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
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