Download The Microsoft Biology Foundation and its Applications Simon Mercer

Survey
yes no Was this document useful for you?
   Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Document related concepts

History of biology wikipedia, lookup

Biology wikipedia, lookup

Transcript
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.