Bosc mercer
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  • Extensibilitycore concepts mapped as interfacescan easily provide alternative implementations or add any missing features you needLanguage Neutralitybuilt on top of .NET – use any supported languagesupports dynamic languages such as IronPythonDesigned and implemented using best practicescommented source code provided so nothing is a black box algorithms all cite publications
  • To use MBF in other environments, you will use Silverlight as your application style and then rely on Mono/Moonlight or the Silverlight plug-in on the OSX platform to run your code. You can still use Visual Studio for your IDE on the Windows platform, or if you are willing to work with the source code, you can use a Mono-based IDE such as MonoDevelop or SharpDevelop. MBF v2 will also support a Silverlight version with a subset of functionality but capable of running wherever Silverlight is supported

Transcript

  • 1. A Framework for Bioinformatics on the Microsoft PlatformSimon MercerDirector, Health & WellbeingMicrosoft Research Connections
    2/25/2011
  • 2. Vision and Community
    To support the genomics workflow from DNA sequencer output to contiguous, fully-annotated genome
    Community consists of ‘scientific programmers’:
    • Continuum of expertise between CS and Bio
    • 3. May be wet-bench scientists themselves
    • 4. Frequently support the lab and analyze the data
    • 5. Commercial scientific programmers often located in dedicated service units, more CS background
  • The Microsoft Biology Foundation– what is it?
    MBF is a Bioinformatics Toolkit
    • built on top of the .NET Framework 4.0
    • 6. open source under the Apache 2.0 license
    • 7. foundation upon which other tools can be built
    Provides various components useful for biological analysis
    • parsers to read and write common bioinformatics formats
    • 8. support for DNA, RNA and protein sequences
    • 9. algorithm framework for analysis and transformation
    • 10. web connector framework for web-service interaction
  • MBF vs. your Application
    MBF is not an application in itself
    • it does not provide any visualization of the data being managed
    • 11. it provides the basis for visualizations to be built on top of
    Your Application
    MBF
    .NET Framework 4.0
  • 12. Cross-Platform Capabilities
    Possible to target non-Windows platforms
    using Silverlight / Mono / Moonlight
  • 13. New in v2
    Advanced Math functions
    Available free to academics via the Intel MKL library and Sho
    Comparative DNA sequence assembly
    Assemble to reference of a related strain or species
    Command line tools
    Exposing MBF features on the command line
    Discovery via Visualization
    Natural navigation and annotation of assembled genomes
    Delight the Developer
    Ability to easily and efficiently create, extend and debug applications
    Grow the Community
    Provide training, easy on-ramps and incentives for contributing to the library
  • 14. Open Source Development
    Source Code
    Community
    Support
    MBF.codeplex.com
  • 15. Building a Community
    Community-Curated Open Source
    • MBF is freely available for commercial and academic use under the Apache 2.0 license
    • 16. Installers and tools available from:http://research.microsoft.com/bio/
    • 17. Source Code and developer community support available from:http://mbf.codeplex.com
    The name is going to change
    The MBF project is NOT guided by Microsoft alone
    The MBF project will NOT be owned by Microsoft: