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Microsoft Research eScience Workshop 2009
Friday, October 16 – Saturday, October 17, 2009


Click the linked titles in the following table to view the presentation videos.

Friday, October 16, 2009 
8:00 Breakfast 

The Fourth Paradigm: Realizing Jim Gray’s Vision for Data-Intensive Scientific Discovery
Tony Hey, Jeff Dozier, Ben Shneiderman, Timo Hannay, Christopher Southan  

Chair: Daron Green

11:00-11:30 Break






Chair: Iain Buchan 

eResearch Services & Applications
Chair: Lee Dirks 

eScience Topics
Chair: Yan Xu 

Advances in Software Support
Chair: Judith Bishop  


Computational Methods for Large-Scale DNA Data Analysis

Xiaohong Qiu, Jaliya Ekanayake, Geoffrey C. Fox, Thilina Gunarathne, Scott Beason - Indiana University

Generating Intelligent Multimedia Presentations from Semantic Mashups Using OAI-ORE and SMIL

Jane Hunter, Anna Gerber - The University of Queensland


Observing Round-the-Clock Expulsion of Matter from a Black Hole: Global Jet Watch

Katherine Blundell - Oxford University

Software Support for Hybrid Computing

Shujia Zhou - University of Maryland, Baltimore County


Tools for Scalable Genome Haplotying in the Windows Azure Cloud

Girish Subramanian - Indiana University

Yogesh Simmhan - Microsoft Research

Comment by Sketch: A Picture Says a Million Words
Stephen Wilson
, Jeremy Frey - University of Southampton

Towards Complete Functional and Structural Imaging of Cortical Circuits

R. Clay Reid, Davi Bock, Wei-Chung Reid - Harvard Medical School

Scaling Simulations Through Declarative Processing
Alan Demers, Oliver Gao, Johannes Gehrke, Christoph Koch, Marcos Vaz Salles, Walker White -
Cornell University


Lunch and Poster Session





Tools for Biology
Chair: Simon Mercer 

Systems for Author & Document Analysis
Chair: Lee Dirks 

Earth & Environment
Chair: Stewart Tansley  

Provenance Management for Scientific Data
Chair: Dean Guo     


Enhancing BLAST Comprehension with SilverMap
Peter Ansell, Lawrence Buckingham, Xin-yi Chua, James Hogan, Scott Mann, Paul Roe - Queensland University of Technology

Scalable Solution for a Comprehensive Appraisal of Contemporary Documents
Rob Kooper, Peter Bajcsy, Kenton McHenry - National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign


Listening to Nature: Acoustic Monitoring of the Environment

Michael Towsey, Birgit Planitz, Paul Roe, Jiro Sumitomo, Ian Williamson, Jason Wimmer, Jinglan Zhang - Queensland University of Technology

Simple Provenance in Scientific Databases

Nolan Li, Alexander Szalay - Johns Hopkins University


Web Service Extension of Computational Biology Application Suite
Robert Bukowksi, Jaroslaw Pillardy - Computational Biology Service Unit, Cornell University 

Author Identity and Social Networking at arXiv
Simeon Warner
, Nathan Woody, Paul Ginsparg - Cornell University

Thorsten Schwander - Los Alamos National Laboratory 

3D Geographical Environments and Geospatial Data Exploration Using Flight Simulators and Geodatabases
Alexandra Diehl
, Horacio Abbate, Marta Mejail, Mercedes Sanchez - Universidad de Buenos Aires

Claudio Delrieux - Universidada Nacional del Sur, Argentina  


Provenir Ontology: Towards a Framework for eScience Provenance Management
Satya Sahoo, Amit Sheth - Wright State University

3:00-3:15   Break 






eScience Research at Microsoft
Chair: David Heckerman 

Chair: Michael Zyskowski 

Semantic Repositories and Modeling
Chair: Evelyne Viegas 

Data Intensive Computing
Chair: Peter Lee

3:15-3:45  The Vedea Visualization Language
Martin Calsyn - Microsoft Research 

Generalized eScience Collaboration Through SharePoint
Marty Humphrey
- University of Virginia

Catharine Van Ingen - Microsoft Research

Deb Agarwal - Lawrence Berkeley National Laboratory 


Facilitating Next Generation Data Intensive Science Using Semantic Technologies

Deborah McGuinness, Peter Fox - Rensselaer Polytechnic Institute 

Data Intensive Scalable Computing: Applying  Google-Style Computing to eScience

Randal E. Bryant -  
Carnegie Mellon University 

3:45-4:15  Tools and Techniques for Computational Biology
Carl Kadie
- Microsoft Research 

Collaborative Data Analysis with Taverna Workflows

Andrea Wiggins, Kevin Crowston - Syracuse University 

Integrating Streaming Data and Semantic Repositories

Alejandro Rodriguez, Yong Liu, James Myers - University of Illinois, Urbana Champaign

Understanding and Maturing the Data-Intensive Scalable Computing Storage Substrate

Garth A. Gibson - Carnegie Mellon University


4:15-4:45  Performing Science in the Cloud: A Haplotype Phasing Case Study
Yogesh Simmhan
- Microsoft Research 

Lessons from myExperiment: Research Objects for Data Intensive Research

David De Roure - University of Southampton

Carole Goble - University of Manchester 

Using Multipartite Graphs for Recommendation and Discovery

Michael Kurtz, Edwin Henneken, Alberto Accomazzi - Harvard-Smithsonian Center for Astrophysics 

Low Power Amdahl Blades for Data Intensive Computing

Alexander Szalay, Andreas Terzis, Alainna White, Jan Vandenberg - Johns Hopkins University

Gordon Bell, Jose Blakeley - Microsoft

Howie Huang - George Washington University



eOcean: The Challenges Ahead and Below the Waves

Ellen Prager, President, Earth2Ocean, Inc
Chair: Harold Javid



Workshop dinner at Carnegie Museum


Click the linked titles in the following table to view the presentation videos.

Saturday, October 17, 2009

8:00 Breakfast

Some Challenges in Natural Science

Stephen Emmott

Chair: Tony Hey

10:00-10:15 Break





Chair: Yogesh Simmhan

Development in Search & Semantics for Chemistry
Chair: Daron Green

Democratizing Semantics for the Scientist
Chair: Evelyne Viegas

Cloud Computing
Chair: Dean Guo


Bayesian Network Modelling of the Factors Influencing the Development of Obesity
David Hoyle, Nicholas Harding, Iain Buchan - University of Manchester

Navigating the Complex Web of Chemistry Using ChemSpider
Antony Williams, Valery Tkachenko - Royal Society of Chemistry

Social and Semantic Computing to Support Citizen Science

Joel Sachs, Tejas Lagvankar, Tim Finnin - University of Maryland-Baltimore County



Construction of a MODIS Scientific Data Reprojection and Reduction Pipeline in Windows Azure Platform

Jie Li - University of Virginia

Youngryel Ryu - University of California, Berkeley

Keith Jackson, Deb Agarwal - Lawrence Berkeley National Laboratory

Catharine Van Ingen - Microsoft Research



Navigating Across Multi-Scale Biological Systems Using Cognitive Modeling and Systems Approaches Conceptualized in Product Engineering
Nagasuma Chandra - Indian Institute of Science

Satish Chandra - National Aerospace Laboratories


The oreChem Project: Integrating Chemistry Scholarship with the Semantic Web and Web 2.0
Carl Lagoze - Cornell University

Prasenjit Mitra, William Brouwer - Penn State University

Mark Borkum - University of Southampton

Tupelo: a Framework for E-Science Knowledge Spaces

Joe Futrelle, Jeff Gaynor, Joel Plutchak, James Myers, Robert McGrath -
National Center for Supercomputing Applications

Cloud Workflow Service: Automatically Scaling Scientific Workflows on Demand
Cui Lin
- Wayne State University

Roger Barga, Dean Guo, Jared Jackson - Microsoft External Research


Improvements in the Determination of Fundamental Principles of RNA Structure and the Prediction of RNA Secondary and Tertiary Structure

Robin Gutell, David Gardner - University of Texas, Austin

Stuart Ozer - Microsoft

Integrative Data Mining For Drug Discovery Using the Semantic Web

Qian Zhu, Marlon Pierce, Geoffrey C. Fox, David J. Wild - Indiana University

Michael S. Lajiness - Eli Lilly and Company


Extraction of NMR Spectra and Structural Data from Documents for Semantic Representation and Reuse

Mark Borkum - University of Southampton

William Brouwer - Penn State University


Data Integration for E-Science Using Correlated Concepts

Lushan Han, Tim Finin, Anupam Joshi, Yelena Yesha - University of Maryland, Baltimore County

Cloud Computing for Planetary Defense
Steven Johnston, Kenji Takeda, Hugh Lewis, Simon Cox, Graham Swinerd - University of Southampton
11:45-12:45  Break





Medical Imaging
Chair: Stewart Tansley

Global Public Health
Chair: Kristin Tolle

Advances in Data Intensive Science
Chair: Yan Xu 

Segmentation of Confocal Stacks and Synaptic Regions for the Connectome Project
Amelio Vazquez-Reina
, Won-Ki Jeong, Roanna Ruiz, Bo Wang, Hanspeter Pfister - Harvard University 

Eric Miller - Tufts University


Current Status of e-Health in Peru

Lady Murrugarra - Universidad Peruana Cayetano Heredia

A New Partnership for Cross-Scale, Cross-Domain eScience

Bill Howe - University of Washington 


A Web-Based System for Biomedical Image Storage, Annotation, Content-Based Retrieval and Exploration

Jorge Camargo, Juan Caicedo, Angel Cruz Roa, Eduardo Romero, Clara Spinel, Fabio Gonzalez - Universidad Nacional de Colombia

David Seligmann, Jessica Forero - Politecnico Grancolombiano


Model-Driven Support for a Vaccine Study in Kathmandu

Jeremy Gibbons, Jim Davies, Steve Harris, Jane Metz, Matthew Snape, Andrew Pollard - University of Oxford

Extracting Natural Laws from Data: Invariants Are Better Than Predictive Models

Michael Schmidt, Hod Lipson - Cornell University 


Incorporating Problem-Based Learning in Medical Image Processing: A Case Study on Computing-Centric Engineering Education
Chang Quo, May Wang - Georgia Institute of Technology 


  From Flops to (Peta)Bytes: the Expanding Role of Data in Scientific Analysis
Nick Nystrom - Pittsburgh Supercomputing Center 
2:15-2:30   Break





Biomedical Modeling
Chair: Kristin Tolle 

Computational Thinking Research
Chair: Tom McMail 

Data Driven Environmental Science
Chair: Christophe Poulain 


SysMO-DB: Just Enough Exchange for Systems Biology Data and Models
Carole Goble, Katy Wolstencroft, Stuart Owen, Sergejs Aleksejevs - University of Manchester

Wolfgang Müller, O. Krebs, Isable Rojas - EML

Jacky Snoep - University of Stellenbosch 


How Optimized Environmental Sensing Helps Address Information Overload on the Web
Carlos Guestrin - Carnegie Mellon University 
Opportunities for Integration of Multi-Model Data for the Water Sciences Community
Yong Liu, David Hill, Barbara Minsker - National Center for Supercomputing Applications 

Healthcare e-Labs: Opening and Integrating Models of Health
Iain Buchan, Carole Goble, David Hoyle, John Ainsworth, Mark Delderfield, Gareth Smith, Lee Kitching - University of Manchester

John Winn, Christopher Bishop - Microsoft Research

Computational Thinking for a Modern Kidney Exchange
Tuomas Sandholm
- Carnegie Mellon University

Modelling Data-Driven CO2 Sequestration Using Distributed HPC CyberInfrastructure
Yaakoub El Khamra - University of Texas at Austin 

Shantenu Jha - Louisiana State University 




Parallel Thinking

Guy Blelloch - Carnegie Mellon University 

Beyond Sensors: Curating Ancillary Data for Carbon-Climate Science

Catharine Van Ingen - Microsoft Research

Marty Humphrey - University of Virginia

Deb Agarwal - Lawrence Berkeley National Laboratory 


From Flops to Petabytes: the Expanding Role of Data in NSF Cyberinfrastructure

Ralph Roskies and Michael Levine

Chair: Peter Lee