, which requires an understanding of how the virus evolves in each individual. The next versions of the biological applications Heckerman is developing will use functions built into MBF. Heckerman's applications will continue to be made available for free download on CodePlex[RK2] .

    In keeping with the bioinformatics community's strong tradition of sharing expertise in support of ongoing discovery, I invite you to download it, use it for your work, and contribute your experience to the global research community.

    Simon Mercer, director, Health & Wellbeing, External Research, a division of Microsoft Research

  • Microsoft Research Connections Blog

    Microsoft Research and Collaborate to Remove Language Barriers


    In Helsinki, Finland, on June 11, during the International Council for Scientific and Technical Information (ICSTI) Annual Conference 2010, it was my honor to participate in the announcement of the official launch of multilingual This new, global resource is the result of collaboration between Microsoft Research and, an international alliance of national science and technology agencies and libraries representing 65 countries. The operating agent for is the U.S. Department of Energy's Office of Scientific and Technical Information. uses Microsoft Translator technology developed by Microsoft Research and pairs it with federated searching technology from Deep Web Technologies.

    Photo source: Jakke Nikkarinen/STT Info Kuva. From left: Walter Warnick, U.S. Department of Energy (Office of Science); Office of Scientific and Technical Information, Director; Yuri Arskiy, All-Russian Institute of Scientific and Technical Information (VINITI), Director; Tony Hey, Microsoft External Research, Corporate Vice President; Richard Boulderstone, British Library, Director of e-Strategy; and Wu Yishan, Institute of Scientific and Technical Information of China (ISTIC), Chief Engineer

    I am excited because multilingual provides unparalleled access to science across what were previously language barriers, enabling real-time searching and translation of multilingual scientific literature. Thanks to Microsoft Research's translation technology, the website can simultaneously search and translate more than 400 million pages of scientific research published in 70 countries around the world, 96.5 percent of which is not available via any other search engine. Initially, multilingual enables users to search non-English databases and content in China, Russia, France, Germany, Japan, and several Latin American countries. Multilingual translates search results into the user's language of choice for native speakers of Chinese, English, French, German, Japanese, Korean, Portuguese, Spanish, and Russian. More languages will be added in coming months.

    Developing technology that ensures that large volumes of translations are available quickly in a breadth of languages is an ongoing priority at Microsoft Research. Translation technology plays an important role in our work to foster open communication and collaboration among researchers. Bringing these goals together in our collaboration with has been especially fulfilling. Together, we are helping to make the world's scientific and technical information easily accessible to researchers, students, and governments across the globe.

    The launch of multilingual adds yet another resource that we all can leverage in support of collaborative relationships. Those relationships, in turn, expedite our ability to drive research that has the power to improve lives around the world. All of us at Microsoft Research look forward to more meaningful contributions to multilingual to make the world's scientific and technical information globally accessible. It has been an honor to be involved in this groundbreaking project.

    I invite you to visit the new, improved website and give it a try. I think you will be impressed.

    Tony Hey, corporate vice president, Microsoft External Research



  • Microsoft Research Connections Blog

    New Award Honors Significance of Open, Available Data


    For several years, Microsoft External Research has been a proud sponsor of the BioMed Central Research Awards. The awards honor excellence in an approach to publishing known as "open access research," whereby content is available not only to subscribers but also to anyone online.

    This year, as a result of  productive discussions with BioMed Central's managing director, Matthew Cockerill, the increasingly significant role data plays in research has been recognized with the first BioMed Central Open Data Award, which was presented last night to Yoosook Lee for her article Ecological and genetic relationships of the Forest-M form among chromosomes and molecular forms of the malaria vector Anopheles gambiae sensu stricto. Since 2007, Lee has been a postdoctoral researcher in the Department of Pathology, Microbiology and Immunology at the School of Veterinary Medicine at the University of California, Davis.

    Selecting Lee's article for the award, which includes a $5,000 prize, was determined in large part by the Panton Principles, which were unveiled in February 2010. The Panton Principles offer guidance for those who want to make data related to their published science free of financial, legal, and technical barriers. The Principles were put to use by the judges as guidelines that they were able to use to help them rate, rank, and reward authors for how openly they were sharing their data with others.  (One of the judges, Cameron Neylon, summarizes the judging process in this blog entry.)

    The term "open data" is literal: It calls for the data supporting research to be open and available to all readers. Making data open and available upon publication has become increasingly popular over the past 15 years and is, in fact, mandated by many in the global research community. While the trend toward making data available is a logical step in the evolution of scholarly communication, it is still in an early stage of incubation. Therefore, it's a special honor for Microsoft External Research to support a practice that will encourage innovation and discovery both within and across domains.

    From all of us at Microsoft External Research, congratulations to Yoosook Lee as well as the other winners of this year's BioMed Central Research Awards.

    Lee Dirks, director, Education & Scholarly Communications, Microsoft External Research

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