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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

    U.K. e-Science Program a ’Jewel’

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    On a gloomy day in December 2009, an international panel of experts met at the unlikely venue of a football stadium on the outskirts of Oxford, U.K. The panel, chaired by Dan Atkins, who recently stepped down as director of the National Science Foundation's (NSF's) Office of Cyberinfrastructure, convened to review the achievements of the U.K. e-Science Programme, which I had the privilege of directing from 2001 to 2005, before I joined Microsoft Research. The venue for the review was chosen to overlap with the 2009 U.K. e-Science All Hands Meeting (AHM). These AHMs were begun in 2002, and their continuation three years after the end of the program's formal funding is, for me, a testament to the passion and strength of the multidisciplinary e-science community that we created. I was present in Oxford to discuss my management and organization of the e-Science Core Programme, and I was curious to see what impression the achievements of U.K. e-science would make on this distinguished panel.

    The review was organized by the U.K. Engineering and Physical Sciences Research Council (EPSRC), which had set up a punishing schedule for the panel-a virtually nonstop series of interviews and visits, with hardly a moment to breathe. The results of the review have now been published on the EPSRC website, and I was delighted that the panel had concluded "that the U.K. e-Science Program is in a world-leading position along the path of building a U.K. Foundation for the Transformative Enhancement of Research and Innovation." They further declared that "the U.K. has created a 'jewel', a pioneering, vital activity of enormous strategic importance to the pursuit of scientific knowledge and the support of allied learning."

    The report concluded with recommendations for action by the United Kingdom and included a plea for the need to support "Crossing the Chasm" between research prototypes and mainstream cyberinfrastructure. Atkins recently presented a summary of the international panel's conclusions to the NSF Advisory Committee for Cyberinfrastructure.

    The NSF's Office of Cyberinfrastructure is developing a detailed implementation plan for U.S. cyberinfrastructure. Ideally, the NSF will take some of the good things from the U.K. e-science experience and avoid some of those that proved less successful!

    -Tony Hey, corporate vice president, External Research, a division of Microsoft Research

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    ScholarLynk facilitates management and sharing of research

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    Regardless of how much content is available to today's researchers, it loses value if it cannot be properly managed and shared. At this week's 14th European Conference on Research and Advanced Technology for Digital Libraries (ECDL) at Glasgow University in Scotland, Microsoft Research will present the prototype of ScholarLynk, a desktop solution designed to help researchers more effectively manage, organize, and share ideas and information.

    One of the main goals of ScholarLynk is to make scholarly data as easy to access and manage as one's personal music collection. Unlike other offerings, ScholarLynk doesn't lock the user into a particular tool or service. Instead, it bridges data silos by enabling the user to manage information across repositories and applications.

       

    ScholarLynk builds on research that was conducted as part of the Research Desktop project at Microsoft Research Cambridge. It leverages the infrastructure that was built as part of the Digital Repository Infrastructure Vision for European Research (DRIVER), a two-phase project funded by the European Union to provide access to over two and a half million publications in 250 repositories located in 33 countries.  Over the last year, DRIVER has also spawned the formation of the Confederation of Open Access Repositories (COAR). Microsoft Research is a sponsor of COAR; Tony Hey, corporate vice president of the External Research Division of Microsoft Research, serves on the organization's advisory board.

    By providing a unified interface for managing desktop and web data sources, ScholarLynk allows researchers to access the content of the DRIVER repositories from within their own computing environment. It also supports a highly collaborative environment, essential for projects being undertaken by more than one researcher. Currently, the prototype offers the ability to create reading lists by tagging the desired resources, seamlessly incorporating remote resources onto the desktop, and to communicate contextually by sharing readings lists and collaborating with other users of ScholarLynk.  Efforts are underway to include additional communication tools that will provide automatic subscription notifications, conversational capabilities, and routine updates when a user's work is edited or cited by others. Such tools will further connect ScholarLynk users with relevant content.

    In addition to connecting to the DRIVER repositories, the long-term vision for ScholarLynk is for it to evolve into a platform that can provide federated access to multiple repositories and portals, such as Microsoft Academic Search, Google Scholar, and CiteULike. Currently in prototype form, ScholarLynk will be available for download by the end of 2010.

    Alex Wade, director for Scholarly Communication, External Research, a division of Microsoft Research

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    Microsoft Researchers Present New Statistical Method for Genetic Analysis

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    A deeper understanding of a disease's genetic underpinnings can lead to better biological insight into the disease and, thus, to improvements in screening, treatment, and drug development. This week, Jennifer Listgarten, David Heckerman, and Carl Kadie of Microsoft Research and Eric E. Schadt of Pacific Biosciences made a significant contribution to researchers' insight into the role genetics plays in human disease. Their article, Correction for Hidden Confounders in the Genetic Analysis of Gene Expression, was published today in Proceedings of the National Academy of Sciences, one of the world's most-cited multidisciplinary scientific serials.

    Their research offers a possible solution to challenges presented by the variety of confounders hidden in genetic data that lead, when improperly addressed, to both spurious and missed associations. The article presents a new statistical method that better captures the true biological signal of interest by removing interfering signals from the data. Applying the method to real and synthetic data, the paper demonstrates the need for a joint correction of two types of confounders and shows the disadvantages of other possible approaches found in the current literature. In particular, the paper demonstrates that a new class of methods has maximum detection power on synthetic data and the best performance when applied to real data, as judged by a commonly accepted bronze standard.  The software used will be available for free download.

    While the article recommends future avenues in which the method could be used, the framework can be applied today on existing data sets with SNP and gene-expression data, two of the most common types of biological data sets. In the future, I believe this new method will become even more relevant in the search for new and improved ways to manage disease. The central problem addressed by this work, of identifying which genetic markers affect the expression of specific genes, leads directly into improving analyses that aim to identify the biological processes that lead to disease. And those future discoveries of biological processes could have a direct impact on identifying the causes of amyotrophic lateral sclerosis, cancer, heart disease, HIV/AIDS, and many other complex diseases that affect many of us.

    -Tony Hey, corporate vice president, External Research, a division of Microsoft Research

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