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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

    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

    Building a Collaborative Research Relationship with the Chinese Academy of Sciences

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    I recently had the great pleasure of visiting with staff at the Chinese Academy of Sciences (CAS) in Beijing, China. CAS is China's leading academic institution and comprehensive research and development center in natural science, technological science, and high-tech innovation. The Asia-Pacific Microsoft Research Connections team has done a terrific job of establishing a relationship with CAS in recent years. That early groundwork paid off in many ways during my visit to the CAS in February.

    Tony Hey, Corporate Vice President, Microsoft Research Connections presents The Fourth Paradigm: Data-Intensive Scientific Discovery.

    Tony Hey, Corporate Vice President, Microsoft Research Connections presents
    The Fourth Paradigm: Data-Intensive Scientific Discovery.

    There are more than 100 institutes under CAS to focus on specific research areas. I visited the Computer Network Information Center (CNIC), which is a public institution that supports networks and information infrastructure for CAS. Professor Tieniu Tan, deputy secretary of CAS, and some researchers from different research institutes that are involved in the eScience program came to CNIC to host my visit. Among the topics we discussed were eScience-related projects and the Academic Cloud Program at Microsoft Research. I found the CAS team very welcoming and ready to share ideas. We will be building on that enthusiasm: as of February, CAS is a key Microsoft Research Connections partner for eScience in China.

    In addition to meeting one-on-one with CAS high-level staff, leading researchers, and executives, I had the pleasure of delivering my presentation, The Fourth Paradigm: Data-Intensive Scientific Discovery. The audience included a diverse student body as well as faculty representing various research fields, such as chemistry, high-energy physics, biotechnology, geography, environment, database, computing, engineering, and automation.

    Although I was there to speak, I was also there to listen. One of my hosts, Professor Mingqi Chen, director of the Information Department of the CAS General Office, presented on cyber-infrastructure and eScience applications in CAS in three categories:

    The goal of the eScience program in CAS is to build an Open Science Cloud that serves CAS researchers and the broader scientific community. Professor Chen presented some typical eScience applications in CAS, including Galactic Wind Simulation, a real-time prediction of sandstorms system, and ChinaFLUX, which includes a large scientific facility, a field sensor-network real-time data-collection system, and an astronomical virtual laboratory.

    My visit ended on a positive note when another of my hosts, Professor Tieniu Tan, approached me to propose that we further our collaboration through a joint eScience workshop. This workshop will take advantage of the eScience experience and resources that both CAS and Microsoft Research have acquired through our past research work. We will meet again soon to work out the details of this next collaborative venture.

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    Tony Hey, Corporate Vice President, Microsoft Research Connections

  • Microsoft Research Connections Blog

    Brazilian Research Celebrated

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    On March 17, Microsoft Research Connections and the São Paulo Research Foundation (better known by its Portuguese acronym: FAPESP) held a workshop to mark the ongoing collaborative efforts of the Microsoft Research-FAPESP Institute. The theme of the workshop—revisiting the past and planning for the future—provided the scientific community with a historical perspective on the Institute's completed projects, its ongoing initiatives, and the prospects for future investments.

    Harold Javid, Director of Microsoft Research Connections, Carlos Henrique de Brito Cruz, Scientific Director of FAPESP and Michel Levy, President of Microsoft Brazil during the meeting MSR-FAPESP Institute Workshop: revisiting the past and planning the future.

    Harold Javid, Director of Microsoft Research Connections, Carlos Henrique de Brito Cruz, Scientific Director of FAPESP and Michel Levy, President of Microsoft Brazil during the meeting MSR-FAPESP Institute Workshop: revisiting the past and planning the future. 

    The presentation of newly funded research projects broke with tradition this year: previously restricted to researchers and teams who are directly involved with the selected projects, the event was opened to all professionals and researchers interested in learning more about the opportunities created by the program. By so doing, the Institute reached out to researchers and scientists from other areas of knowledge, while simultaneously stressing the role of information technology in accelerating scientific research on priority themes.

    The event was attended by Carlos Henrique de Brito Cruz, scientific director of FAPESP, and Michel Levy, president of Microsoft Brazil. Leonardo de Moura, a senior researcher at Microsoft Research in the United States who specializes in theorems and the optimization and verification of software, presented the first lecture, "Symbolic Reasoning @ Microsoft: Tackling Impossible Tasks." Harold Javid, the director of Microsoft Research Connections (a division of Microsoft Research) explored the theme of e-science, addressing such fertile areas for collaboration as medical imaging research, a new approach to creating digital narratives, and compelling possibilities for sharing "big time" views of history.

    Announced at the workshop were the four projects that were selected in the latest call for proposals. The researchers who were responsible for the approved proposals then made brief presentations of their studies.

    • Eleanor Patricia Cerdeira Morellato, Bioscience Institute of Universidade Estadual Paulista (Unesp), presented the e-Phenology project, which implements new technologies to monitor ecology and climate change in the tropics. This multidisciplinary project combines research in computer science and phenology, a branch of ecology that studies the development cycle of living organisms and its relation to such environmental conditions as temperature, light, and humidity.
    • Junia Coutinho Anacleto, Center of Exact Sciences and Technologies at Universidade Federal de São Carlos (UFSCar), presented a project that will use natural user interface (NUI) technology to help patients develop their social skills. Developed in partnership with the Center for Intensive Attention to Health (CAIS) and Clemente Ferreira, a hospital that serves people with neurological and psychiatric disorders, the project also seeks to improve the interaction between health professionals.
    • Ronaldo Fumio Hashimoto, Institute of Mathematics and Statistics at the University of São Paulo (USP), presented a project that will use math and computational modeling to examine the biological processes that underlie molecular organization and the regulatory relationships of molecules and genes. The research will use new computational and statistical techniques to understand how biological processes occur and how to prevent those that cause disease from taking place.
    • Regina Célia de Matos Pires, Instituto Agronômico (IAC), presented a project that will use environmental monitoring and genetic modeling to calculate the potential of sugarcane cultivars based on the availability of groundwater. This research is important in light of forecasts that predict expanded cultivation of sugarcane in arid regions of Brazil. Pires intends to use sensors that monitor the interactions of climate, soil, and water with the development of plants, in order to understand the dynamics that are involved in the transfer of water among the soil, plant, and atmosphere, and to illuminate its interactions in the production system.

    All of these endeavors align perfectly with the mission of the Microsoft Research-FAPESP Institute for IT Research, which is to support bold, innovative projects that apply technology to enable or accelerate research that will help humanity.

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    —Juliana Salles, Senior Program Manager, Microsoft Research Connections

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