The Microsoft Biology Foundation and its Applications Simon Mercer

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]

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Computational Biology Service Unit

Computational Biology Applications Suite for High Performance Computing (BioHPC)

Acknowledgements •

MBF Team –

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Microsoft Research –

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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

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