The Microsoft Biology Foundation and its Applications

Simon MercerDirector for Health & Wellbeing

Microsoft External Research

MICROSOFT EXTERNAL RESEARCH - SOFTWARE

• Phil Bourne • Lynn Fink

Ontology Add-in for Word

Source code and binary:http://research.microsoft.com/ontology/

Relationships:Ontology browser

Intent: Term recognition & disambiguation

• John Wilbanks

Services: Ontology download web service

NodeXL

Binary and source code:http://nodexl.codeplex.com

3D Molecule Viewer

Binary and source code:http://3dmoleculeviewer.codeplex.com/

•PDB File Viewer•Written in C# using WPF

The Trident Scientific Workflow Workbench

• Built on top of Windows Workflow Foundation

• Write once, deploy and run anywhere…

• Visually program workflows

• Libraries of activities and workflows

• Automatic provenance capture

A visual workflow environment that allows researchers to better manage, evaluate and interact with even the most complex scientific datasets

Available at: http://research.microsoft.com/en-us/collaboration/tools/trident.aspx

Origins of a Platform

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)

Previous bioinformatics project outputs

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 Windows-

based tools, under development using MBF (H1 FY11)

+ Cancer Bioinformatics in ERMarty 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 Weekand NPR

Microsoft BiologyFoundation

• Beta 1: Nov 5, 2009 (MS Connect)• Beta 2: Feb 10, 2010 (CodePlex)• V1 release: July 2010

• Early adopters from industry and academia

• 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

Convergence on a Strategic Platform for Bioinformatics

Azure engagement through XCG(Azure BLAST, PhyloD services)

Product engagement and prototyping use by TC, HSG

• 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• Sequences• Alphabets• Alignments• Genomic Intervals• Phylogeny

Bio.IO• FASTA / FASTQ• GenBank• NEXUS• …

Bio.Algorithms• Translation• Alignment• Sequence Assembly• …

Bio.Web• BLAST• ClustalW• BioHPC• …

Objectives

• Modular by design• Commonly used features• Exceptionally well-

documented• 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 non-commercial use and modification under the MS-PL license (http://opensource.org/licenses/ms-pl.html)

• Community-DevelopedMoved to CodePlex, Creating advisory board and building a community

• Community-CuratedModify code, find bugs, contribute new features

• V1 ReleaseLate June 2010

• Build executables– Visual Studio

• Office add-in– BioExcel

• Commandline scripting access– Iron Python, PowerShell

• Workflow Activities– Trident, WF

• Services on the Cloud– Azure

Different Styles of Usage

mbf.codeplex.com

18

Selecting Restriction Endonucleases: DNA PReDuST(Aditi Technologies)

Fragment Size Distribution Graph

Restriction Map [Circular DNA]

Computational Biology Applications Suite for High Performance Computing (BioHPC)Computational Biology

Service Unit

• MBF Team– Mike Zyskowski, Chris Wu

• Microsoft Research– David Heckerman, Bob Davidson, Carl Kadie, Yogesh Simmhan,

Jennifer Listgarten, Jonathan Carlson

• Cornell University– Jarek Pillardy

• Queensland University of Technology– Jim Hogan

• University of Texas at Austin– Robin Gutell

• Aditi Technologies– Vivek Kumar

• Illumina Corporation– Scott Kahn

• Johnson & Johnson Pharmaceutical Research Division LLC.– Dimitris Agrafiotis, Victor Lobanov, Jeremy Kolpak

Acknowledgements

mbf.codeplex.com

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