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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

    Presenting the History of Everything

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    ChronoZoom: an infinite canvas in time

    Today, March 14—Einstein’s birthday no less—marks the release of the beta version of an incredible new tool for the study of history: ChronoZoom. This powerful open-source tool, a joint effort of the University of California, Berkeley; Moscow State University; the Outercurve Foundation; and Microsoft Research Connections, will be unveiled at the Northwest Council for Computer Education (NCCE) Conference and is available for download.

    What, you might ask, is so wonderful about ChronoZoom? After all, history resources abound. There are thousands of digital repositories, collections, libraries, and websites full of images, videos, documents, facts, and figures—not to mention the wealth of content squirreled away in private offices, personal computers, and university servers. But the sheer volume and disparate locations of these resources confound researchers, educators, and students, who spend untold hours searching this information, seeking to better understand history and its lessons for our future. What if we had a tool that could bring all these resources together?

    Moreover, despite increasing collaboration, the sciences and humanities are still largely taught and researched in silos. For example, when I took an East Asian Studies course in college, I learned what was happening in China in the 1400s, but not what was going on in the Middle East or Africa or Latin America, or what was taking place in the scientific realms of physics and chemistry. If we brought these worlds together, would we ask different questions? Would we arrive at new understandings of the past, resulting in different innovations and insights today?

    Such are the questions we hope to answer with ChronoZoom, which makes time relationships between different studies of history clear and vivid. In the process, it provides a framework for exploring related electronic resources, including videos, text, charts, schematics, images, articles, and other multimedia content. ChronoZoom thus serves as a "master timeline," tying together all kinds of specialized timelines and electronic resources, and it aspires to bridge the gap between the humanities and the sciences. In the spirit of “make no small plans,” ChronoZoom seeks to unify all knowledge of the past and to make this information easy to understand.

    In so doing, ChronoZoom emerges as a potentially vital tool in the evolving field of Big History, which attempts to unify the past—all of the past, from the beginning of time, some 13.7 billion years ago, to the present—through the four major regimes: cosmic history, Earth history, life history, and human history. Big History offers a broad understanding of how the past has unfolded, and it lets us explore the unifying characteristics that can bridge the intellectual chasm between the humanities and the sciences.

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    Today’s release of ChronoZoom is especially exciting for me because this tool was made by the academic community for the academic community. There’s no other timeline tool today that is supported by such a vast number of experts in different disciplines around the world. ChronoZoom has two communities that are led by two outstanding universities:

    • The content community, which provided the digital content to populate and share on ChronoZoom, led by Professor Walter Alvarez and Roland Saekow at the University of California, Berkeley
    • The development community, which built the feature set to bring ChronoZoom to life, led by Dr. Sergey Berezin at Moscow State University.

    In addition, significant student involvement sets ChronoZoom apart. On the dev side, more than 80 percent of ChronoZoom is the work of undergraduate and graduate computer science students at Moscow State. The amazing application you can explore today was developed in three months by these students with support from Microsoft Research engineers. Similarly, 90 percent of the content in ChronoZoom was organized and developed by students at Cal Berkeley. 

    Today’s release is a call to action to the academic community to try ChronoZoom in their classrooms and then vote on its features and let us know what could make the tool even more useful. For academic experts and digital collection owners, it’s an opportunity to help determine the content that should be in ChronoZoom. For computer science institutions and developers around the world, it’s a call to join our open-source community and help us build the next set of features.

    ChronoZoom has a long history and has gone through different phases of development. In the spring of 2009, Roland Saekow had the good fortune of taking Professor Alvarez's Big History course. During the course, Professor Alvarez used a variety of tools, from log scales to multi-sheet paper timelines, to convey the vast time scales of Big History.

    Luckily, Saekow remembered a TED talk about a new computer zoom technology called Seadragon. He approached Professor Alvarez after class, and they started brainstorming about how a zoomable timeline would function. With the help of the Industry Alliances group on campus, they got in touch with Microsoft Research and Microsoft Live Labs, which helped produce the first prototype version of ChronoZoom.

    Today, with feedback from other Big History, humanities, and science professors around the world, we are focused on creating an all-new ChronoZoom that is a great educational tool for the classroom and research tool for academics. After creating the first version of ChronoZoom, we worked in collaboration with universities, professors, and students to make this tool easier to use in the classroom, but we definitely encourage feedback. This is why we are making the ChronoZoom beta version available to the community—hoping for significant feedback and collaboration to create a great tool that helps students, educators, and researchers really understand the history of everything.

    We’re pleased to announce that the ChronoZoom project is now 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. The foundation’s four galleries—the Research Accelerators, ASP.NET Open Source, Data, Languages and Systems Interoperability, and Innovators Galleries—support the collaborative development of software in open-source communities, yielding faster results and improved community development for organizations and research groups worldwide

    If you’re attending the NCCE Conference, I hope you’ll visit me today as I launch ChronoZoom beta in a training workshop for educators. And wherever you are, please try out the ChronoZoom beta in the weeks ahead, as we hope to get more than 500,000 users providing feedback over the next six months. If you want to help with content or development, please email us at chronozoomproject@outercurve.org.

    Zoom away!

    Rane Johnson-Stempson, Education and Scholarly Communication Principal Research Director, Microsoft Research Connections

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    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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