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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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    Creating Better Software for Next-Generation Computer Architectures

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    Computers are everywhere, controlling everything from phones and traffic lights to airplanes and buildings. And inside each computer is software: line after line of complex code that tells the program, and any attached hardware, what to do.

    It’s amazing how the world has come to rely on software.

    Testing is a vital step in software development, but it’s hard to test every possible path through millions of lines of code. For example, in 2003 the northeastern United States and Canada experienced a blackout that affected more than 50 million people due to an obscure problem in the energy management system software. It was admitted afterwards that even extensive testing would not have found this problem. So we need more formal methods to determine such program behavior in advance. This software verification—the science of deducing whether a program will execute correctly—is crucial for reliability in complex programs.

    Much of the existing work in software verification does not consider the processor design itself, which is a problem because new multi-core processors and more complex computer architectures are being designed for next-generation computing platforms—from mobile phones and tablet devices to cloud computing data centers. A new collaboration between Koç University in Turkey, Microsoft Research, and the Barcelona Supercomputer Centre is taking a unique multidisciplinary approach, bringing together world-leading researchers in computer architecture, formal methods, and systems to produce a coherent, end-to-end, robust methodology for computer architecture design.

    Dr. Serdar Tasiran from Koç University leads the discussion with his research team: Hassan Salehe Matar, Cansu Erdogan, Umit Can Bekar, Omer Subasi, Zeynep Su Kurultay, and Emre Gul.

    Dr. Serdar Tasiran from Koç University leads the discussion with his research team:
    Hassan Salehe Matar, Cansu Erdogan, Umit Can Bekar, Omer Subasi, Zeynep Su Kurultay, and Emre Gul.

    Research leader at Koç University, Serdar Taşıran, is excited about this new project, “After working together for many years, it is tremendous that we are beginning this formal collaboration between Microsoft Research and Barcelona Supercomputer Centre to look at the whole problem of software verification from the processor-up.” This follows a strong history of working closely with Microsoft Research in Redmond, Cambridge, and India.

    The team aims to create a holistic, robust approach to the development of novel computer architectures. This is required to simultaneously push the state-of-the-art while permitting application-driven scenarios to be taken into account at an early stage in the hardware design.

    Tim Harris, a senior researcher at Microsoft Research Cambridge, explains “Modern programming languages such as F# rely on multiple layers of software for activities such as garbage collection and managing parallel work items. This collaboration will help us develop new hardware techniques to accelerate these activities, while ensuring that the correctness of programs is not compromised."

    Mateo Valero, director of Barcelona Supercomputing Center, adds, “This collaboration simultaneously targets the three requirements that modern multi-core computing faces today: processors should be fast and efficient, they should be easy to program, and they should compute in a verifiable and correct way."

    Fabrizio Gagliardi, director of Microsoft Research Connections Europe, the Middle East, and Africa (EMEA), is delighted. “This is a strong partnership that brings together world experts in software verification and computer architecture to solve this hugely challenging problem,” he says. “We look forward to this project paving the way to more reliable software on tomorrow’s hardware.”

    Kenji Takeda, Solutions Architect and Technical Manager, Microsoft Research Connections EMEA

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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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