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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

    Join the Microsoft Biology Foundation v2.0 Development Preview

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    Microsoft Biology FoundationYou may be familiar with the Microsoft Biology Foundation (MBF), an open source bioinformatics .NET library that is designed to provide core functionality for genomics research from commonly-used file parsers to algorithms and web connectors. We're pleased to announce that we are continuing to invest in the project in the coming year.

    We recently posted a preview of MBF v2.0, which can be downloaded for development evaluation purposes. (Please note that this release is limited to source code only.) This release resolves a number of previously reported and identified issues. We also implemented-and in some cases, improved-many new features, including:

    • BAM extension scenarios and paired end support
    • Object model changes to use ISequence : IList<byte>

    We also optimized some features for MBF v2.0, including:

    • Memory profiling and analysis on MBF
    • Parallel de Novo Assembler (PaDeNA) memory optimizations
    • Sequence optimizations (including non-string and non-character)
    • MUMmer optimization based on sequence
    • Object model optimizations
    • Additional scenarios for the collection of memory and performance profiles

    We are now in the process of implementing additional features. We will discuss those in greater detail at a future date. In the meantime, we invite you to participate in the MBF v2.0 development preview and provide feedback through our community forums.

    For best performance and to avoid any conflicts, we strongly recommend that you completely uninstall MBF v1.0 before you install MBF v2.0. Also, please note that we have identified the following issues that may affect your ability to install the code:

    • The DLL version of MBF is incorrectly reported as 1.0.0.0
    • The installer installs MBF in a directory named 2.1; it should be 2.0

    The recommended (stable) MBF v1.0 code and corresponding v1.0 binaries are still available for download if you prefer to work with the earlier code. Either way, we encourage you to help us improve MBF by providing feedback in the forums.

    For more information:

    MBF download locations:

    -Beatriz Diaz Acosta, Senior Research Program Manager, Microsoft Research

  • 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

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