Powerful new resources and tools for biological scientists from Microsoft Research

imageGood news for biological scientists and programmers.  Tomorrow, July 10th, in Boston, the External Research division of Microsoft Research will introduce the Microsoft Biology Initiative, resources designed to help biological scientists and programmers conduct research more efficiently and affordably. These include the first post-beta release of the Microsoft Biology Foundation (MBF), a language-neutral bioinformatics tool kit built as an extension to the Microsoft .NET Framework. In addition to a new genome assembler, performance enhancements, and other improvements, MBF builds upon the vision and goals that drove the development of the beta versions. Those included a commitment to community involvement, extensibility, cross-platform and interoperable functionality, language neutrality, and support for best practices. While there are other libraries of biological functionality available, MBF supports universally accepted standards of the bioinformatics community and implements a range of unique functionality derived from original Microsoft research. The code for MBF and supporting documents is available on CodePlex[RK1] .

One example of MBF at work is the research undertaken by my colleague David Heckerman, senior director of the eScience group within Microsoft Research. HealthBlog readers may recall a video presentation I did with Dr. Heckerman a while back.

imageHeckerman, an expert in machine learning, is working on the design of HIV vaccines, which requires an understanding of how the virus evolves in each individual.  One of the enduring challenges in HIV vaccine design is the remarkable rate of viral mutation and adaptation, which limits the immune system’s ability to mount a lasting, effective response. The HIV group at Microsoft Research is developing models of evolution that allow researchers to identify and visualize the complex, yet encouragingly consistent, patterns of adaptation that suggest novel vaccine strategies.  The next versions of the biological applications Heckerman is developing will use functions built into MBF. Dr. Heckerman's applications will continue to be made available for free download on CodePlex[RK2] .

The Microsoft Biology Initiative initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT).

The Microsoft Biology Foundation (MBF) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework, initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, and documentation are freely downloadable.

The Microsoft Biology Tools (MBT) are a collection of tools targeted at helping the biology and bioinformatics researcher be more productive in making scientific discoveries. The tools provided here take advantage of the capabilities provided in the Microsoft Biology Foundation, and are good examples of how MBF can be used to create other tools.

For more information and to download the Microsoft Biology Foundation and Tools, visit the Microsoft Biology Initiative pages at Microsoft Research.  Also see the Microsoft Research External Team Blog.

Bill Crounse, MD       Senior Director, Worldwide Health      Microsoft

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