Bosc mercer
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This document discusses the Microsoft Biology Foundation (MBF), an open source bioinformatics toolkit built on the .NET Framework. MBF provides components for working with biological data formats, sequences, and algorithms. It is intended as a foundation for other tools and applications to build upon, rather than an application itself. The community around MBF consists of scientific programmers with a range of expertise. MBF is cross-platform, with new features in version 2 including advanced math functions, comparative assembly, command line tools, and visualization capabilities. The source code and community are hosted on Codeplex to encourage open source development of the toolkit.
Bosc mercer
- 1. A Framework for Bioinformatics on the Microsoft PlatformSimon MercerDirector, Health & WellbeingMicrosoft Research Connections2/25/2011
- 2. Vision and CommunityTo support the genomics workflow from DNA sequencer output to contiguous, fully-annotated genomeCommunity 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 backgroundThe Microsoft Biology Foundation– what is it?MBF is a Bioinformatics Toolkitbuilt 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 builtProvides various components useful for biological analysisparsers 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 interactionMBF vs. your ApplicationMBF is not an application in itselfit does not provide any visualization of the data being managed
- 11. it provides the basis for visualizations to be built on top ofYour ApplicationMBF.NET Framework 4.0
- 12. Cross-Platform CapabilitiesPossible to target non-Windows platformsusing Silverlight / Mono / Moonlight
- 13. New in v2Advanced Math functionsAvailable free to academics via the Intel MKL library and ShoComparative DNA sequence assemblyAssemble to reference of a related strain or speciesCommand line toolsExposing MBF features on the command lineDiscovery via VisualizationNatural navigation and annotation of assembled genomesDelight the DeveloperAbility to easily and efficiently create, extend and debug applicationsGrow the CommunityProvide training, easy on-ramps and incentives for contributing to the library
- 14. Open Source DevelopmentSource CodeCommunitySupportMBF.codeplex.com
- 15. Building a CommunityCommunity-Curated Open SourceMBF 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.comThe name is going to changeThe MBF project is NOT guided by Microsoft aloneThe MBF project will NOT be owned by Microsoft:
Editor's Notes
- #4: 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
- #6: 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