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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.

  • Microsoft Research Connections Blog

    Colombian Center for Bioinformatics and Computational Biology Established

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    As we approached the holiday season in Colombia, we had already received one of the biggest gifts on our wish-list: on November 12, the government of Colombia officially committed to the establishment of the Center for Bioinformatics and Computational Biology in the city of Manizales, an important academic hub located in west-central Colombia. The Center is an ambitious project that aims to provide scientific and technical support to businesses, public organizations, universities, and research centers throughout Colombia. It will offer much-needed technology for processing and storing data, and will strengthen the country's research capacity by providing computational capability to other centers of excellence in Colombia and, potentially, across Latin America.

    The government's action confirmed the Center as a legal entity, which enables it to receive funding and to initiate the selection of the final site and begin the planning, design, and building of its infrastructure. The venture brings together government and private parties including the Ministry of Information Technologies and Communications (known by its Spanish initials, MINTIC) and the Administrative Department of Science, Technology, and Innovation (better known as Colciencias) from the government side; and Microsoft Colombia, Microsoft Research, and a group of prestigious universities including the University of Caldas, the Autonomous University of Manizales, the University of Manizales, Quindío University, the University of Technology of Pereira, and Tolima University.

    Speaking at the commitment announcement, ICT Minister Diego Molano Vega underscored the significance of the Center's establishment: "This is an important step for the government, the consolidation of a project that we believe allows Colombia to position itself as a country that enhances the use of information technology in such strategic areas as biotechnology and biodiversity."1

    With a government investment of 4.6 million Colombian pesos (US$2.5 million) for the first year, and a commitment to comparable funding for each of the next two years, the Center is well positioned to embark on its first major project. Since its main goals include research in biology and computer science, the Center intends to focus on Colombian biodiversity, with the goal of creating synergies and knowledge-sharing among researchers at universities, government agencies, and private industry.

    Microsoft has been involved in the Center since its very beginning, helping to conceptualize the project with MINTIC, Colciencias, and a group of international experts. Microsoft Research has offered to support the Center in designing its technical architecture and to provide bioinformatics research tools based on high-performance computing (HPC) and the cloud. 

    Orlando Ayala, corporate vice president and chairman of emerging markets at Microsoft, said that "the creation of this Center is a great opportunity for the country to generate research and scientific development." Ayala emphasized Microsoft's commitment to the biodiversity research project, which will, he noted, "establish a direct bridge between Microsoft Research and the Center for Bioinformatics and Computational Biology."1

    Microsoft External Research's involvement in this project aligns perfectly with the group's charter to harness the power of science and technology by fostering collaboration worldwide among academia, industry, and governments.

    —Jaime Puente, Director, Microsoft External Research, a division of Microsoft Research

    __________

    1. "Nace primer Centro de Bioinformática y Biología Computacional," Dinero.com, accessed December 20, 2010. Machine translated as "Born first Center for Bioinformatics and computational biology."

  • 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

  • Microsoft Research Connections Blog

    Virtual Fire System Aids Firefighters in Wildfire Combat and Prevention

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    When a wildfire strikes, every second counts. Time lost can all too often be measured in lost life, deforestation, and property damage. Enter the Virtual Fire application, based on Microsoft Bing Maps, ESRI ArcGIS, and other software. This web geographic information system (GIS) platform is designed to support wildfire early warning, control, and civil protection by sharing information and tools produced by the Geography of Natural Disasters Laboratory at the University of the Aegean in Greece.

    With these new tools, firefighting personnel, emergency crews, and other authorities can design an operational plan to contain the forest fire, pinpointing the best ways to put it out with new levels of precision. Fire management professionals can locate fire service vehicles and other resources online and in real-time. Fire patrol aircrafts use Global Positioning System (GPS) tracking and communications to send coordinates for each item to Virtual Fire, which depicts them on a web GIS. Cameras can augment this data by transmitting images of high-risk areas into the Virtual Fire system.

    One of the compelling advantages of Virtual Fire is that it enables fire management professionals to take advantage of GIS capabilities without extensive training on complicated GIS applications. The platform enables end-users to query the databases and get answers immediately, locate points of interest in high-resolution satellite images, and download information to their portable computers or GPS devices.

    But the Virtual Fire application offers services beyond simple coordination of emergency efforts. Remote automatic weather stations and a weather forecasting system based on the SKIRON weather model (developed by the Atmospheric Modeling and Weather Forecasting group at the University of Athens) provide crucial data needed for fire prevention and early warning. Virtual Fire provides geographical representation of the fire risk potential and identifies high-risk areas at different local regions daily, based on a high performance computing (HPC) pilot application that runs on Windows HPC Server.

    "Virtual Fire hosts and visualizes models used for predicting forest fire risk and behavior to understand how the fire is likely to spread, based on the actual meteorological data, vegetation, and landscape morphology," says Kostas Kalabokidis, geography professor at University of the Aegean and principal investigator of the Virtual Fire initiative. "These prediction data—along with a plethora of other information spanning roads, location of water tanks, the positioning of aircrafts and vehicles, vegetation types, and weather data—will be visualized over online maps such as Bing Maps. This will enable fire fighters in control centers, or on-site via handheld devices, to more effectively manage forest fires and deal with any other emergencies situations that may arise."

    The system runs on servers that were donated by Hewlett Packard (three quad-core computing nodes: one head node and two computing nodes). By using the FARSITE and FlamMap fire behavior software (created by Missoula Fire Sciences Laboratory), maps are produced on demand to graphically represent the spread and intensity of a forest fire at different times and places. In addition, user feeds and email messages provide effective communication between users and administrators for reporting events.

    During the course of its development, the Virtual Fire platform delivered some early successes in combating and even deterring wildfires. On July 8, 2009, an extremely dangerous wildfire broke out on Lesvos Island. The Virtual Fire system—which was at its initial stage, only partly operational with the fire-risk probability index and the weather forecasting and monitoring—provided the fire service with a better grasp of local topography and details of current and imminent weather as well as the high-risk prediction map. This resulted in a prompt initial response that prevented the fire from uncontrolled enlargement and encroachment to nearby sensitive ecological preserves and a military base camp. Virtual Fire successfully predicted the fire risk for the particular area where the event took place, which led to its status as a preferred fire risk prediction tool in 2010.

    During the 2010 fire season (from April to October), no serious fire breakouts developed on Lesvos Island, in contrast to other Greek islands such as Samos. Almost all of the fire events were promptly confronted; fires were not permitted to overgrow and they responded to initial efforts to subdue them. Evidence currently under investigation suggests that Virtual Fire played an important role in these improved results, offering the local fire service valuable information to utilize for decision support with their own considerable operational experience and knowledge.

    Coordinating Prefecture Board of Lesvos, Mytilene, in Greece

    Coordinating Prefecture Board of Lesvos, Mytilene, in Greece

    The results of the Virtual Fire initiative were presented July 6, 2010, at the Coordinating Prefecture Board of Lesvos, Mytilene, in Greece. Event attendees included the prefect and counsellors of Lesvos Prefecture, mayors and representatives of the Municipalities of Lesvos Island, heads of Civil Protection, officers and fire fighters of the North Aegean and Mytilene Fire Services, staff of Lesvos Forest Service, commanders and officers of military and public service authorities, representatives of social services and fire-fighting volunteer organizations of Lesvos Island, and the partners of the project from University of the Aegean, University of Athens, Microsoft Research, Microsoft Hellas, and Microsoft Innovation Center—Greece. For more information, read the press release.

    —Scarlet Schwiderski-Grosche, Research Program Manager, External Research division of Microsoft Research, Cambridge

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