A Framework for Bioinformatics on the Microsoft PlatformSimon MercerDirector, Health & WellbeingMicrosoft Research Connect...
Vision and Community<br />To support the genomics workflow from DNA sequencer output to contiguous, fully-annotated genome...
May be wet-bench scientists themselves
Frequently support the lab and analyze the data
Commercial scientific programmers often located in dedicated service units, more CS background</li></li></ul><li>The Micro...
open source under the Apache 2.0 license
foundation upon which other tools can be built</li></ul>Provides various components useful for biological analysis<br /><u...
support for DNA, RNA and protein sequences
algorithm framework for analysis and transformation
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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
  • Bosc mercer

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