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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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    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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    Preserving Mayan Language into the Next B'ak'tun

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    Mayan calendarThe best way to describe how I’m feeling is deeply honored and emotionally moved. This is the feeling I get every time we start a Microsoft Translator Hub project in language preservation or translation because it is always an honor and privilege to work on preserving a language. Whether it’s in Fresno, California, working to preserve Hmong, or in distant Dhulikhel, Nepal, working to provide translations for Nepali, the feeling’s the same—a visceral sense of making an impact. I can attest that this feeling is a distinct benefit of being a part of the Microsoft Research Connections team.

    The last week of September, I visited the Mexican states of Yucatan and Quintana Roo—or more accurately, I was warmly welcomed to these homelands of the Mayan people. Together with my colleagues Erick Stephens, director of technology at Microsoft Mexico, and Adrian Hernandez Becerril, a program manager at Microsoft Mexico, I came to the Universidad Intercultural Maya de Quintana Roo to finalize a project to preserve the Mayan language. Our visit marked the culmination of months-long discussions with the university and various government officials and was, in my opinion, a significant day on any calendar (more on calendars below).
     
    The future of the Mayan language is uncertain. University president Francisco Javier Rosado-May said it best when we first spoke back in May at the 2012 Latin American Faculty Summit in Cancun: “If we do not do anything to stop it, Mayan will be extinct within two generations.” President Rosado-May is extremely motivated to turn the tide, to change the future of the Mayan language, and his enthusiasm is infectious. So we and our partners in Microsoft Mexico decided to sponsor a project at his university along with Assistant Professor Martin Esquivel-Pat, to enable Mayan to survive the present and leap into the next b'ak'tun (in other words, the next long cycle of the Mayan calendar).
     
    For those of you who are concerned that the Mayan calendar predicts the end of the world this December 20, let me assure you, as my hosts in Quintana Roo assured me, this is simply the end of a time period in the Mesoamerican Long Count calendar developed by the Mayans—a timekeeper more accurate than our own Julian calendar, by the way. What the Mayans say is that this December 21, we will be starting the next b'ak'tun, and with that, we hope, an era where Mayan remains a viable language for generations to come.

    On arrival at the university, we were greeted by Javier Díaz Carvajal, head of the Secretariat of Economic Development for Quintana Roo, who, on behalf of the governor, extended me the honor of being made an “adopted citizen” of Quintana Roo. Afterwards, we signed an agreement with the government and the university to work on developing a Mayan language translation system that is solely built by the community and shared only when they decide to do so. And that is the real benefit of the Microsoft Translator Hub: it places the power of developing automatic translation models into the hands of the community where it belongs.

    For the remainder of the day and the one that followed, we gave presentations and trained our hosts, professional translators, and students at the university on using the Microsoft Translator system, both through the Hub interface (which any bilingual person can use with a little training) and programmatically (which requires some technical knowledge). The latter is significant, as the university is looking to establish a computer and information science program, and this programmatic work with the Microsoft Translator Hub can help them build expertise in this area. My colleagues and I wanted to assist them in this endeavor in every way possible.
     
    But back to building the language translation system. Microsoft Translator Hub makes the process easy, but it still takes time and commitment from the community—it doesn’t just happen overnight. It took our partners at California State University of Fresno and the Hmong Language Partners more than seven months to collect and add enough parallel data (between Hmong and English), upload it to the system, train, build, and release the Hmong translator.

    We got a preview of how the Mayan translation system might work at a workshop we ran in Quintana Roo—which focused largely on building a translator system between Spanish and Yucatec (a local Mayan dialect). Participants employed another distinguishing feature of the Microsoft Translator Hub that enables you to build translation systems directly between any two languages instead of pivoting (and propagating errors) through English. How long it will take to build a functional Mayan translator is unknown right now, but I know the community is very motivated to get it done early in the next b'ak'tun!

    I believe it is vital to future of the human race that we remember and preserve our past. My colleagues and I are thrilled to have the opportunity to play even a small part in making that happen.

    Kristin Tolle, Director, Natural User Interactions Team, Microsoft Research Connections

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