Agenda - Microsoft Research

UK e-Science: a Jewel or a Thousand Flowers
Malcolm Atkinson, e-Science Institute
The global digital revolution provides a fertile and turbulent ecological environment in which e-Science is a small but vital element. There is a deep history of e-Science, but coining the term and injecting leadership and modest funds had a huge impact. A veritable explosion of activity has led to a global burst of new e-Science species. Our challenge is to understand what will enable them to thrive and yield maximum benefit as the digital revolution continues to be driven by commerce and media.

Webcast

2:45–3:45

Session MA1

Senses Across Scales

Webcast

Session MA2

Data Analysis Through Visualization

Webcast

Session MA3

Health & Wellbeing I

Webcast

Exploration of Real-Time Provenance-Aware Virtual Sensors Across Scales for Studying Complex Environmental Systems
Yong Liu, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign

Abstract

Development and Application of Network of Geosensors for Environmental Monitoring
Rafael Santos, INPE – Brazilian National Institute for Space Research

Abstract

BLAST Atlas: A Function-Based Multiple Genome Browser
Lawrence Buckingham, Queensland University of Technology

Abstract

DIVE: A Data Intensive Visualization Engine
Dennis Bromley, University of Washington

Abstract

Simplifying Oligonucleotide Primer Design Software to Keep Pace with an Ever Increasing Demand for Assay Formats
Kenneth "Kirby" Bloom, Illumina Corporation

Abstract

Integration of Sequence Analysis into Third Dimension Explorer Leveraging the Microsoft Biology Framework
Jeremy Kolpak, Janssen Pharmaceutical Companies of Johnson & Johnson

Abstract

3:45–4:45

Session MA5

From Environmental Science to Public Policy

Webcast

Session MA6

Complex Biological Systems in Action

Webcast

Session MA7

Data-Intensive Science

Webcast

Session MA8

Health & Wellbeing II

Webcast

Achieving an Ecosystem Based Approach to Planning in the Puget Sound

Stephen Stanley, Washington Department of Ecology

Abstract

Adapting Environmental Science Methods to Public Policy and Decision Support
Rob Fatland, Microsoft Research

Abstract

An Interactive Modeling Environment for Systems Biology of Aging
Pat Langley, Arizona State University

Abstract

Analyzing the Process of Knowledge Dynamics in Sustainability Innovation: Towards a Data-Intensive Approach to Sustainability Science
Masaru Yarime, University of Tokyo

Abstract

Data-Intensive Science for Safety, Trust, and Sustainability

Shuichi Iwata, The University of Tokyo

Abstract

BL!P: A Tool to Automate NCBI BLAST Searches and Customize the Results for Exploration in Live Labs Pivot
Vince Forgetta, McGill University

Abstract

GenoZoom: Browsing the genome with Microsoft Biology Foundation, Deep Zoom, and Silverlight
Xin-Yi Chua, Queensland University of Technology

Abstract

4:45–5:30

No pre-planned workshop activities

5:30–9:00

Reception and dinner
Jim Gray eScience Award Presentation
This year, Microsoft Research presents the Jim Gray eScience Award to a researcher who has made an outstanding contribution to the field of data-intensive computing. The award—named for Jim Gray, a Technical Fellow for Microsoft Research and a Turing Award winner who disappeared at sea in 2007—recognizes innovators whose work truly makes science easier for scientists.

Webcast

Making Open Science Real
Adam Bly, Seed
The future of science is open, not because it ought to be but because it needs to be. Today, science's potential is hindered by the disconnected nature of the world's scientific information and the closed architecture of science itself. So how do we get from here to there? How can technology make open science real?

Webcast

Tuesday, October 12

Time	Event
9:00–10:00	Tuesday Keynote Presentation The Reaming of Life Philip Bourne, University of California, San Diego Anyone can punch a hole in a piece of metal, but a reamer is needed to accurately size and finish that hole. Digital computers are the reamers of life, bringing together a vast array of disparate bits of data to provide an accurate picture of life that can be smoothly transcended across scales—from molecules to populations. Sounds heady, so why do we not fully understand the molecular basis of cancer? Why can’t we accurately model the impact of an oil spill on marine life? Why can’t we decide whether there is a tree of life or a network of life? "Well tonight we are going to sort it all out, for tonight it’s the reaming of life." Webcast
10:00–11:00	Session TM1 Data from Ocean to Stars Webcast	Session TM2 Health & Wellbeing III Webcast	Session TM3 Tools to Get Science Done Webcast
Data, Data, Everywhere, nor Any Drop to Drink: New Approaches to Finding Events of Interest in High Bandwidth Data Streams Mark Abbott, Oregon State University Abstract Extreme Database-centric Computing in Science Alex Szalay, Johns Hopkins University Abstract	Model-Driven Cloud Services for Cancer Research Marty Humphrey, University of Virginia Abstract Cloud-Based Map-Reduce Architecture for Nuclear Magnetic Resonance-Based Metabolomics Paul Anderson, Wright State University Abstract	MyExperimentalScience, Extending the “Workﬂow” Jeremy Frey, University of Southampton Abstract The Conversion Software Registry Michal Ondrejcek, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign Abstract
11:00–12:00	Session TM5 Cloud Computing and Chemistry Webcast	Session TM6 Health & Wellbeing IV Webcast	Session TM7 Database Diversity Webcast
oreChem: Planning and Enacting Chemistry on the Semantic Web Mark Borkum, University of Southampton Abstract Accelerating Chemical Property Prediction with Cloud Computing Hugo Hiden, Newcastle University Abstract	Remote Computed Tomography Reconstruction Service on GPU-Equipped Computer Clusters Running Microsoft HPC Server 2008 Timur Gureyev, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Abstract e-LICO: Delivering Data Mining to the Life Science Community Simon Jupp, University of Manchester Abstract	SQL is Dead; Long Live SQL: Lightweight Query Services for Ad Hoc Research Data Bill Howe, University of Washington Abstract SinBiota 2.0 – Planning a New Generation Environmental Information System João Meidanis, University of Campinas Abstract
1:30–3:00	Session TA1 Enabling Scientific Discovery Webcast	Session TA2 Health & Wellbeing V Webcast	Session TA3 Virtual Research Environments and Collaboration Webcast	Session TA4 Applications in Digital Humanities Webcast
Enhancing the Quality and Trust of Citizen Science Data Jane Hunter, The University of Queensland Abstract Scientist-Computer Interfaces for Data-Intensive Science Cecilia Aragon, Lawrence Berkeley National Laboratory Abstract Enabling Scientific Discovery with Microsoft SharePoint Kenji Takeda, University of Southampton Abstract	Genome-Wide Association of ALS in Finland Bryan Traynor, National Institute on Aging, National Institutes of Health Abstract A Framework for Large-Scale Modelling of Population Health John Ainsworth, University of Manchester Abstract GREAT.stanford.edu: Generating Functional Hypotheses from Genome-Wide Measurements of Mammalian Cis-Regulation Gill Bejerano, Stanford University Abstract	Medici: A Scalable Multimedia Environment for Research Joe Futrelle, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign Abstract BlogMyData: A Virtual Research Environment for Collaborative Visualization of Environmental Data Andrew Milsted, University of Southampton Abstract RightField: Rich Annotation of Experimental Biology Through Stealth Using Spreadsheets Matthew Horridge, University of Manchester Abstract	musicSpace: Improving Access to Musicological Data mc schraefel, University of Southampton Abstract Quantifying Historical Geographic Knowledge from Digital Maps Tenzing Shaw, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign Abstract Data Intensive Research in Computational Musicology David De Roure, Oxford e-Research Centre Abstract
3:30–4:30	Session TA5 Agriculture, Digital Watersheds and Heterogeneous Climate Data Webcast	Session TA6 Health & Wellbeing VI Webcast	Session TA7 eScience in Systems Webcast	Session TA8 Archaeo Informatics
Scaling Information on ‘Biosphere Breathing’ from Chloroplast to the Globe Dennis Baldocchi, University of California-Berkeley Abstract Agrodatamine: Integrating Analysis of Climate Time Series and Remote Sensing Images Humberto Razente, UFABC Abstract	Correction for Hidden Confounders in Genetic Analyses Jennifer Listgarten, Microsoft Research Abstract BioPatML.NET and Its Pattern Editor: Moving into the Next Era of Biology Software James Hogan, Queensland University of Technology Abstract	GRAS Support Network, Its Implementation, Operation, and Use Fritz Wollenweber, EUMETSAT Abstract Data Intensive Frameworks for Astronomy Jeffrey Gardner, University of Washington Abstract	Experiences and Visions on Archaeo Informatics Christiaan Hendrikus van der Meijden, IT group, Veterinary Faculty, Ludwig Maximilians University; Peer Kröger, Hans-Peter Kriegel, Department of Computer Science Database Systems Group, Ludwig Maximilians University Abstract
4:45–6:00	Poster Session

Time

Event

9:00–10:00

Tuesday Keynote Presentation
The Reaming of Life
Philip Bourne, University of California, San Diego
Anyone can punch a hole in a piece of metal, but a reamer is needed to accurately size and finish that hole. Digital computers are the reamers of life, bringing together a vast array of disparate bits of data to provide an accurate picture of life that can be smoothly transcended across scales—from molecules to populations. Sounds heady, so why do we not fully understand the molecular basis of cancer? Why can’t we accurately model the impact of an oil spill on marine life? Why can’t we decide whether there is a tree of life or a network of life? "Well tonight we are going to sort it all out, for tonight it’s the reaming of life."

Webcast

10:00–11:00

Session TM1

Data from Ocean to Stars

Webcast

Session TM2

Health & Wellbeing III

Webcast

Session TM3

Tools to Get Science Done

Webcast

Data, Data, Everywhere, nor Any Drop to Drink: New Approaches to Finding Events of Interest in High Bandwidth Data Streams
Mark Abbott, Oregon State University

Abstract

Extreme Database-centric Computing in Science
Alex Szalay, Johns Hopkins University

Abstract

Model-Driven Cloud Services for Cancer Research
Marty Humphrey, University of Virginia

Abstract

Cloud-Based Map-Reduce Architecture for Nuclear Magnetic Resonance-Based Metabolomics
Paul Anderson, Wright State University

Abstract

MyExperimentalScience, Extending the “Workﬂow”

Jeremy Frey, University of Southampton

Abstract

The Conversion Software Registry

Michal Ondrejcek, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign

Abstract

11:00–12:00

Session TM5

Cloud Computing and Chemistry

Webcast

Session TM6

Health & Wellbeing IV

Webcast

Session TM7

Database Diversity

Webcast

oreChem: Planning and Enacting Chemistry on the Semantic Web

Mark Borkum, University of Southampton

Abstract

Accelerating Chemical Property Prediction with Cloud Computing

Hugo Hiden, Newcastle University

Abstract

Remote Computed Tomography Reconstruction Service on GPU-Equipped Computer Clusters Running Microsoft HPC Server 2008
Timur Gureyev, Commonwealth Scientific and Industrial Research Organisation (CSIRO)

Abstract

e-LICO: Delivering Data Mining to the Life Science Community

Simon Jupp, University of Manchester

Abstract

SQL is Dead; Long Live SQL: Lightweight Query Services for Ad Hoc Research Data
Bill Howe, University of Washington

Abstract

SinBiota 2.0 – Planning a New Generation Environmental Information System
João Meidanis, University of Campinas

Abstract

1:30–3:00

Session TA1

Enabling Scientific Discovery

Webcast

Session TA2

Health & Wellbeing V

Webcast

Session TA3

Virtual Research Environments and Collaboration

Webcast

Session TA4

Applications in Digital Humanities

Webcast

Enhancing the Quality and Trust of Citizen Science Data
Jane Hunter, The University of Queensland

Abstract

Scientist-Computer Interfaces for Data-Intensive Science
Cecilia Aragon, Lawrence Berkeley National Laboratory

Abstract

Enabling Scientific Discovery with Microsoft SharePoint

Kenji Takeda, University of Southampton

Abstract

Genome-Wide Association of ALS in Finland
Bryan Traynor, National Institute on Aging, National Institutes of Health

Abstract

A Framework for Large-Scale Modelling of Population Health

John Ainsworth, University of Manchester

Abstract

GREAT.stanford.edu: Generating Functional Hypotheses from Genome-Wide Measurements of Mammalian Cis-Regulation
Gill Bejerano, Stanford University

Abstract

Medici: A Scalable Multimedia Environment for Research
Joe Futrelle, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign

Abstract

BlogMyData: A Virtual Research Environment for Collaborative Visualization of Environmental Data
Andrew Milsted, University of Southampton

Abstract

RightField: Rich Annotation of Experimental Biology Through Stealth Using Spreadsheets
Matthew Horridge, University of Manchester

Abstract

musicSpace: Improving Access to Musicological Data
mc schraefel, University of Southampton

Abstract

Quantifying Historical Geographic Knowledge from Digital Maps
Tenzing Shaw, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign

Abstract

Data Intensive Research in Computational Musicology
David De Roure, Oxford e-Research Centre

Abstract

3:30–4:30

Session TA5

Agriculture, Digital Watersheds and Heterogeneous Climate Data

Webcast

Session TA6

Health & Wellbeing VI

Webcast

Session TA7

eScience in Systems

Webcast

Session TA8
Archaeo Informatics

Scaling Information on ‘Biosphere Breathing’ from Chloroplast to the Globe
Dennis Baldocchi, University of California-Berkeley

Abstract

Agrodatamine: Integrating Analysis of Climate Time Series and Remote Sensing Images

Humberto Razente, UFABC

Abstract

Correction for Hidden Confounders in Genetic Analyses
Jennifer Listgarten, Microsoft Research

Abstract

BioPatML.NET and Its Pattern Editor: Moving into the Next Era of Biology Software
James Hogan, Queensland University of Technology

Abstract

GRAS Support Network, Its Implementation, Operation, and Use
Fritz Wollenweber, EUMETSAT

Abstract

Data Intensive Frameworks for Astronomy
Jeffrey Gardner, University of Washington

Abstract

Experiences and Visions on Archaeo Informatics
Christiaan Hendrikus van der Meijden, IT group, Veterinary Faculty, Ludwig Maximilians University; Peer Kröger, Hans-Peter Kriegel, Department of Computer Science Database Systems Group, Ludwig Maximilians University

Abstract

4:45–6:00

Poster Session

Wednesday, October 13

Time	Event
8:30–10:00	Session WM2 Challenges of Data Standards & Tools Webcast	Session WM3 Data and Visualization Webcast	Session WM4 Health & Wellbeing VII Webcast
8:30–10:00	Panel: Challenges of Data Standards and Tools Deb Agarwal, LBNL/UCB; Bill Howe, University of Washington; Alex James, Microsoft; Yong Liu, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign; Maryann Martone, UCSD; Yan Xu, Microsoft Research Abstract	Scientific Data Sharing and Archiving at UC3/CDL: the Excel Add-in Project and More John Kunze, California Digital Library/California Curation Center; Tricia Cruse, California Digital Library/California Curation Center Abstract Visualizing All of History with Chronozoom David Shimabukuro, University of California-Berkeley; Roland Saekow, University of California-Berkeley Abstract	Proteome-Scale Protein Isoform Characterization with High Performance Computing Jake Chen, Indiana University Abstract Answering Biological Questions by Querying k-Mer Databases Paul Greenfield, CSIRO Mathematics, Informatics and Statistics Abstract
10:00–11:45	Closing Keynote Presentations
10:00–10:30	OpenSource & Microsoft: Beyond Interoperability Sam Ramji, Apigee Microsoft's open source strategy has shifted over the years, from ignore to fight to interoperate. Recently they have changed course to use open source as an engine of innovation and growth for core businesses. This talk will cover details of projects that showcase the shifts in strategy and expose the underlying dynamics of open source in the software industry. Webcast
10:30–11:45	Scaling the Science Garrison Sposito, U.C. Berkeley; Mark Stacey, U.C. Berkeley; Stephanie Carlson, U.C. Berkeley; Charlotte Ambrose, NOAA's National Marine Fisheries Service; James Hunt, U.C. Berkeley The current opportunities in the physical and biological sciences and their technological applications require the means to fundamentally understand processes at the molecular scale and to extend those processes to predict performance at larger scales. As examples, material science is using resolution at the scale of an atom to predict and design devices that are orders of magnitude larger, and biological processes are dictated by interactions at molecular, cellular, organismal, population, and ecosystem levels. Spatial and temporal scaling across orders of magnitude requires analysis tools that are available for computation, aggregation, and visualization. eScience is developing approaches for conducting this scaling and has been essential in addressing fundamental questions in biology and astronomy. While additional applications remain in the basic sciences, these fields have demonstrated pathways for advances in the applied environmental and social sciences, where the linkages between scales and disciplines require focused contributions from the eScience community. This workshop provides opportunities to observe how eScience has provided the scaling across various fields and to explore some of the challenges that remain. Webcast
Close of 2010 Microsoft Research eScience Workshop
1:00–3:30	Tutorial WT1 CoSBiLab: Enabling Simulation-Based Science Abstract Webcast	Tutorial WT2 Scientific Data Visualization using WorldWide Telescope Abstract Webcast	Tutorial WT3 Data-Intensive Research: Dataset Lifecycle Management for Scientific Workflow, Collaboration, Sharing, and Archiving Abstract Webcast	Tutorial WT4 OData – Open Data for the Open Web Abstract Webcast
3:30	Event concludes

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