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December, 2010

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.

December, 2010

  • Microsoft Research Connections Blog

    How Microsoft Technology and Research Are Helping Create a Clearer Picture of HIV

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    Nearly 30 years since its discovery, the human immunodeficiency virus (HIV) continues to prove a difficult virus to pin down because it mutates so rapidly—a trait which, so far, has made an effective vaccine for this often-deadly condition impossible to develop.

    That might change, thanks in part to new Microsoft tools that are being used to construct maps of the mutating virus, which may in turn help identify prospective vaccine candidates.

    HIV mutates at such a high rate that the virus is distinct for each individual patient. The level of viral variation in one HIV patient is comparable to the worldwide level of variation during the course of an influenza epidemic.

    The PhyloD Viewer draws proteins as circles to reveal mutation patterns that could aid in HIV vaccine design.

    The PhyloD Viewer draws proteins as circles to reveal mutation patterns
    that could aid in HIV vaccine design.

    A first step in overcoming this challenge is to identify consistent patterns in viral adaptation. Tools such as PhyloD, PhyloD Viewer, and Phylo Detective can be used to identify and visualize HIV covariation and adaptation. By identifying patterns and constraints in HIV evolution, scientists are able to focus on HIV's weaknesses, with the goal of designing a vaccine that will be resistant to HIV mutation. The arcs in the circle pictured above, developed with the PhyloD Viewer, represent how HIV in a single patient is connected to itself as parts of it mutate.

    This research delivered a statistical approach that could help further research into HIV mutation. It also led to the observation that patterns of HIV evolution are broadly predictable based on host immunogenetic profiles. In other words, we found a promising consistency in the way that HIV adapts to the human immune response, which could pave the way for vaccine design. 

    It's worth noting that this work is built on the Microsoft Biology Foundation, which provides consistent file formats, statistical packages, and resources to farm out computations to clusters of machines—permitting scientists to focus on the science of modeling the virus and identifying its vulnerabilities.

    —Jonathan Carlson, Researcher for Microsoft Research, eScience

  • Microsoft Research Connections Blog

    .NET Gadgeteer Redefines What Gadget Fans Can Do with Modular Components and Object-Oriented Programming

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    This example of the Gadgeteer main board has several modules attached through standard connectors. The modules include a display, an LED, button, an Ethernet connection, and a Zigbee radio.Once upon a time, being a "gadget fanatic" usually meant you were an early adopter of new technologies, someone who'd own the latest multi-megapixel digital camera or high-powered handheld device. A rare few with engineering and embedded development programming skills might push this a bit further, creating something new from hardware components by soldering, wiring, and coding a new gizmo into existence. But such aspirations were out of reach for many hobbyists and potential inventors.

    All that is about to change. Before long, gadget groupies will be able to reach the level of custom hardware configuration thanks to the .NET Micro Framework and the forthcoming .NET Gadgeteer rapid prototyping platform. Perhaps best described as building blocks for electronics, an aspiring gadget maker can connect various hardware components (no soldering required), develop functionality by using object-oriented Microsoft .NET programming, and even design a novel enclosure for a custom device. Functions can include sensing the environment, taking pictures, displaying images, playing sounds, and even communicating with other devices and the Internet.

    In the coming year, .NET Micro Framework hardware modules—including displays, sensors, cameras, radios, MP3 players, and Ethernet ports—are expected to become available for purchase through third-party partners. The prototype hardware, available in kits to select researchers, was recently shared at the 2010 New York Maker Faire event for do-it-yourself technologists. The platform's inventor, Nicolas Villar, demonstrated the system with his Microsoft Research colleagues James Scott, Steve Hodges, and Kerry Hammil, together with the product unit manager for the .NET Micro Framework, Colin Miller. Attendees were impressed by the Gadgeteer demos, which included an MP3 player, a Simon-type matching game, and a remote sensing system that enabled users to control a camera. One attendee became so enthralled with the technology that he picked it up and started demoing it to others! The booth went on to win the Maker Faire "Editor's Choice Best-in-Show" and "Most Interactive Demo" awards.

    This is an exploded view of the Simon game (which was made as a demo for Maker Faire) showing the Gadgeteer modules and the custom case.Since Maker Faire, Microsoft Research has been developing the infrastructure needed to further develop Gadgeteer as a product and partnering with high school and university teachers to bring Gadgeteer to students. At an internal Microsoft "science fair" event, it beat out tough technological competitors to take the "President's Award" given by Terry Crowley, a technical fellow and the director of development for Microsoft Office.

    If you're interested in seeing the .NET Gadgeteer in action, you can view the Channel 9 video demonstration and the Make Magazine video from Maker Faire. Additional opportunities to see Gadgeteer in person are planned for the TEI 2011 Conference in January 2011 and Microsoft Research Software Summit in April 2011. If you're an educator who is interested in Gadgeteer, visit the .NET Micro Framework Academic page to get involved.

    —Scarlet Schwiderski-Grosche and Stewart Tansley, Research Program Managers in the External Research division of Microsoft Research

    P.S. Here's a festive example (semantic Christmas lights!) of what you can do with .NET Micro Framework, which should be even easier with Gadgeteer.

  • Microsoft Research Connections Blog

    Preparing for Transformation: How Convergence in Computer Science and Biology Could Fuel the Next Healthcare Revolution

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    Computers have increased the reach of biological science, altering the path of medicine with such revolutions as human genome sequencing—which is already causing a shift in treatment approach from epidemiological (based on patterns in the general population) to care that is tailored to individuals.

    Center for Computational and Systems BiologyResearchers attending the fifth anniversary of the Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI) believe it's time to take a more active role in developing the computer systems and tools needed to further transform the healthcare industry. The event, which took place November 30 through December 3 in Trento, Italy, examined the topic "Merging Knowledge: From Programming Languages to Personalized Healthcare."

    "It appears that systems medicine will transform medicine over the next 5 to 20 years from its currently reactive state to a mode that is proactive—medicine that is predictive, personalized, preventive, and participatory (P4)," says Leroy Hood, president of the Institute for Systems Biology. "P4 medicine will have striking implications for healthcare costs as well as leading to a transformation of the healthcare industry."

    Success will require a change in approach and investment in the right technologies. "There is great excitement and potential for the use of computer-science solutions to enhance biology-related disciplines, both in the scientific community and in the industrial community," states Corrado Priami, COSBI president and CEO. "Therefore, our idea of investing in the design and development of an integrated artificial plug-in based biological laboratory, connecting computational modeling with experiments, and built on top of a (programming) language for biology is the right strategy to lead the innovation wave at which we will assist in the next years."

    In particular, the study of nutrigenomics—or interactions between nutrients and genes—could unlock the key to more effective treatment and prevention of diabetes, obesity, and cardiovascular diseases. "Developing individual risk factors in light of the genetic diversity of human populations; the complexity of foods, culture, and lifestyle; and the variety of metabolic processes that lead to health or disease are significant challenges for personalizing dietary advice for healthy or medical treatments for individuals with chronic disease," reports James Kaput of the U.S. Food and Drug Administration. "New research and application strategies are needed for creating knowledge for personalizing nutrition advice and healthcare."

    Achieving these results is possible only with the proper set of conceptual and computational tools, which can extract knowledge from data—as happened in major scientific fields in recent years with the move to eScience methods of distributed computing and collaboration.

    At the conference, top speakers from the center's scientific reference community discussed recent findings that can enable and propel personalized healthcare with system-level understanding of interactions between molecular machinery of organisms and diseases, between drugs and multi-signaling networks, between nutrients and metabolism of organisms, and between food production and environment through the exploitation of programming language technology.

    Here are some highlights:

      • Tony Hoare described Process Algebra, a model that formulates abstract mathematical equations that describe general properties of an important class of phenomena in the real world. Originally, Process Algebra was applied primarily to what happens inside computers and computer networks, but now it has been extended and is applied to biological phenomena at various scales of granularity and abstraction.
      • Leroy Hood explained how emerging computing technology can dramatically impact system biology and system medicine.
      • Andrew Herbert spoke on "Medical and Biological Topics at Microsoft Research Cambridge" (watch a webcast on this topic).
      • Jeannette M. Wing, President’s Professor of Computer Science and department head of the School of Computer Science at Carnegie Mellon University, gave a visionary talk on how computing is creating a new revolutionary computational thinking paradigm.
      • Daron Green, general manager of the External Research division of Microsoft Research, described how existing tools can be used to improve the way in which data and information are discovered/shared/visualized. He also discussed lessons learned from collaborative research engagements that are associated with realizing External Research's vision for the Computational Paradigm.

    —Fabrizio Gagliardi, Director of EMEA (Europe, Middle East, Africa), the External Research division of Microsoft Research

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