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November, 2012

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.

November, 2012

  • Microsoft Research Connections Blog

    Cloud Computing Unlocks Drug Discovery


    Helping scientists discover new drugsAntibiotics, antivirals, NSAIDs—the list of modern “wonder drugs” goes on and on. And yet many diseases remain resistant to drug therapy, and in other instances, the side effects of drug treatment are as bad as or worse than the disorder. Why, the public wonders, aren’t more new and better drugs coming to market? 

    The answer, in a word, is cost. Modern drug discovery involves identifying likely candidates and then screening them for biological efficacy and potential toxicity. This process is enormously, often prohibitively, expensive.

    Toxicity prediction in particular remains one of the great challenges of drug discovery. Even after decades of unprecedented funding, scientists still struggle to predict the toxic side effects for any given compound. Traditional statistical models that are based on empirical data, while wonderful in theory, have one key shortcoming. Unless researchers have access to either a state-of-the-art corporate datacenter or one of the world’s few supercomputers, there’s just too much data to analyze efficiently. The identification of compounds that will cause a desired biological effect requires a huge investment in technical infrastructure.

    At least it did until recently. Now, the power of cloud computing offers a relatively inexpensive alternative to the huge up-front costs of building out a high-powered computing infrastructure. Researchers from Molplex, a small drug-discovery company; Newcastle University; and Microsoft Research Connections are working together to use cloud computing to help scientists across the globe deliver new medicines faster and at lower cost. This collaborative partnership has helped Molplex develop Clouds Against Disease, an offering of high-quality drug discovery services based on a new molecular discovery platform that draws its power from Windows Azure.

    The Clouds Against Disease computational platform runs algorithms to calculate, rapidly, the numerical properties of molecules. As a result, Molplex has been able to produce drug discovery results on a much larger scale than has ever been seen before.

    The Molplex method enables researchers to address practical issues when screening compounds. Will the compound be toxic? Will it pass safely through the human intestine? Will it stay in the body long enough? The Molplex process features extreme front loading that identifies viable drug candidates early in the research process. Contrast this with the traditional approach, which involves a great deal of up-front experimental work that is wasted when the researchers later learn that the hoped-for drug is toxic.

    Access to Windows Azure, Microsoft’s cloud platform, was critical to the success of Clouds Against Disease. Molplex can take advantage of 100 or more Windows Azure nodes, which are in effect virtual servers, to process data rapidly. The physical-world alternative would be to source, purchase, provision, and then manage 100 or more physical servers, which represents a significant financial investment. Scientists taking this traditional approach would have to raise hundreds of thousands, or even millions of dollars before they could begin drug research. That’s a huge barrier for scientists around the world who want to engage in drug discovery. Windows Azure helps to eliminate start-up costs by allowing new companies to pay for only what they use in computing resources.

    One of the biggest potential impacts of Clouds Against Disease lies in its ability to make drug discovery affordable for tropical diseases and niche disorders—categories that have long been low priority for drug companies, due to their limited commercial payoff. The requirement of a multi-million dollar investment before even going into the clinic doesn’t work for scientists studying drugs to combat such diseases. Radically reducing the cost of drug discovery makes it feasible for scientists to tackle these scourges and bring hope to countless sufferers around the world.

    Fabrizio Gagliardi, Cloud Engagements in EU, Microsoft Research Connections

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    Fighting Wildfires with Data


    When wildfires strike, all eyes turn to the clouds, hoping for a downpour that will quench the flames. Now, wildfire prevention teams on the Greek island of Lesvos are looking to a different kind of cloud for help, thanks to the VENUS-C Fire application and the computing power of Windows Azure.

    The Fire app determines the daily wildfire risk on Lesvos during the months of May to October, when the annual dry season turns the island’s forests into a tinder box. The application not only alerts fire prevention teams of the risk, it also enables firefighters to design and coordinate an effective response when a wildfire breaks out. As a result, the island’s fire prevention personnel have been better prepared to predict, respond to, and stop fires, preventing potential loss of life and property.

    The Fire app integrates Bing Maps, Microsoft Silverlight, and Windows Azure in a single system that enables users to see the potential of an emerging fire
    The Fire app integrates Bing Maps, Microsoft Silverlight, and Windows Azure in a single system that enables users to see the potential of an emerging fire

    Developed by the Geography of Natural Disasters Laboratory at the University of Aegean in Greece, the Fire app is designed to calculate and visualize the risk of wildfire ignition and to simulate fire propagation. The end users are primarily emergency responders, including the fire service, fire departments, and civil protection agencies that address wildfires on the island of Lesvos.

    The app was built with functionality from multiple resources, giving it both technological depth and a visual interface that is accessible to non-technical users. It integrates Bing Maps, Microsoft Silverlight, and Windows Azure in a single system that enables users to see the potential of an emerging fire.

    All of the Fire app’s data is stored in the cloud via Windows Azure. And a lot of data it is, including information on topography, vegetation, weather patterns, and past fire patterns. This is “big data,” and crunching it requires the computing power of a large cloud infrastructure, such as Windows Azure.

    Professor Kostas Kalabokidis of University of the Aegean calls Windows Azure essential to the app, noting that “the cloud provides us with the necessary processing power and storage that is required. That means the real end users for the fire department do not need to have any huge processing power or storage capabilities locally.” Indeed, on the end-user side, all that’s needed to access the tool is a regular computer or laptop, an Internet connection, and a web browser that supports Silverlight.

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    The Geography of Natural Disasters Laboratory team built the Fire app in 2011. Microsoft Research partnered with the lab during the development phase, providing funding, high-performance computing resources, and cloud computing infrastructure. As part of that collaboration, Microsoft built a tool called the Generic Worker (GW) that greatly simplified the challenges faced by Kalabokidis’ team.

    GW was critical, according to Professor Kalabokidis, who states that “Generic Worker provides a robust environment for job execution that fulfilled the requirements of the University of the Aegean’s scenario for running forest fire risk and fire propagation models in the cloud. GW provides interoperability through OGF [Open Grid Forum] Basic Execution Service, which is very important in the Aegean scenario to execute tasks in a hybrid cloud environment, such as VMs [virtual machines] of different cloud solutions. Furthermore, GW provides scalability: for example, VMs are increased or decreased according to the needs of deployment. Users are also notified about the status of the job, which is important for the execution of the fire propagation simulation.”

    The Fire app is just one of many big data projects that benefit from Windows Azure’s scalability, storage capacity, and computational power. There’s no question but that cloud computing is having a significant impact throughout the research world, as information from instruments, online sources, and social media are combining to create a data tsunami. This has ushered in the era of data-intensive science—what the late Jim Gray predicted would be the Fourth Paradigm of scientific research—and Windows Azure is in the forefront of making it possible.

    Cloud computing, and the processing power that accompanies it, has made it possible for researchers to reduce processing job times from months to just hours. The thing that excites me about my job is the possibility that we can change the way science is conducted. I believe that cloud computing is a revolutionary change in an era of big data and the exploration of large data collections.

    Dennis Gannon, Director of Cloud Research Strategy, Microsoft Research Connections

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    Chinese Edition of "The Fourth Paradigm" Released


    Over the past two years, I have watched eScience take root in China. The movement advanced in the first and second Chinese eScience forums and in various eScience projects that were developed by the Computer Network Information Center (CNIC) of the Chinese Academy of Sciences (CAS). During this time, Microsoft Research collaborated closely with the CAS, exchanging ideas through joint workshops, student contests, and lectures such as the keynote that Tony Hey, vice president of Microsoft Research Connections, delivered at the CAS meetings in 2010. 

    Chinese edition of "The Fourth Paradigm"Through these channels, a foundational concept of eScience—that we are entering a new fourth paradigm for science where discovery advances through data-intensive computing—was introduced to the Chinese eScience community and attracted the attention of the CAS. In late 2010, Xiaolin Zhang, the executive director of the National Science Library of the CAS, proposed a Chinese translation of The Fourth Paradigm, a seminal collection of essays that describe the practice and promise of data-intensive science. I am happy to report that through the efforts of the CAS and the support of Microsoft Research, the Chinese edition of The Fourth Paradigm premiered in Beijing on October 23.

    Tony Hey and Stewart Tansley, two of the book’s co-editors, joined Lolan Song, Steve Yamashiro, and me at the launch event. On behalf of Microsoft Research, Tony donated copies of the book to more than 80 Chinese university libraries, observing that "The advance of science depends on how well researchers collaborate with one another, and marry science with technology." I, for one, am confident that the publication of the Chinese edition of The Fourth Paradigm will foster just such endeavors.

    Xiaolin Zhang and Tony Hey celebrate the release of the Chinese edition of "The Fourth Paradigm"Jiaofeng Pan, the deputy secretary-general of the CAS and one of the book’s Chinese translators, spoke highly of the Chinese edition. “Building on the studies from the field of eScience, the book proposes the fourth paradigm for scientific research: data-intensive science as well as academic exchange based on big data. This book opens the door to a new paradigm of scientific research, greatly enhancing awareness of the huge impact of the digital revolution in the research and information network.”

    Through the release of the Chinese edition, we sincerely hope to help Chinese researchers in a variety of fields to understand and utilize this revolutionary development in research methodology. To further speed the adoption of data-intensive approaches to research, Microsoft Research has agreed to donate 2 million hours of access to Windows Azure cloud resources, as well as 15 terabytes of Windows Azure storage space, to research projects at the CNIC over the next two years, which will enable Chinese researchers to apply the concepts of the fourth paradigm by using the Windows Azure platform.

    In 2013, the IEEE International Conference on e-Science and the Microsoft eScience Workshop will be held jointly in Beijing. Looking forward to those events, we anticipate even more progress in eScience research in China.

    Guobin Wu, Research Program Manager, Microsoft Research Asia

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