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October, 2011

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.

October, 2011

  • 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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    Kinect for Windows SDK Beta Makes It Big in the Big Apple

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    The Kinect for Windows SDK beta was honored as one of the “10 Most Innovative Tech Products of 2011” earlier this week at the 2011 Popular Mechanics Breakthrough Awards ceremony held at the Hearst Tower in New York City. Gavin Jancke, general manager of Engineering for Microsoft Research, who led the engineering and release for the Microsoft Research release of the Kinect for Windows SDK beta, accepted the award on behalf of Microsoft.

    Award recipients were invited to demonstrate their technologies at a reception following the seventh annual ceremony. Gavin presented the SDK (software development kit) from a developer perspective discussing, among other things, skeletal tracking and raw sensor data. Jacob Vanderplas, an astronomer at the University of Washington, further illustrated the potential applications of the SDK in natural user interface (NUI) technologies with a presentation of the Kinect-controlled WorldWide Telescope concept demonstrator.

    From left to right: Jim Meigs, editor in chief of Popular Mechanics; Gavin Jancke, general manager, Engineering, Microsoft Research;  Bill Congdon, publisher of Popular Mechanics, pictured at the Popular Mechanics Breakthrough Awards ceremony

    From left to right: Jim Meigs, editor in chief of Popular Mechanics; Gavin Jancke, general manager of Engineering for Microsoft Research; and Bill Congdon, publisher of Popular Mechanics, pictured at the Popular Mechanics Breakthrough Awards ceremony

    The ceremony was our second visit to New York City in as many months. Previously, we were pleased to present the SDK at the World Maker Faire 2011, which was held at the New York Hall of Science in late September. Maker Faire is an inspiring showcase of creativity and cool technology that celebrates technology enthusiasts of all ages. This year’s event attracted 35,000 attendees, up 40 percent from the previous year.

    Presenting at Maker Faire 2011

    We were joined at this year’s Maker Faire by our colleagues from Microsoft Robotics and Microsoft .NET Gadgeteer. Our teams jointly exhibited in a combined tent. We offered attendees just a taste of our technologies that are available for hobbyists, enthusiasts, and educators. The showpieces in our tent were the newly launched Robotics Developer Studio 4 beta and a new reference design robot, EDDIE, available from Parallax, Inc. We also presented two Kinect SDK beta demos: on-board robot sensing and NUI robot control—including a roving “party photographer” robot that proved very popular with young and old alike.

    In addition to demonstrating our technologies, we were also honored with two awards at the Maker Faire: an inaugural “Makey” award for Kinect, and an “Editor’s Choice” blue ribbon for our combined booth. It was fantastic to see so many people inspired by technology, including our own. We continue to look forward to seeing your inventions and ideas come to fruition.

    Stewart Tansley, Director of Natural User Interface, Microsoft Research Connections

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    FIRST Adds Kinect Technology to Robotics Competition Tool Kit

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    I’m thrilled to be part of a new phase of the partnership between Dean Kamen’s FIRST (For Inspiration and Recognition of Science and Technology) organization and Microsoft (including the Microsoft Research Connections group). Last week, FIRST announced that Microsoft’s Kinect for Xbox 360 sensor and the Kinect for Windows SDK beta software will be included in the standard robotics Kit of Parts for the 2012 FIRST Robotics Competition (FRC) season.

    Dean Kamen, an American entrepreneur, inventor, and founder of FIRST, reveals Kinect as part of the 2012 FRC competitionDean Kamen, an American entrepreneur, inventor, and founder of FIRST, reveals Kinect as part of the 2012 FRC competition

    FRC is a unique “Varsity Sport for the Mind,” which is designed to help young people discover the interesting and rewarding aspects of engineering and research, while challenging teams and their mentors to solve problems in a six-week timeframe by using a standard Kit of Parts and a common set of rules. The 2012 kit will include Kinect technology, enabling competitors to not just control the robot, but to “be the robot.”

    By combining the Kinect technology with robotics, competitors will be able to control their robots by using a natural user interface—with potentially no joystick, game controller, or other input device required. Teams will have the option of programming their robots to respond to custom gestures that their human teammates create, or by using default code and gestures. Kinect will be beta tested by using robots built by FIRST students in the coming weeks in preparation for the 2012 competition.

    Kinect for Windows SDK beta
    “This is an awesome capability to incorporate into a robot,” said Bill Miller, director of FIRST Robotics Competition. “By working with Microsoft, we are able to provide FRC students with an additional high-level sensor capability, adding to the options for our students’ strategy on the field as well as delivering a unique robotics experience. This experience will take the competition to a new level, while also helping equip students with the skills and tools to innovate in the twenty-first century.”

    During the 2011 season, 2,072 FRC teams, totaling 51,800 students, competed at 59 events in the United States, Canada, and Israel. Participants are eligible to apply for nearly US$15 million in scholarships at more than 140 colleges and universities. An estimated 60,000 competitors will have access to Kinect technology in the 2012 competition.

    “By putting the amazing capabilities of the Kinect sensor in students’ hands, FIRST is able to provide a compelling and powerful new technology for the teams,” said Tony Hey, corporate vice president, Microsoft Research Connections. “With so many students already familiar with Kinect for Xbox 360 at home, in school, and lately even on their PCs via the Kinect for Windows SDK beta, I’m sure it will be a popular choice.”

    We are honored to partner with the amazing FIRST organization and their thousands of student, educator, and parent participants. It is exciting to see so many young people inspired by these technologies and we look forward to being amazed by their creativity during the upcoming competition!

    Stewart Tansley, Director of Natural User Interface, Microsoft Research Connections

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