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March, 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.

March, 2011

  • Microsoft Research Connections Blog

    Microsoft Research and TWAS-AAS Recognize Outstanding Young African Scientists

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    (from left to right) Fayçal Djeffal, Konrad Scheffler, Moustafa Youssef received the 2010 TWAS-AAS-Microsoft Award in a ceremony held in Nairobi, Kenya.

    (from left to right) Fayçal Djeffal, Konrad Scheffler, Moustafa Youssef received the
    2010 TWAS-AAS-Microsoft Award in a ceremony held in Nairobi, Kenya.

    On February 26, 2011, three African scientists received the 2010 TWAS-AAS-Microsoft Award in a ceremony held in Nairobi, Kenya. The award, funded by Microsoft Research Connections, recognizes outstanding research in computer sciences that was conducted by African scientists and has had—or promises to have—an impact on the developing world. The award was established in 2009 as a partnership among Microsoft Research; TWAS, the academy of sciences for the developing world; and the African Academy of Sciences (AAS). This year's winners, each of whom received a cash prize of €7,000, are:

    Fayçal Djeffal, associate professor in the Department of Electronics, Faculty of Technology, at the University of Batna in Batna, Algeria. Djeffal was recognized for his contributions to the development of new approaches to study nanoscale electronic devices and circuits. His research group developed a series of novel soft-computing-based approaches (neural networks, genetic algorithms, particle-swarm computations, neural-space mapping, fuzzy logic, and experts systems) for the modeling of nanoscale electronics devices, now widely employed in many research laboratories.

    Konrad Scheffler, associate professor in the Computer Science Division, Department of Mathematical Sciences, Stellenbosch University, in Matieland, South Africa. Scheffler was honored for his contributions to the fields of bioinformatics and computational biology, particularly the modeling of molecular evolution in HIV and other organisms. His work applies computational techniques and probabilistic modeling to gain insight into the selective forces that drive the evolution of HIV as it adapts to changes in its environment; for example, changes resulting from drugs aimed at suppressing the virus or from the different immune systems of its hosts.

    Moustafa Youssef, assistant professor in the Department of Computer Science and Engineering, Egypt-Japan University of Science and Technology (E-JUST), in Alexandria, Egypt. Youssef was recognized for his contributions to the fields of mobile and wireless networks, particularly in the design, analysis, and implementation of location determination systems. His work covers different layers of the protocol stack from the physical layer up to the application layer, with specific projects that target location determination systems, sensor networks, protocol modeling and analysis, peer-to-peer systems, network measurements, and security.

    The TWAS-AAS-Microsoft Award is open to researchers of any nationality, provided they have resided in Africa for at least two years prior to their nomination. In addition, nominees must have received their most recent degree—either a master's or a doctorate—within the previous 10 years. The selection of winners is handled by TWAS in collaboration with AAS. As noted above, the award is funded by Microsoft Research Connections, the division of Microsoft Research that drives collaboration with academic researchers and institutions.

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    —Luisa Marie Küppers, EMEA Business Manager, Microsoft Research Connections

  • Microsoft Research Connections Blog

    Free MBF Workshop at RENCI in North Carolina

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    Microsoft Biology FoundationWe recently posted a preview of the Microsoft Biology Foundation (MBF) for development evaluation purposes. Now, we're following up with a special, free, two-day MBF workshop from April 19 to 20, 2011, at the Renaissance Computing Institute in Chapel Hill, North Carolina, hosted by the Microsoft Biology Initiative. The workshop includes a quick introduction to Microsoft Visual Studio 2010, the Microsoft .NET Framework, C#, and the MBF Object Model. Plus, our hands-on lab will give you the opportunity to write a sample application that employs the file parsers, algorithms, and web connectors in MBF. For complete details about the event, or to register, please see the MBF Workshop website.

    We will also cover some MBF training modules throughout the day, including:

    • Module 1: Introduction to Visual Studio 2010 and C#. This comprehensive introduction to the Microsoft Visual Studio programming environment and Microsoft .NET will teach you how to create a project, get started with C#, and perform runtime debugging. Also, you will get hands-on lab experience by building applications in Visual Studio 2010.
    • Module 2: Introduction to the Microsoft Biology Foundation. This overview will introduce you to MBF basics through discussions of its scenarios and architectures and includes a starter project. The starter project is a hands-on lab that will help you get the experience you need to work with sequences, parsers, formatters, and the transcription algorithm that is supplied in MBF.
    • Module 3: Working with Sequences. In this module, you'll learn more about the Sequence data type in MBF, including how to load sequences into memory and save them, the different sequence types that are available, how to use sequence metadata, and how data virtualization support enables support for large data sets in a hands-on lab setting.
    • Module 4: Parsers and Formatters. In Parsers and Formatters, you'll explore MBF's built-in sequence parsers, formatters, alphabets, and encoders. This module will also introduce the method of expanding MBF with custom alphabets, parsers, and formatters. The hands-on lab will walk you through the steps that are required to build a simple custom parser and formatter for a fabricated biology data format.
    • Module 5: Algorithms. In this module, you will examine the algorithms that are defined in MBF for sequence alignment, multi-sequence alignment, sequence fragment assembly, transcription, translation, and pattern matching against sequences. You'll also learn how to create custom algorithms. The hands-on lab will walk you through the steps that are required to build an application to run algorithms against sequences loaded with MBF and will teach you how to perform sequence alignment, assembly, and transformations.
    • Module 6: Web Services. This module will introduce Microsoft .NET web services, the web service architecture in MBF, the built-in web service support in MBF for BLAST (Basic Local Alignment Search Tool), and ClustalW. You will also learn how to call these services asynchronously and build custom service wrappers. In the hands-on lab, you'll build an application that executes the BLAST algorithm by using web services against handlers for BLAST, pass sequences and sequence fragments to BLAST, change the BLAST parameters, and display the results from a BLAST run.

    We hope you will join us for this free two-day event. Whether your goal is to get trained on MBF or simply to evaluate MBF and its Microsoft .NET model, you can expect to get a tremendous return on your time investment.

    We look forward to meeting you on April 19 in Chapel Hill.

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     Swatee Surve, Research Program Manager, Health and Wellbeing, Microsoft Research Connections

  • Microsoft Research Connections Blog

    InnerEye: Visual Recognition in the Hospital

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    The neurosurgeon hovers over the patient, preparing to excise a life-threatening brain tumor. In this delicate operation, there is no margin for error: the tumor needs to be cut out with minimal damage to the surrounding healthy tissue. By using simple hand gestures, the surgeon signals a computer to display high-resolution scans of the patient’s brain, showing the physician where to place her scalpel, detailing the boundaries between diseased and healthy tissue. No longer must the neurosurgeon stop to refer to the patient’s image data during the operation, removing her gloves and potentially compromising the sterile surgical field. The upshot for the patient: reduced time under anesthesia and a lower risk of introduced infection.

    Interactive Segmentation of CT and MR Scans

    Science fiction? Far from it. This scenario and others like it are on the verge of realization thanks to ground-breaking InnerEye project being conducted by Microsoft Research and a host of collaborators, including Johns Hopkins Medical Institute, The University of Oxford, Cornell Medical School, Massachusetts General Hospital, the University of Washington, Kings College London, and Cambridge University Hospitals

    The analysis of medical images is essential in modern medicine. As images have achieved higher and higher resolutions, the increasing amount of patient data has presented new challenges and opportunities, from diagnosis to therapy. The InnerEye research shows how a single, underlying image-recognition algorithm can enable a multitude of clinical applications, such as semantic image navigation, multimodal image registration, quality control, content-based image search, and natural user interfaces for surgery.

    InnerEye takes advantage of advances in computer-human interactions that have put computers on a path to work for us and collaborate with us. The development of a natural user interface (NUI) enables computers to adapt to you and be more integrated into your environment via speech, touch, and gesture. As NUI systems become more powerful and are imbued with more situational awareness, they can provide beneficial, real-time interactions that will be seamless and naturally suited to your context—in short, systems will understand where you are and what you’re doing.

    At this year’s TechFest—the annual event that showcases the latest work from Microsoft Research’s labs around the world—InnerEye is one of several projects that show where Microsoft is headed with NUI technologies, and how “futuristic” computing experiences are quickly becoming a reality. Building on the success of Kinect—a prime example of NUI technology reaching consumer scale—Microsoft Research continues to explore technologies that will enable the coming shift in how humans will communicate with machines, and vice versa. The possibilities are seemingly endless in how we approach the integration of computing into our lives and can enable a new era of creativity, social interaction, and technological scenarios.

    Antonio Criminisi, Researcher, Microsoft Research and Kristin Tolle, Director, Natural User Interface Team, Microsoft Research Connections division of Microsoft Research

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