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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 Evolves into New Toolkit: .NET Bio

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    .NET Bio logoThe Microsoft Biology Foundation (MBF) has undergone a significant transformation since it was first released. Over time, it’s become clear that a new name was also in order. So today, I am pleased to announce that MBF will now be known as .NET Bio. In addition to the new name, .NET Bio will also have a new location: the Outercurve Foundation. This move is the next logical step in the life of the project: transferring its ownership to a nonprofit foundation that is dedicated to open-source software underscores our community-led philosophy; while Microsoft will continue to contribute to the code, it will do so as one among a growing community of users and contributors.

    About .NET Bio

    .NET Bio is a bioinformatics toolkit that was built using the Microsoft 4.0 .NET Framework. It is designed for use by developers, researchers, and scientists, making it simpler to build applications to meet the needs of life scientists. This open-source platform features a library of commonly used bioinformatics functions plus applications built upon that framework, and can be extended by using any Microsoft .NET language, including C#, F#, Visual Basic .NET, and IronPython.
     
    Users can perform a range of tasks with .NET Bio, including:

    • Importing DNA, RNA, or protein sequences from files with a variety of standard data formats, including FASTA, FASTQ, GFF, GenBank, and BED.
    • Constructing sequences from scratch.
    • Manipulating sequences in various ways, such as adding or removing elements or generating a complement.
    • Analyzing sequences by using algorithms such as Smith-Waterman and Needleman-Wunsch.
    • Submitting sequence data to remote websites (for example, a Basic Local Alignment Search Tool [BLAST] website) for analysis.
    • Outputting sequence data in any supported file format, regardless of the input format.

    Like other frameworks (for example, BioJava and BioPython), .NET Bio can help reduce the level of effort that is required to implement bioinformatics applications through the provision of a range of pre-written functionality.

    In addition to enhancements to the performance and capacity of the basic features contained in the previous version, the new version will provide a range of new features and demo applications. This includes:

    • Access to advanced math functions by using Sho scripting
    • A comparative DNA sequence assembler sample application
    • A range of command-line utilities

    .NET Bio is now in use by both academic and commercial organizations—including Microsoft—worldwide.

    Simon Mercer, Director of Health of Wellbeing, Microsoft Research Connections


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  • Microsoft Research Connections Blog

    The Promise of Games in Lifelong Learning

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    We are pleased to announce the launch of a program that is designed to support collaborations between Microsoft Research Connections and major research institutions to build the foundations for a unified game layer for education. Our first official project is Just Press Play, an experiment to craft gameful experiences for the students of Rochester Institute of Technology (RIT) undergraduate game design program. (Gameful experiences incorporate the use of game play mechanics that focus on the user's intrinsic motivation, engaging the user in a way that can produce long-lasting and powerful results.) You can learn more about the project by visiting the Just Press Play developer blog.

    Just Press Play: Students bringing gameful experiences to education.

    Just Press Play: Students bringing gameful experiences to education.

    Microsoft Research has a long-standing commitment to games for learning, which began more than a decade ago with our support of Henry Jenkins and the MIT Education Arcade through programs like Games to Teach and iCampus. This work complemented games research that was being performed by Michel Pahud, Andy Wilson, and other Microsoft researchers. More recently, we founded the Games for Learning Institute, a consortium of 8 universities, 14 principal investigators, and a small army of graduate students whose mission is to find out what makes games fun, what makes them educational, and to develop patterns that assist developers in the creation of effective educational games.

    One of those principal investigators is Andrew Phelps, director of the RIT School of Interactive Games and Media. Andy began his experiments with games for learning in 2003, when he created the Multi-User Programming Pedagogy for Enhancing Traditional Study (MUPPETS) to teach computational thinking through 3-D graphics and animation. More recently, he and Jessica Bayliss began pushing the boundaries of games in the classroom by conducting an experiment to award experience points to students in lieu of grades. In collaboration with Elizabeth Lawley, director of the RIT Lab for Social Computing and creator of the citizen heritage experiment, Picture the Impossible, he began to develop a much more ambitious idea: create a “frame game” that wraps around the most common activities that are inherent to student life at RIT. In other words, he is developing a platform that deeply integrates with the school’s core student information systems in order to create gameful experiences for students that pervade their online experience, versus their person-to-person interactions. By using this platform and the resulting experiences, he can gather data on student activities, improve student motivation, and reduce attrition in the IGM freshman class.

    The Just Press Play experiment is an important first step in bringing gameful experiences to education, but it is only the beginning. Throughout the year, we intend to announce additional partnerships with other researchers and organizations to build out the foundations of a unified game layer for education. This layer is similar to the social layer developed in the first decade of the twenty-first century to support a unified representation of identity and social networks across websites and applications. The social layer is arguably complete with the creation of the Open Graph protocol and applications such as Bing Social Search. Now we need to begin work on another layer, one that will instrument our everyday experiences, transform these experiences into gameful experiences and, by doing so, provide the inputs to entirely new capabilities such as e-portfolios, adaptive learning, and project-based learning.

    Intrinsic motivation is a primary goal of the game layer, but there are other benefits as well. Because a great deal of data is needed to power these gameful experiences, we are encouraging participants to instrument their the online experience versus person-to-person interactions in a way similar to how Foursquare encourages players to keep track of the places they visit. This instrumentation provides entirely new insights into the worlds of students and educators. It enables large-scale longitudinal studies that span the many institutions of learning that we travel through over the course of our lives. It is the promise of true lifelong learning environments to teach twenty-first-century skills and guide our students along a rewarding journey of lifelong learning. We look forward to inviting you to the game!

    Donald Brinkman, Research Program Manager, Games for Learning, Digital Heritage, Digital Humanities, Microsoft Research Connections

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    ChronoZoom Named Top Educational Resource at 2013 SXSW Interactive

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    When Microsoft Research teamed up with the University of California Berkeley to create a digital tool for exploring the history of everything, we knew we had the potential to build a killer educational app. After all, a tool that can reveal the cross-currents of history, revealing the interdependencies that cut across disciplines, geographies, and cultures, would offer a major advance in the understanding of Big History—the history of not just humanity, but of life, Earth and, ultimately, the cosmos. Moreover, it would provide researchers with a tool to derive unique insights based on multidisciplinary connections between vastly disparate data sets.

    ChronoZoom wins the 2013 SXSW Interactive Award for Education

    On March 12, the resulting tool, ChronoZoom—a dynamic, zoomable timeline that starts with Big Bang and ends with modern history—won first prize in the Educational Resources category of the 2013 SXSW Interactive Awards. As described on the SXSW website, the SXSW Interactive Awards competition “uncovers the best new digital work, from mobile and tablet apps to websites and installations, while celebrating those who are building tomorrow's interactive trends.”

    ChronoZoom was developed to make time relationships between different studies of history clear and vivid. In the process, it provides a framework for exploring related electronic resources. It thus serves as a “master timeline,” tying together all kinds of specialized timelines and electronic resources, and aspires to bridge the gap between humanities and the sciences and to bring together and unify all knowledge of the past. With the planned addition of in-browser content and authoring tools, we hope to enable educators and researchers to build timelines; explore rich, multidisciplinary contextual spaces; and to tell and share stories based on authoritative data.

    Donald Brinkman, Roland Saekow, and Michael Zyskowski accept the 2013 SXSW Interactive Award for Education
    Donald Brinkman, Roland Saekow, and Michael Zyskowski accept the 2013 SXSW Interactive Award for Education 

    The prestigious SXSW Interactive Award for Education recognizes the educational value of this amazing open-source product. Moreover, it honors the multidisciplinary team that came together to make ChronoZoom a reality: software engineers, program managers, and project leaders at Microsoft Research Connections in Redmond, Washington, and students and professors at Moscow State University in Russia and at UC Berkeley and University of Washington in the United States. This distributed team developed cutting-edge HTML5 and JavaScript code and implemented services on Windows Azure to create a rich, visual database full of historical events and timelines.

    The ChronoZoom project is part of the Outercurve Foundation’s Research Accelerators Gallery. The Outercurve Foundation, a non-profit, open-source foundation, provides software IP management and project development governance to 22 open-source projects.  Developers can get involved by visiting the source code project on GitHub.

    In his acceptance speech, Michael Zyskowski dedicated the award to Lee Dirks, who strongly believed in and supported the ChronoZoom project.

    I encourage you to experience the power of ChronoZoom for yourself. But be forewarned—it can be addictive!

    Donald Brinkman, Program Manager, Microsoft Research Connections


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