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The Microsoft Biology Foundation and its Applications Simon Mercer Director for Health & Wellbeing Microsoft External Research MICROSOFT EXTERNAL RESEARCH - SOFTWARE Ontology Add-in for Word Services: Ontology download web service • John Wilbanks Intent: Term recognition & disambiguation • Phil Bourne • Lynn Fink Relationships: Ontology browser Source code and binary: http://research.microsoft.com/ontology/ NodeXL Binary and source code: http://nodexl.codeplex.com 3D Molecule Viewer •PDB File Viewer •Written in C# using WPF Binary and source code: http://3dmoleculeviewer.codeplex.com/ The Trident Scientific Workflow Workbench A visual workflow environment that allows researchers to better manage, evaluate and interact with even the most complex scientific datasets • • • • • Built on top of Windows Workflow Foundation Write once, deploy and run anywhere… Visually program workflows Libraries of activities and workflows Automatic provenance capture Available at: http://research.microsoft.com/en-us/collaboration/tools/trident.aspx Origins of a Platform Previous bioinformatics project outputs Jaroslav Pillardy, Computational Biology Service Unit, Cornell University • BioHPC: Suite of 28 applications modified and adapted for efficient use in an Windows HPC environment with ASP.NET interface • Currently supports the areas of DNA sequence analysis, protein structure prediction, population genetics and phylogenetics Jim Hogan, SilverMap: Queensland University of Technology • MQUTer supports research into bioinformatics, sensor networks, visualization and parallelism on the Microsoft platform • 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) Robin Gutell, Center for Computational Biology and Bioinf., UT Austin • Suite of tools to explore evolutionary relationships and predict function of RNA molecules • Available as a website – also a complementary open-source suite of Windowsbased tools, under development using MBF (H1 FY11) + Cancer Bioinformatics in ER Marty Humphrey, Department of Computer Science, University of Virginia • The caBIG platform 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. • 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. Fighting HIV and AIDS • Four-year collaboration between Bruce Walker at Harvard and David Heckerman’s team (Microsoft Research) • Discovered three key insights to fight HIV: – Immune system is led astray by decoy epitopes (Nature Medicine, 2006) – Frameshift epitopes exist (JEM, 2010) – Natural killer cells directly attack HIV (Nature Medicine, in review) • 40+ publications, including Nature and Science • Walker has obtained $110M+ subsequent funding • 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 • Numerous press stories including Business Week and NPR Convergence on a Strategic Platform for Bioinformatics Microsoft Biology Foundation • Beta 1: Nov 5, 2009 (MS Connect) • Beta 2: Feb 10, 2010 (CodePlex) • V1 release: July 2010 • Early adopters from industry and academia Azure engagement through XCG (Azure BLAST, PhyloD services) Product engagement and prototyping use by TC, HSG • Bio-IT Alliance partner • Leveraging Microsoft assets: Pivot, NodeXL, TRIDENT, Iron Python, etc • Showcasing Microsoft products: Excel/Office, Visual Studio 2010, .NET 4.0, WPF, Silverlight • V1 launch June 2010 • Keynote presentations planned • Training course in prep • Community ownership • Foundation of future MSR genomics projects • Foundation of all future ER genomics engagements with academia What is The Microsoft Biology Foundation? An open-source library of reusable bioinformatics algorithms, services and functions built on the .NET platform Benefits: Easy to parallelize algorithms Easy to distribute computations and workflows Easy to visualize massive data sets Ability to leverage greater strength from existing use of other MS technologies Provides transition from local to cloud-based computation and data storage Architecture: Namespaces Bio Bio.IO • Sequences • Alphabets • Alignments • Genomic Intervals • Phylogeny • FASTA / FASTQ • GenBank • NEXUS •… Bio.Algorithms Bio.Web • Translation • Alignment • Sequence Assembly •… • BLAST • ClustalW • BioHPC •… Objectives • Modular by design • Commonly used features • Exceptionally welldocumented • Extensible • Interoperable Initial Areas of Focus • Genomics – Sequencing – Analysis and Annotation • Advanced Research – Phylogenetics – Genome Wide Association – Haplotype reconstruction • Next Targets – Visualization – Large data sets mbf.codeplex.com • Open Source Available free of charge for commercial and noncommercial use and modification under the MS-PL license (http://opensource.org/licenses/ms-pl.html) • Community-Developed Moved to CodePlex, Creating advisory board and building a community • Community-Curated Modify code, find bugs, contribute new features • V1 Release Late June 2010 Different Styles of Usage • Build executables – Visual Studio • Office add-in – BioExcel • Commandline scripting access – Iron Python, PowerShell • Workflow Activities – Trident, WF • Services on the Cloud – Azure mbf.codeplex.com Selecting Restriction Endonucleases: DNA PReDuST (Aditi Technologies) Fragment Size Distribution Graph Restriction Map [Circular DNA] 18 Computational Biology Service Unit Computational Biology Applications Suite for High Performance Computing (BioHPC) Acknowledgements • MBF Team – • Microsoft Research – • Vivek Kumar Illumina Corporation – • Robin Gutell Aditi Technologies – • Jim Hogan University of Texas at Austin – • Jarek Pillardy Queensland University of Technology – • David Heckerman, Bob Davidson, Carl Kadie, Yogesh Simmhan, Jennifer Listgarten, Jonathan Carlson Cornell University – • Mike Zyskowski, Chris Wu Scott Kahn Johnson & Johnson Pharmaceutical Research Division LLC. – Dimitris Agrafiotis, Victor Lobanov, Jeremy Kolpak mbf.codeplex.com © 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. 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.