7th IEEE International Conference on e-Science

5 Dec 2011, 08:00 → 8 Dec 2011, 18:00 Europe/Stockholm

City Conference Center

See http://www.escience2011.org/ for details.

Monday 5 December

09:00 → 10:30 Microsoft eScience Workshop Plenary: Advancing Environmental Understanding; the Role of eScience

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

09:00 → 10:30 Workshop on Interoperability in Scientific Computing

See http://
www.cs.ox.ac.uk/david.johnson/wisc11/ for details

10:30 → 11:00 Coffee Break

11:00 → 12:30 Microsoft eScience Workshop: Citizen Science on Windows Phone 7 Platform

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

11:00 → 12:30 Microsoft eScience Workshop: Scientific Programming for Biologists (and Everyone Else)

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

11:00 → 12:30 Workshop on Interoperability in Scientific Computing

See http://
www.cs.ox.ac.uk/david.johnson/wisc11/ for details

11:00 → 12:30 Workshop: Computing advances in Life Sciences

See http://www.scalalife.eu/content/ieee-escience-2011-
workshop-computing-advances-life-science for details

11:00 → 12:30 Workshop: Measuring the Impact of eScience Research

See http://www.ci.uch
icago.edu/MESR/ for details.

12:30 → 13:30 Lunch Break

13:30 → 15:00 Microsoft eScience Workshop: Community Capability Model for Data-Intensive Science

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

13:30 → 15:00 Microsoft eScience Workshop: VENUS-C: eScience in the Cloud

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

13:30 → 15:00 Workshop on D3Science (data-intensive, distributed, and dynamic)

See http://www.c
i.uchicago.edu/D3Science/ for details

13:30 → 15:00 Workshop: Computing advances in Life Sciences

See http://www.scalalife.eu/content/ieee-escience-2011-
workshop-computing-advances-life-science for details

13:30 → 15:00 Workshop: Distributed Multiscale Computing

See http:/
/www.computationalscience.nl/dmc2011/ for details.

13:30 → 15:00 Workshop: Measuring the Impact of eScience Research

See http://www.ci.uch
icago.edu/MESR/ for details.

15:00 → 15:30 Coffee Break

15:30 → 17:00 Microsoft eScience Workshop: Cloud Computing: Real-World Experiences

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

15:30 → 17:00 Microsoft eScience Workshop: Developing Communication Maturity Models for Data-Intensive Science

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

15:30 → 17:00 Workshop on D3Science (data-intensive, distributed, and dynamic)

See http://www.c
i.uchicago.edu/D3Science/ for details

15:30 → 17:00 Workshop: Computing advances in Life Sciences

See http://www.scalalife.eu/content/ieee-escience-2011-
workshop-computing-advances-life-science for details

15:30 → 17:00 Workshop: Distributed Multiscale Computing

See http:/
/www.computationalscience.nl/dmc2011/ for details.

15:30 → 17:00 Workshop: Measuring the Impact of eScience Research

See http://www.ci.uch
icago.edu/MESR/ for details.

17:30 → 21:30 Microsoft Workshop Dinner and Jim Gray Award

Tuesday 6 December

09:00 → 09:30 Opening

09:30 → 10:30 Keynote: Computational Biomedicine: A Challenge for the 21st Century, Peter Coveney, UCL

Much scientific research and innovation requires a wide
range of data intensive computations--including high
performance computing (HPC)--to be run as part of a
complex workflow, for example with different steps for data
access, data acquisition, data transfer, data processing and
compute-intensive simulation. To simplify the process for
the user, we can orchestrate these steps using a workflow
manager and provide seamless access to remote resources
using audited credential delegation and the application
hosting environment. This talk will outline several
biomedical applications our group has been working on to
enable better medical/clinicial treatments which draw on
the use of HPC inter alia. These include patient specific HIV
drug therapy, personalized treatment of aneurysms in the
brain and patient specific cancer therapy. In this talk I will
describe the e-Science techniques used in each project and
will make a case for an integrated computational
infrastructure (data storage, networks and computational
resources) to ensure the successful development of future
biomedical applications. I will also provide an overview of the
developments at the EU level to further computational
biomedicine through the FP7 Virtual Physiological Human
(VPH) Initiative. VPH projects in which we are involved
include VPH-SHARE, which aims to provide robust cloud
based infrastructure for translational biomedical research
and clinical usage, and p-medicine, where we process large
amounts of federated medical data from different sources to
provide personalized clinical decision support. Such scenarios
require a heterogeneous computational infrastructure,
comprising secure resources from the desktop (within a
hospital) to the very largest supercomputers available
nationally and internationally, in new and disruptive ways,
for example to deliver urgent results on demand.

slides PVC-IEEE-2011b.pdf

10:30 → 11:00 Coffee Break

11:00 → 12:30 Microsoft eScience Workshop: Digital Humanities 1

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

11:00 → 12:30 Microsoft eScience Workshop: Semantics in Action with Data Enrichment

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

11:00 → 12:30 Workshop: Towards a Global Research Data Infrastructure

For more information see the workshop website.

11:00 → 12:30 e‐Science Paper Session 1A (Bioinformatics and Health/Tools)

11:00 A Virtual Research Environment for Cancer Imaging

Maria Susana Avila Garcia, Anne Trefethen, Xin Xiong, Charles Crichton, Andrew Tsui, Pin Hu

11:30 An Open‐source Collaboration Environment for Metagenomics Research

Xiaoquan Su, Yongzheng Ma, Hongwei Yang, Xingzhi Chang, Kai Nan, Jian Xu, Kang Ning

12:00 rCAD: A Novel Database Schema for the Comparative Analysis of RNA

Stuart Ozer, Kishore Doshi, Weijia Xu, Robin Gutell

11:00 → 12:30 e‐Science Paper Session 1B (Tools)

11:00 A national grid submission gateway for eScience

Shunde Zhang, Paul Coddington, Andrew Wendelborn

11:30 Investigating the Use of Gadgets, Widgets, and OpenSocial to Build Science Gateways

Zhenhua Guo, Raminderjeet Singh, Marlon Pierce, Yan Liu

12:00 A Chemistry‐Inspired Workflow Management System for Scientific Applications in Clouds

Cedric Tedeschi, Hector Fernandez, Thierry Priol

12:30 → 13:30 Lunch Break

13:30 → 15:00 International eScience Coordination (closed)

13:30 Intro

Speaker: Erwin Laure (PDC-HPC)

13:40 Sweden

Speakers: Prof. Dan Henningson (KTH Mechanics), Nyström Ingela

13:47 UK

Speakers: Anne Trefethen, David De Roure

13:54 Finland

Speaker: Per Öster

14:01 Australia

Speaker: David Abramson

14:08 Nordic

Speaker: Sverker Holmgren

14:15 Netherlands

Speaker: Jacob de Vlieg

14:22 Microsoft

Speaker: Tony Hey

14:30 Discussion

13:30 → 15:00 Microsoft eScience Workshop: Digital Humanities 2

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

13:30 → 15:00 Microsoft eScience Workshop: Semantics in Action via Services and Policies

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

13:30 → 15:00 Workshop: Towards a Global Research Data Infrastructure

For more information see the workshop website.

13:30 → 15:00 e‐Science Paper Session 2A (Bioinformatics and Health/Tools)

13:30 A Cloud‐based Dynamic Workflow for Mass Spectrometry Data Analysis

Ashish Nagavaram, Gagan Agrawal, Michael Freitas, Gaurang Mehta, Rajiv Mayani, Ewa Deelman

14:00 Creating a Cloud‐based Life Science Gateway

Wenjun Wu, Hui Zhang, Zhenan Li, Yaokuan Mao

14:30 Optimizing Phylogenetic Analysis Using SciHmm Cloud‐based Scientific Workflow

Kary Ocana, Daniel Oliveira, Eduardo Ogasawara, Jonas Dias, Marta Mattoso

13:30 → 15:00 e‐Science Paper Session 2B (Climate and Earth Sciences)

13:30 Wireless sensing networks for environmental monitoring: two case studies from tropical forests

Arturo Sanchez‐Azofeifa, Cassidy Rankine, Mario Do Espirito Sanchez, Robert Fatland, Milton Garcia

14:00 On the Powerful Use of Simulations in the Quake‐Catcher Network to Efficiently Position Low‐cost Earthquake Sensors

Kyle Benson, Trilce Estrada, Michela Taufer, Jesse Lawrence, Elizabeth Cochran

14:30 Communicating Coastal Risk Analysis in an Age of Climate Change

John McGee, Brian Blanton, Oleg Kapeljushnik

15:00 → 15:30 Coffee Break

15:30 → 17:00 Microsoft eScience Workshop: Software for Science

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

15:30 → 17:00 e‐Science Paper Session 3A (Bioinformatics and Health/Tools)

15:30 Application of Data Mining in Research of Avian Influenza Virus Cross‐Species Infection

Shasha Li, Yuanchun Zhou, Jianhui Li, Ze Luo, Zheng Kou, Tianxian Li, Baoping Yan

16:00 Fostering Scientific Workflow Preservation Through Discovery of Substitute Services

Khalid Belhajjame, Carole Goble, Stian Soiland‐Reyes, David de Roure

16:30 A Novel Framework for Monitoring and Analyzing Quality of Data in Simulation Workflows

Michael Reiter, Uwe Breitenbuecher, Schahram Dustdar, Dimka Karastoyanova, Frank Leymann, Hong‐Linh Truong

15:30 → 17:00 e‐Science Paper Session 3B (Climate and Earth Sciences)

15:30 Transient modeling of permafrost dynamics in changing climate scenarios

Andrew Frampton, Georgia Destouni, Ylva Sjöberg, Scott Painter

16:00 Evolving Inversion Methods in Geophysics with Cloud Computing ‐ a case study of an eScience collaboration

Craig Mudge, Graham Heinson, Pinaki Chandrasekhar, Stephan Thiel

16:30 Assessing the Value of Cloudbursting: A Case Study of Satellite Image Processing on Windows Azure

Marty Humphrey, Zach Hill, Keith Jackson, Catharine van Ingen, Youngryel Ryu

19:00 → 21:00 Reception at City Hall

Wednesday 7 December

09:00 → 10:00 Keynote: eScience: Past, Present and Future, Tony Hey, Microsoft Research

The talk will review the origins of the eScience initiative
starting with the John Taylor’s ambitious £250M program in
the UK. One strand of the eScience agenda concerns data-
intensive science and ‘big data’. In Europe and the UK, and
also globally, the particle physicists used complex
middleware to build a grid of centers to move data from
CERN and to share data and computing resources for the
analysis of the LHC experiments. Other scientific
communities also have big data challenges: Jim Gray and
Alex Szalay’s pioneering work with the Sloan Digital Sky
Survey and their creation of the SkyServer Database were
major landmarks for ‘big data’ astronomy. The global
astronomy community also came together to create ‘Virtual
Observatories’ as a forum for collaboration and exchange of
data.



Both particle physics and astronomy have significant
amounts of data yet do not present the same challenge for
discovery and insight that is needed for the analysis of
genetic and bioinformatics data. There, the goal is to extract
new knowledge from very disparate types of data ranging
from gene sequences to 3-D protein structures. Similar
remarks can be made about biomedical data where
understanding features in medical images and integrating
this information with many other types of medical data is a
major challenge. In these last two examples, computer
science technologies such as Machine Learning and
Computer Vision clearly have a key role to play. Finally the
increasing deployments of sensor networks and the use of
satellite imagery are transforming many areas of
environmental science. In all these cases there is a need to
use advanced IT to assist scientists in managing, visualizing
and analyzing their data.



The eScience agenda is not only about very big data in the
Terabyte and Petabyte range. The need to collaborate, re-
use and mine many small data sets is a common feature of
many different fields and eScience covers the tools and
technologies required to make this possible. The tools must
cover the entire data life cycle, from acquisition to archive.
Furthermore, the tools needed by scientists can incorporate
advanced computer science algorithms but they also need
to be robust and reliable - not just research prototypes
beloved by computer science researchers!



Increasingly eScience technologies will be relevant to the
Humanities and Social Sciences and perhaps the term
eResearch, as in the Australian eResearch program, is a
more appropriate name. The explosive growth in scientific
data will also affect scholarly publishing and libraries. In
addition to the scientific data revolution we are also seeing a
transformation in how we publish scientific data and how
we assign credit for such tasks as data curation.



After a brief survey of the state of eScience today with
some examples of what Jim Gray called the ‘Fourth
Paradigm’ for scientific research, the talk concludes with a
look to the future where semantic computing technologies
and Cloud services are certain to play an increasingly
important role.

slides (Dec11)_TonyHey_-_Stockholm_e-Science_Talk_(final).pdf

10:00 → 10:30 Coffee Break

10:30 → 12:00 Microsoft eScience Workshop: Is NUI "Natural" for Scientists?

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

10:30 → 12:00 Microsoft eScience Workshop: Open Data for Open Science – An Environmental Informatics Workshop (part 1)

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

10:30 → 12:00 Workshop: Cloud Interfaces and Virtualization for e-Science and Industry

For more information see the workshop website.

10:30 → 12:00 e‐Science Paper Session 4A (Data Management and Digital Repositories)

10:30 A Provenance approach to trace scientific experiments on a grid infrastructure

Ammar Benabdelkader, Mark Santcroos, Souley Madougou, Antoine van Kampem, Silvia Delgado Olaba

11:00 The SinBiota 2.0 Biodiversity Information System

Cleber Mira, Pedro Feijao, Tiago Duque‐Estrada, Joao Meidanis, Carlos Joly

11:30 Large Scale Participatory Acoustic Sensor Data Analysis: Tools and Reputation Models to Enhance Effectiveness

Anthony Truskinger, Haofan Yang, Jason Wimmer, Jinglan Zhang, Ian Williamson, Paul Roe

10:30 → 12:00 e‐Science Paper Session 4B (Arts, Humanities and e‐Social Science)

10:30 Preparing DARIAH

Andreas Aschenbrenner, Tobias Blanke, Michael Priddy

11:00 e‐Science and the Archaeological Frontier

Aaron Gidding, Yuma Matsui, Thomas Levy, Tom DeFanti, Falko Kuester

11:30 Building a Semantic Knowledge Base for Painting Conservators

Jane Hunter, Suleiman Odat

10:30 → 12:00 e‐Science Paper Session 4C (Physical Sciences and Engineering)

10:30 Building and operating a distributed regional centre for LHC computing and data storage

Oxana Smirnova, Gerd Behrmann, Michael Gronager, Daniel Johansson, Josva Kleist, Aleksandr Konstantinov, Balazs Konya, Henrik Thostrup Jensen

11:00 iGrid: Interactive Grid

Marco Meoni

11:30 Chinese e‐VLBI Network: a multi‐purpose e‐science platform

Weimin Zheng

12:00 → 13:00 Lunch Break

13:00 → 14:30 Microsoft eScience Workshop: Open Data for Open Science – An Environmental Informatics Workshop (part 2)

See http://research.microsoft.com/en-
us/events/escience2011/ for details.

13:00 → 14:30 Workshop: Cloud Interfaces and Virtualization for e-Science and Industry

For more information see the workshop website.

13:00 → 14:30 e‐Science Paper Session 5A (Data Management and Digital Repositories)

13:00 Adaptive Inference of Fine‐grained Data Provenance to Achieve High Accuracy at Lower Storage Costs

Mohammad Rezwanul Huq, Andreas Wombacher, Peter Apers

13:30 A Scalable Architecture for e‐Science Data Management

Salman Toor, Manivasakan Sabesan, Sverker Holmgren, Tore Risch

14:00 The Adaptive Collection and Analysis of Distributed Multimedia Sensor Data

Paul Roe

13:00 → 14:30 e‐Science Paper Session 5B (Tools)

13:00 Collaborative eResearch in a Social Cloud

Ashfag Thaufeeg, Kris Bubendorfe, Kyle Chard

13:30 Dynamic Handling for Cooperating Scientific Web Services

Reginald Cushing

14:00 In Situ Data Provenance Capture in Spreadsheets

Hazeline Asuncion

13:00 → 14:30 e‐Science Paper Session 5C (Physical Sciences and Engineering)

13:00 HELIO: Discovery and Analysis of Data in Heliophysics

Donal Fellows, John Brooke, Robert Bentley Andre Csillaghy, Anja Le Blanc, Gabriele Pierantoni, Marco Soldati, Mauro Messerotti

13:30 Scaling Dalton, a molecular electronic structure program

Xavier Aguilar, Michael Schliephake, Olav Vahtras, Judit Gimenez, Erwin Laure

14:00 Dynamic Pipeline Changes in Scienitifc Data Processing

Johnson Mwebaze

14:30 → 15:00 Coffee Break

15:00 → 16:00 eScience Keynote: 2011 Nobel Laureate Brian P. Schmidt

16:15 → 17:15 Keynote: ...ye who here enter...., Pär Strand, Chalmers University, Sweden

e-Science and activities that build on e-infrastructure has
emerged on the scientific arena the last ten years or so. It
is continuing to grow in an ever increasing pace and is
gaining more and more impact on both science and society.
The underpinning of this development is the availability and
robustness of the underlying infrastructures and the ability,
often seeded by EU level project funding, to bring large scale
collaborative teams together to pursue science issue son
the infrastructures.
There are a number of challenges for a new community to
access e-infrastructures. Some of the challenges are purely
technical – the tools of the new community need to be
adapted to the infrastructure. Other challenges come from
new computational or technical requirements introduced to
the infrastructure pushing it into new realms of operation or
access paradigms. Bridging the societal differences of
individuals of sometimes very different backgrounds both
technical and cultural is a harder challenge than often is
appreciated.
A lot of these challenges will be polarized as larger scale
projects with strong e-Science and e-Infrastructure
components are starting up in Europe. We will look at these
issues taken input from our experience in bringing the
fusion community closer to the e-science and e-
infrastructure activities in Europe.

slides e-science2011_strand.pdf

17:15 → 18:15 eScience Steering Committee (closed)

18:30 → 22:00 Gala Dinner

Thursday 8 December

09:00 → 10:00 Keynote: The Name is Science, d-Science, Yannis Ioannidis, University of Athens and ATHENA Research Center

Having passed through the empirical/observational, the
theoretical/experimental, and the computational paradigms,
science is now conducted predominantly following the data
exploration paradigm. Data is the key in modern scientific
endeavor! Incredible amounts of it of great complexity is
generated, which is then analyzed in an automatic or semi-
automatic fashion; this results in identification of common
patterns and trends or rare phenomena, which often
constitute new scientific discoveries or lead to those. In this
talk, we will present several contemporary scientific efforts
of major importance that are critically dependent on data
exploration. We will also outline some key relevant data-
management challenges that arise in the context of these
efforts and require significant advances in current
technology. At the end of the talk, it should be obvious that
the "e-Science 2012" Conference should be renamed into
"d-Science 2012"!

slides ioannidis@eScience.pdf

10:00 → 10:30 Coffee Break

10:30 → 16:30 EGI Council meeting (closed)

For more information see https://www.eg
i.eu/indico/event/653

10:30 → 12:00 Workshop: Computing for Citizen Science

See http://itee.uq.edu.au/~eresearch/worksho
ps/compcitsci2011/index.html for details.

10:30 → 12:00 Workshop: EU-IndiaGrid2

For more details see the workshop
homepage.

10:30 → 12:00 e‐Science Paper Session 6A (Data Management and Digital Repositories)

10:30 Enforcing scientific data sharing agreements

Michael Wilson, Shirley Crompton, Brian Matthews, Alexey Orlov

11:00 A Mosaic of Software

Kenton McHenry, Rob Kooper, Luigi Marini, Michael Ondrejcek, Peter Bajcsy

11:30 Creating Infrastructure for Tool‐Independent Querying and Exploration of Scientific Workflows

Lena Strömbäck, Valentina Ivanova

10:30 → 12:00 e‐Science Paper Session 6B (Data Management/Climate and Earth Sciences)

10:30 Towards an e‐Infrastructure for Urban Research Across Australia

Richard Sinnott, Martin Tomko, Gerson Galang, Ribert Stimson

11:00 A Linked Data Approach to Publishing Complex Scientific Workflows

Arif Shaon, Sarah Callaghan, Bryan Lawrence, Brian Matthews, Andrew Woolf, Timothy Osborn, Colin Harpham

11:30 Experiences Using GlideinWMS and the Corral Frontend Across Cyberinfrastructures

Mats Rynge, Gideon Juve, Ewa Deelman, Krista Larson, Burt Holzman, Igor Sfiligoi, Frank Würthwein, G. Bruce Berriman, Scott Callaghan

10:30 → 12:00 e‐Science Paper Session 6C (Physical Sciences and Engineering)

10:30 Large‐scale simulations of turbulence: HPC and numerical experiments

Philipp Schlatter, Johan Malm, Geert Brethouwer, Arne Johansson, Dan Henningson

11:00 The Saaz Framework for Turbulent Flow Queries

Alden King, Eric Arobone, Scott Baden, Sutanu Sarkar

11:30 Parallel finite element operator application: Graph partitioning and coloring

Katharina Kormann, Martin Kronbichler

12:00 → 13:00 Lunch Break

13:00 → 14:30 Workshop: Computing for Citizen Science

See http://itee.uq.edu.au/~eresearch/worksho
ps/compcitsci2011/index.html for details.

13:00 → 14:30 Workshop: EU-IndiaGrid2

For more details see the workshop
homepage.

13:00 → 14:30 e‐Science Paper Session 7A (Education and e‐Science Practice)

13:00 Cyberinfrastructure Internship and its application to e‐Science

David Abramson

13:30 Cyberinfrastructure and e‐Science Application Practices in Chinese Academy of Sciences

Xiangyang Huang, Ze Luo, Baoping Yan

14:00 e‐Science Practice for Wild Birds' Monitoring and Protection in Qinghai Lake Region

Ze Luo, Baoping Yan, Yuanchun Zhou, Jian LI, Haiming Zhang, Jing Shao, Shasha Li

13:00 → 14:30 e‐Science Paper Session 7B (Tools)

13:00 A Social Cloud for Public eResearch

Koshy John, Kris Bubendorfe, Kyle Chard

13:30 User‐orientated electronic laboratory notebook for retrieval and extraction of provenance information for EUROCHAMP‐2

Zulkifly Mohd Zaki, Peter Dew, Lydia MS Lau, Michael Pilling

14:00 A Framework for Efficient Text Analytics through Automatic Configuration and Customization of Scientific Workflows

Matheus Hauder, Yolanda Gil, Yan Liu

13:00 → 14:30 e‐Science Paper Session 7C (Physical Sciences and Engineering)

13:00 Design of a parallel hybrid direct/iterative solver for CFD problems

Jonas Thies, Fred Wubs

13:30 CarbBuilder: An Adjustable Tool for Building 3D Molecular Structures of Carbohydrates for Molecular Simulation

Michelle Kuttel, Göran Widmalm, Yue Mao, Magnus Lundborg

14:00 An Approach to Optimize the Execution of RTM algorithm in Multicore Machines

Alexandre Sena, Aline Nascimento, Cristina Boeres, Vinod Rebello, André Bulcão

14:30 → 15:00 Coffee Break

15:00 → 16:30 Workshop: Computing for Citizen Science

See http://itee.uq.edu.au/~eresearch/worksho
ps/compcitsci2011/index.html for details.

15:00 → 16:30 Workshop: EU-IndiaGrid2

For more details see the workshop
homepage.