eScience Workshop 2010

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.

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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.

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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?

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Microsoft Biology Foundation: An Open-Source Library of Re-usable Bioinformatics Functions and Algorithms Built on the .NET Platform

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Scientific Data Visualization using WorldWide Telescope

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Data-Intensive Research: Dataset Lifecycle Management for Scientific Workflow, Collaboration, Sharing, and Archiving

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Parallel Computing with Visual Studio 2010 and the .NET Framework 4

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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

Development and Application of Network of Geosensors for Environmental Monitoring

Rafael Santos, INPE – Brazilian National Institute for Space Research

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BLAST Atlas: A Function-Based Multiple Genome Browser

Lawrence Buckingham, Queensland University of Technology

DIVE: A Data Intensive Visualization Engine

Dennis Bromley, University of Washington

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Simplifying Oligonucleotide Primer Design Software to Keep Pace with an Ever Increasing Demand for Assay Formats

Kenneth “Kirby” Bloom, Illumina Corporation

Integration of Sequence Analysis into Third Dimension Explorer Leveraging the Microsoft Biology Framework

Jeremy Kolpak, Janssen Pharmaceutical Companies of Johnson & Johnson

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Achieving an Ecosystem Based Approach to Planning in the Puget Sound

Stephen Stanley, Washington Department of Ecology

Adapting Environmental Science Methods to Public Policy and Decision Support

Rob Fatland, Microsoft Research

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An Interactive Modeling Environment for Systems Biology of Aging

Pat Langley, Arizona State University

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Analyzing the Process of Knowledge Dynamics in Sustainability Innovation: Towards a Data-Intensive Approach to Sustainability Science

Masaru Yarime, University of Tokyo

Data-Intensive Science for Safety, Trust, and Sustainability

Shuichi Iwata, The University of Tokyo

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

Vince Forgetta, McGill University

GenoZoom: Browsing the genome with Microsoft Biology Foundation, Deep Zoom, and Silverlight

Xin-Yi Chua, Queensland University of Technology

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.”

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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

Extreme Database-centric Computing in Science

Alex Szalay, Johns Hopkins University

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Model-Driven Cloud Services for Cancer Research

Marty Humphrey, University of Virginia

Cloud-Based Map-Reduce Architecture for Nuclear Magnetic Resonance-Based Metabolomics

Paul Anderson, Wright State University

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MyExperimentalScience, Extending the “Workflow”

Jeremy Frey, University of Southampton

The Conversion Software Registry

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

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oreChem: Planning and Enacting Chemistry on the Semantic Web

Mark Borkum, University of Southampton

Accelerating Chemical Property Prediction with Cloud Computing

Hugo Hiden, Newcastle University

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Remote Computed Tomography Reconstruction Service on GPU-Equipped Computer Clusters Running Microsoft HPC Server 2008

Timur Gureyev, Commonwealth Scientific and Industrial Research Organisation (CSIRO)

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

Simon Jupp, University of Manchester

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SQL is Dead; Long Live SQL: Lightweight Query Services for Ad Hoc Research Data

Bill Howe, University of Washington

SinBiota 2.0 – Planning a New Generation Environmental Information System

João Meidanis, University of Campinas

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Enhancing the Quality and Trust of Citizen Science Data

Jane Hunter, The University of Queensland

Scientist-Computer Interfaces for Data-Intensive Science

Cecilia Aragon, Lawrence Berkeley National Laboratory

Enabling Scientific Discovery with Microsoft SharePoint

Kenji Takeda, University of Southampton

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Genome-Wide Association of ALS in Finland

Bryan Traynor, National Institute on Aging, National Institutes of Health

A Framework for Large-Scale Modelling of Population Health

John Ainsworth, University of Manchester

GREAT.stanford.edu: Generating Functional Hypotheses from Genome-Wide Measurements of Mammalian Cis-Regulation

Gill Bejerano, Stanford University

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Medici: A Scalable Multimedia Environment for Research

Joe Futrelle, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign

BlogMyData: A Virtual Research Environment for Collaborative Visualization of Environmental Data

Andrew Milsted, University of Southampton

RightField: Rich Annotation of Experimental Biology Through Stealth Using Spreadsheets

Matthew Horridge, University of Manchester

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musicSpace: Improving Access to Musicological Data

mc schraefel, University of Southampton

Quantifying Historical Geographic Knowledge from Digital Maps

Tenzing Shaw, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign

Data Intensive Research in Computational Musicology

David De Roure, Oxford e-Research Centre

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Scaling Information on ‘Biosphere Breathing’ from Chloroplast to the Globe

Dennis Baldocchi, University of California-Berkeley

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

Humberto Razente, UFABC

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Correction for Hidden Confounders in Genetic Analyses

Jennifer Listgarten, Microsoft Research

BioPatML.NET and Its Pattern Editor: Moving into the Next Era of Biology Software

James Hogan, Queensland University of Technology

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GRAS Support Network, Its Implementation, Operation, and Use

Fritz Wollenweber, EUMETSAT

Data Intensive Frameworks for Astronomy

Jeffrey Gardner, University of Washington

Dennis Baldocchi, University of California-Berkeley

Experiences and Visions on Archaeo InformaticsChristiaan 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

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.

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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.

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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

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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

Visualizing All of History with Chronozoom

David Shimabukuro, University of California-Berkeley; Roland Saekow, University of California-Berkeley

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Proteome-Scale Protein Isoform Characterization with High Performance Computing

Jake Chen, Indiana University

Answering Biological Questions by Querying k-Mer Databases

Paul Greenfield, CSIRO Mathematics, Informatics and Statistics

CoSBiLab: Enabling Simulation-Based Science

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Scientific Data Visualization using WorldWide Telescope

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Data-Intensive Research: Dataset Lifecycle Management for Scientific Workflow, Collaboration, Sharing, and Archiving

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OData – Open Data for the Open Web

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