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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.

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    EPA Cooperative R&D: Technology for Aquatic Ecosystem Restoration

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    “Despite its size, Puget Sound is ecologically delicate; and while its symptoms of trouble are not easily visible, they are undeniable and getting worse.”
    —The Puget Sound Partnership

    Tony Hey, vice president, Microsoft Research Connections, and Dennis McLerran, regional administrator, EPA Region 10 sign the agreement.We at Microsoft Research Connections have begun work on a cooperative research and development (R&D) project with the U.S. Environmental Protection Agency (EPA) that centers on the restoration of large aquatic ecosystems, particularly Puget Sound. On Friday, November 30, we got together and put our respective imprimaturs on the Cooperative Research and Development Agreement (CRADA), the formal agreement for this partnership. Now all that remains is to do the actual work! Here are some details about the project, which was created under the auspices of the Federal Technology Transfer Act, and why it is so exciting for us.

    As you may know, we have a history—under the leadership of Vice President Tony Hey—of collaborating with researchers outside of Microsoft. Often, we collaborate with academicians doing research in computer science or—in my case—using technology to cope with environmental and geoscience data. We’re also very interested in how science registers in the public domain. For example: land-use policy can benefit from scientific insight, and we think that if technology can help scientists do data-intensive research, it should also help us manage resources, find better ways to preserve habitat, and better share this information with farmers, tribes, municipalities, and the general public. Taking an active role in the stewardship of our shared environment is what the EPA is about, so we began talking with them about working together.

    Tony Hey, vice president, Microsoft Research Connections, and Dennis McLerran, regional administrator, EPA Region 10, shake on the agreement.
    Tony Hey, vice president, Microsoft Research Connections, and Dennis McLerran, regional administrator, EPA Region 10, shake on the agreement.

    It can be difficult to comprehend how big our environment is and yet how tiny its essential elements are. Viewing Puget Sound from 40,000 feet above, it is a vast, beautiful expanse of waterways, inlets, islands, and peninsulas that are crisscrossed with the indelible stamp of cities, roads, and ferry boats supporting the lives of a few million people. Drop your perspective to the shoreline of Fir Island (Washington), and you find green strands of eelgrass washed up on the beach; under a microscope, these strands explode into millions of nodules of chlorophyll, the stuff that converts sunlight into sugar and powers the entire food web all the way up through the salmon. My point is that we inhabit the land and we depend on the health of our natural environment: from the great waterways we use for shipping to the smallest microbes and molecules. As the Puget Sound Partnership has stated, we have work to do to restore and protect the ecological health of Puget Sound, but where to begin?

    The idea of this new cooperative R&D project with the EPA is to explore how available data and technology might be fused to help us better understand and meet the needs of the restoration community, including the kinds of cooperative relationships the community members want to build between the public, the land-holders, the decision makers at the county and city level, and so on. From this learning perspective, we are confident that we can imagine and build proof-of-concept solutions that would be openly available for further development and adoption. For example, we imagine (from preliminary work) applying PhotoSynth technology to the challenge of creating a more robust depiction of the shoreline. Human-built structures like sea walls are distributed throughout Puget Sound and can impact habitat, particularly for grazing fish that spawn in shallow water. More broadly, we see similar efforts at organizations like the Northwest Association of Networked Ocean Observing Systems (NANOOS) that aim to assemble and disseminate data about sea conditions, tides, and weather to help commercial fishing operations become more efficient.

    What more can be done? The opportunities are boundless! What is really exciting is that our colleagues at EPA and in the broader Puget Sound community share a passion for this work; we feel very fortunate to be a part of it and are enthusiastic about the opportunity to contribute.

    Rob Fatland, Senior Research Program Manager, Microsoft Research Connections

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    TouchDevelop in Your Browser

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    TouchDevelopAre you looking for a little extra cash for the upcoming holidays? Then you might be interested in creating some cool apps to sell in the Windows Store. Or maybe you’re simply curious and want to try your hand at developing for Windows 8 and Windows Phone. In either case, the newly released TouchDevelop Web App is for you.

    TouchDevelop Web App is a development environment to create apps on your tablet or smartphone, without requiring a separate PC. Scripts written by using TouchDevelop can access data, media, and sensors on the phone, tablet, and PC. The script can interact with cloud services, including storage, computing, and social networks. TouchDevelop lets you quickly create fun games and useful tools, turning your scripts into true Windows Phone and Windows 8 apps.
     
    A year ago, Microsoft Research released TouchDevelop for Windows Phone, which is being used by enthusiasts, students, and researchers to program their phones in fun, inventive, and interesting ways. These scripts are available at TouchDevelop for anyone to download and use.

    Ever since we released TouchDevelop, we’ve been eyeing the tablet form factor and working on a version for the browser. Now, with the release of TouchDevelop Web App, the wait is over: the tablet version is ready, so go play around with it.

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    All TouchDevelop scripts that are developed on the smartphone can be downloaded to the tablet and run (if hardware allows). Any script that is developed on the tablet can also be accessed on the phone. And scripts can be converted to Windows Phone or Windows 8 apps and submitted to the Windows Phone Store or Windows Store, respectively.

    TouchDevelop Web App’s editor and programming language have been designed for tablet devices with touchscreens, but you can also use a keyboard and a mouse. So grab your web-enabled device and give the TouchDevelop Web App a try. It’s fun and easy, and could even put a little cash in your holiday-depleted wallet. Or at least give you bragging rights at family get-togethers.

    Arjmand Samuel, Senior Research Program Manager, Microsoft Research Connections

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    Predicting the Effects of Changes on Living Systems

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    Predicting the Effects of Changes on Living SystemsCan scientists predict what happens when they introduce a change into a living system—for example, if they change the structure of a gene or administer a drug? Just as changing one letter can completely change the meaning of a word, the change of a single letter of the genetic code (referred to as a single nucleotide polymorphism, or SNP) can subtly affect the meaning of a gene’s instructions or alter them completely, making the effect of any change extremely hard to predict. Such changes are thought to be responsible for much of the variation between members of a single species—for example, in susceptibility to different diseases. The ability to successfully predict the effect of such changes would accelerate drug discovery and provide a deeper understanding of the processes of life.

    In collaboration with Jasmin Fisher at Microsoft Research Cambridge, professor Yanay Ofran and his colleagues at Bar Ilan University have embarked on a program of scientific research that aims to resolve some of the questions underlying this overall goal, and some of their early results have now been published.

    One of the researchers’ first tasks was to determine whether it is possible to predict how a complex network of biochemical interactions will change when a SNP (pronounced “snip”) alters the function of one of the network’s components. In an August 2012 paper entitled, “Static Network Structure Can Be Used to Model the Phenotypic Effects of Perturbations in Regulatory Networks” (available at Bioinformatics with paid subscription), the authors describe their success in analyzing static models of biological networks and correctly predicting the response to changes more than 80 percent of the time. This enables the functions of the network to be deduced, the foundation for building a more expressive dynamic model.

    Building static networks is a challenge in itself; before beginning this work, the researchers needed to understand which genes are active in a particular cell and what they do. In their latest publication entitled, “Assessing the Relationship between Conservation of Function and Conservation of Sequence Using Photosynthetic Proteins” (available at Bioinformatics with paid subscription), the Ofran lab has shown that, while sets of related genes with similar structure diverge in function more quickly than previously thought, selected smaller pieces of each gene may still be useful in predicting function.

    There are many unresolved challenges along the way to the eventual goal of predicting the effect of a SNP—understanding which genes are switched on in which cells and how drugs interact with proteins are just two active areas of investigation—but once the goal is reached, an understanding of the functions of all genes and how changes affect biological systems could lead to the development of computational models to predict and cure many diseases.

    Simon Mercer, Director of Health and Wellbeing, Microsoft Research Connections

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