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Mercer bosc2010 microsoft_framework

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Mercer bosc2010 microsoft_framework

  1. 1. The Microsoft Biology Foundation and its Applications<br />Simon Mercer<br />Director for Health & Wellbeing<br />Microsoft External Research<br />
  2. 2. Microsoft External Research - Software<br />
  3. 3. Ontology Add-in for Word<br />Services: Ontology download web service<br /><ul><li>John Wilbanks
  4. 4. Phil Bourne
  5. 5. Lynn Fink</li></ul>Intent: Term recognition & disambiguation<br />Relationships: Ontology browser<br />Source code and binary:<br />http://research.microsoft.com/ontology/<br />
  6. 6. NodeXL<br />Binary and source code:<br />http://nodexl.codeplex.com<br />
  7. 7. 3D Molecule Viewer<br /><ul><li>PDB File Viewer
  8. 8. Written in C# using WPF</li></ul>Binary and source code:<br />http://3dmoleculeviewer.codeplex.com/<br />
  9. 9. The Trident Scientific Workflow Workbench<br />A visual workflow environment that allows researchers to better manage, evaluate and interact with even the most complex scientific datasets<br />Built on top of Windows Workflow Foundation <br />Write once, deploy and run anywhere…<br />Visually program workflows<br />Libraries of activities and workflows<br />Automatic provenance capture<br />Available at: http://research.microsoft.com/en-us/collaboration/tools/trident.aspx<br />
  10. 10. Origins of a Platform<br />
  11. 11. Previous bioinformatics project outputs<br />Jaroslav Pillardy, Computational Biology Service Unit, Cornell University<br />BioHPC: Suite of 28 applications modified and adapted for efficient use in an Windows HPC environment with ASP.NET interface<br />Currently supports the areas of DNA sequence analysis, protein structure prediction, population genetics and phylogenetics<br />Jim Hogan, SilverMap: Queensland University of Technology<br /><ul><li>MQUTer supports research into bioinformatics, sensor networks, visualization and parallelism on the Microsoft platform
  12. 12. Six new tools – the latest under development using MBF and Silverlight 3 which visualizes DNA sequence similarity and is integrated into MBF (and will shortly be available as an Excel plug-in)</li></ul>Robin Gutell, Center for Computational Biology and Bioinf., UT Austin<br /><ul><li>Suite of tools to explore evolutionary relationships and predict function of RNA molecules
  13. 13. Available as a website – also a complementary open-source suite of Windows-based tools, under development using MBF (H1 FY11)</li></ul>+ Cancer Bioinformatics in ER<br />Marty Humphrey, Department of Computer Science, University of Virginia<br /><ul><li>The caBIGplatform connects consumers, the care delivery system, and the research community. Close to 60 NCI-designated Cancer Centers are deploying caBIG® infrastructure and tools, as are 16 Community Cancer Centers that in the aggregate touch 20 million lives.
  14. 14. This project pilots caBIG clients on Windows, leveraging and extending MBF, and tutorials demonstrating the value of Microsoft technologies to the caBIG developer and user community.</li></li></ul><li>Fighting HIV and AIDS<br /><ul><li>Four-year collaboration between Bruce Walker at Harvard and David Heckerman’s team (Microsoft Research)
  15. 15. Discovered three key insights to fight HIV:
  16. 16. Immune system is led astray by decoy epitopes (Nature Medicine, 2006)
  17. 17. Frameshift epitopes exist (JEM, 2010)
  18. 18. Natural killer cells directly attack HIV (Nature Medicine, in review)
  19. 19. 40+ publications, including Nature and Science
  20. 20. Walker has obtained $110M+ subsequent funding
  21. 21. PhyloD.Net, a tool for inferring HIV evolution in an individual, is used by 100+ HIV researchers and is now part of Microsoft Biology Foundation
  22. 22. Numerous press stories including Business Week and NPR</li></li></ul><li>Convergence on a Strategic Platform for Bioinformatics<br />Microsoft BiologyFoundation<br /><ul><li>Beta 1: Nov 5, 2009 (MS Connect)
  23. 23. Beta 2: Feb 10, 2010 (CodePlex)
  24. 24. V1 release: July 2010
  25. 25. Early adopters from industry and academia
  26. 26. Bio-IT Alliance partner
  27. 27. Leveraging Microsoft assets: Pivot, NodeXL, TRIDENT, Iron Python, etc
  28. 28. Showcasing Microsoft products: Excel/Office, Visual Studio 2010, .NET 4.0, WPF, Silverlight
  29. 29. V1 launch June 2010
  30. 30. Keynote presentations planned
  31. 31. Training course in prep
  32. 32. Community ownership
  33. 33. Foundation of future MSR genomics projects
  34. 34. Foundation of all future ER genomics engagements with academia</li></ul>Azure engagement through XCG(Azure BLAST, PhyloD services)<br />Product engagement and prototyping use by TC, HSG<br />
  35. 35. What is The Microsoft Biology Foundation?<br />An open-source library of reusable bioinformatics algorithms, services and functions built on the .NET platform<br />Benefits:<br /><ul><li>Easy to parallelize algorithms
  36. 36. Easy to distribute computations and workflows
  37. 37. Easy to visualize massive data sets
  38. 38. Ability to leverage greater strength from existing use of other MS technologies
  39. 39. Provides transition from local to cloud-based computation and data storage</li></li></ul><li>Architecture: Namespaces<br />
  40. 40. Objectives<br />Modular by design<br />Commonly used features<br />Exceptionally well-documented<br />Extensible<br />Interoperable<br />
  41. 41. Initial Areas of Focus<br />Genomics<br />Sequencing<br />Analysis and Annotation<br />Advanced Research<br />Phylogenetics<br />Genome Wide Association<br />Haplotype reconstruction<br />Next Targets<br />Visualization<br />Large data sets<br />
  42. 42. mbf.codeplex.com<br />Open SourceAvailable free of charge for commercial and non-commercial use and modification under the MS-PL license (http://opensource.org/licenses/ms-pl.html)<br />Community-DevelopedMoved to CodePlex, Creating advisory board and building a community<br />Community-CuratedModify code, find bugs, contribute new features<br />V1 ReleaseLate June 2010<br />
  43. 43. Build executables<br />Visual Studio<br />Office add-in<br />BioExcel<br />Commandline scripting access<br />Iron Python, PowerShell<br />Workflow Activities<br />Trident, WF<br />Services on the Cloud<br />Azure<br />Different Styles of Usage<br />
  44. 44. mbf.codeplex.com<br />
  45. 45. 18<br />Selecting Restriction Endonucleases: DNA PReDuST(Aditi Technologies)<br />Fragment Size Distribution Graph<br />Restriction Map [Circular DNA]<br />
  46. 46. Computational Biology Applications Suite for High Performance Computing (BioHPC)<br />Computational Biology Service Unit<br />
  47. 47. MBF Team<br />Mike Zyskowski, Chris Wu<br />Microsoft Research<br />David Heckerman, Bob Davidson, Carl Kadie, Yogesh Simmhan, Jennifer Listgarten, Jonathan Carlson<br />Cornell University<br />Jarek Pillardy<br />Queensland University of Technology<br />Jim Hogan<br />University of Texas at Austin<br />Robin Gutell<br />Aditi Technologies<br />Vivek Kumar<br />Illumina Corporation<br />Scott Kahn<br />Johnson & Johnson Pharmaceutical Research Division LLC.<br />Dimitris Agrafiotis, Victor Lobanov, Jeremy Kolpak<br />Acknowledgements<br />mbf.codeplex.com<br />
  48. 48. © 2008 Microsoft Corporation. All rights reserved. Microsoft, Windows, Windows Vista and other product names are or may be registered trademarks and/or trademarks in the U.S. and/or other countries.<br />The information herein is for informational purposes only and represents the current view of Microsoft Corporation as of the date of this presentation. Because Microsoft must respond to changing market conditions, it should not be interpreted to be a commitment on the part of Microsoft, and Microsoft cannot guarantee the accuracy of any information provided after the date of this presentation. MICROSOFT MAKES NO WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, AS TO THE INFORMATION IN THIS PRESENTATION.<br />

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