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The workshop is located in the
Houston Hall on the
University of Pennsylvania campus at
3417 Spruce Street.
All research sessions will be held in the Bodek Lounge.
The Welcome Reception and poster/demo session will be held in the
Hall of Flags,
and the Banquet in the Logan Terrace adjacent to
Houston Hall.
Transportation Information
Keynote speakers
Program
| Time |
Activity |
| Wednesday,
June 27 (Bodek Lounge) |
| 8-9 am |
Breakfast |
| 9-9:15 am |
Welcome (Susan Davidson) |
| 9:15-10:15 am
|
Keynote session
Chair: Chris Stoeckert
Keynote:
Ken Buetow, National Cancer Institute
Enabling the Molecular
Medicine Revolution through Network-Centric
Biomedicine
Slides
|
| 10:15-10:45 am |
Coffee |
| 10:45-12:15 pm |
New architectures and experience on using
systems I
Chair: Bertram Ludaescher
- The Allen Brain Atlas: Delivering
Neuroscience to the Web on a Genome Wide Scale
Chinh Dang, Andrew Sodt,
Chris Lau, Brian
Youngstrom, Lydia Ng,
Leonard Kuan,
Sayan Pathak, Allan Jones,
Mike Hawrylycz
Slides
- Toward an Integrated RNA Motif Database
Jason T. L. Wang, Dongrong Wen, Bruce A.
Shapiro, Katherine G. Herbert, Jing Li, Kaushik
Ghosh
Slides
- B-Fabric: A Data and Application
Integration Framework for Life Sciences Research
Can Turker, Etzard Stolte, Dieter Joho,
Ralph Schlapbach
Slides
|
| 12:15-2:00 pm |
Lunch (boxed) |
| 2:00-3:00 pm |
New architectures and experience on using
systems II
Chair: Sarah Cohen-Boulakia
- myGrid and UTOPIA: an Integrated Approach
to Enacting and Visualising In Silico
Experiments in the Life Sciences
Steve Pettifer,
Katy Wolstencroft, Pinar Alper,
Teresa Attwood,
Alain Coletta, Carole
Goble,
Peter Li, Philip
McDermott, James Marsh,
Tom Oinn, James Sinnott,
David Thorne
Slides
- SWAMI: Integrating Biological Databases
and Analysis Tools within User Friendly
Environment
Rami Rifaieh, Roger Unwin, Jeremy Carver,
Mark A. Miller
Slides
|
| 3:00-3:30 pm |
Coffee |
| 3:30-5:15 pm
|
Selected poster/demo (short
talks)
Chair: Val Tannen
-
Jump-Starting Data
Integration in Biomedicine
Peter Mork, Jean Stanford, Len Seligman, Jeff
Hoyt and Ken Smith
Slides
- Discovering relevant sequential
associations between heterogeneous features of
proteins
Bastien Rance, Frédérique Lisacek,
Christine Froidevaux
Slides
- Using GO and MeSH Annotations to Find
Meaningful Associations
Woei-Jyh Lee, Louiqa Raschid and Padmini
Srinivasan
Slides
- Querying Biologically Relevant Provenance
information in Scientific Workflow Systems with
Zoom*UserViews
Sarah Cohen-Boulakia, Olivier Biton,
Susan Davidson
Slides
- VisTrails: Using
Provenance to Streamline Data Exploration
Erik Andersen, Steven P. Callahan, David A.
Koop, Emanuele Santos, Carlos E. Scheidegger,
Huy T. Vo, Juliana Freire and Claudio T. Silva
Slides
- CleanTAX: A Framework and System for
Automated Reasoning with Taxonomies and
Articulations
David Thau, Sichen Bao,Bertram Ludaescher
Slides
|
| 6-8 pm |
Poster/demo session and
Welcome reception (Hall of Flags) |
| |
|
|
Thursday,
June 28 (Bodek Lounge) |
| 8-9 am |
Breakfast |
| 9-10 am |
Managing and Designing Scientific Workflows I
Chair: Peter Mork
- A High-Throughput Bioinformatics Platform
for Mass Spectrometry-Based Proteomics
Thodoros Topaloglou, Moyez Dharsee, Rob
Ewing, Yury Bukhman
Slides
- Bioinformatics Service Reconciliation By
Heterogeneous Schema Transformation
Lucas Zamboulis, Nigel Martin, Alexandra
Poulovassilis
Slides
|
| 10:00-10:30am
|
Coffee |
| 10:30-12:00 |
Managing and Designing Scientific Workflows
II
Chair: Thodoros Topaloglou
- A Formal Model of Dataflow Repositories
Jan Hidders, Natalia Kwasnikowska, Jacek
Sroka, Jerzy Tyszkiewicz, Jan Van den Bussche
Slides
- Project Histories: Managing Data
Provenance Across Collection-Oriented Scientific
Workflow Runs
Shawn Bowers, Timothy McPhillips, Martin Wu,
Bertram Ludaescher
Slides
- Automatically Constructing a Directory of
Molecular Biology Databases
Luciano Barbosa, Sumit Tandon, Juliana Freire
Slides
|
| 12:00-1:30 pm |
Lunch (boxed) |
| 1:30-3:00 pm |
Mapping and matching techniques
Chair: Juliana Freire
- Fast approximate Duplicate Detection for
2D-NMR Spectra
Bjorn Egert, Steffen Neumann, Alexander
Hinneburg
Slides
- Ontology - Supported Machine Learning and
Decision Support in Biomedicine
Alexey Tsymbal, Sonja Zillner, Martin Huber
- Instance-based matching of large life
science ontologies
Toralf Kirsten, Andreas Thor, Erhard Rahm
Slides
|
| 3:00-3:30 pm |
Coffee |
| 3:30-4:30 pm |
Modeling of life science data
Chair: Louiqa Raschid
- Data Integration and Pattern-finding in
Biological Sequence with TESS's Annotation
Grammar and Extraction Language (AnGEL)
Jonathan Schug, Max Mintz, Christian J.
Stoeckert
Slides
- Accelerating Disease Gene Identification
Through Integrated SNP Data Analysis
Paolo Missier, Suzanne Embury, Cornelia
Hedeler, Mark Greenwood, Joanne Pennock, Andy
Brass
Slides
|
| 6-10 pm |
Banquet (Logan Terrace) |
| |
|
Friday,
June 29 (Bodek Lounge) |
| 8-9 am |
Breakfast |
| 9-10:00 am |
Keynote session
Chair: Susan Davidson
Keynote:
Junhyong Kim, University of Pennsylvania
Phyl-O'Data (POD) from Tree
of Life: Integration Challenges from Yellow Slimy
Things to Black Crunchy Stuff
Slides
|
| 10:00-10:30 am
|
Coffee |
| 10:30-12:00 |
Annotation in Data Integration
Chair: Val Tannen
- What's new? What's certain? -- Scoring
Search Results in the Presence of Overlapping
Data Sources
Philipp Hussels, Silke Trissl,
Ulf Leser
Slides
- Using Annotations from Controlled
Vocabularies to Find Meaningful Associations
Woei-Jyh Lee, Louiqa Raschid, Padmini
Srinivasan, Nigam Shah,
Daniel Rubin, Natasha Noy
Slides
- CONANN: An Online Biomedical Concept
Annotator
Lawrence Reeve,
Hyoil Han
Slides
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