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Events/GCC2012/Program

2012 Galaxy Community Conference (GCC2012), Chicago, Illinois, July 25-27, 2012


Program

The 2012 Galaxy Community Conference included two full days of accepted talks, lightning talks, breakout sessions, and networking time. The conference was preceded by a full day of training sessions that cover 10 topics over four 90 minute sessions.

Summaries

Day 0: July 25, Wednesday, Training Day

Training Day

The 2012 Galaxy Community Conference was preceded by a Training Day, featuring 3 parallel tracks, each featuring four, 90 minutes workshops and covering 10 different topics.

See the Training Day page for complete details on each session.

Day 1: July 26, Thursday

The main meeting started on Thursday, July 26, and featured submitted talks from the Galaxy Community and Galaxy Team.

Time

Topic

8:00-9:00

Continental Breakfast, Registration Open

9:00-9:10

Welcome
William Hendrickson
University of Illinois at Chicago (UIC)

9:10-10:40

Session 1
Moderator: Tin Lap Lee, Chinese University of Hong Kong

9:10

Slides, Video (start @ 7:10)
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project

9:40

Slides, Video (start @ 31:55)
Integration of S-MART, a toolbox to aid RNA-seq data analysis in Galaxy
Yufei Luo, Unité de recherche en Génomique-Info, INRA

10:00

Slides, Video part 1 (start @ xx:yy), part 2
Connecting Galaxy to a Data Repository
Richard Park, Boston University & Center for Biomedical Informatics at Harvard Medical School

10:20

Slides, Video (starts @ 11:45)
Role of Galaxy in a bioinformatic plant breeding platform
Vincent Maillol and Jean-Francois Dufayard, INRA and CIRAD

10:40-11:10

Break

11:10-12:30

Session 2
Moderator: Ann Black-Ziegelbein, University of Iowa

11:10

Galaxy Pipeline for Faster Whole Genome Genotype Calling on the GeneTitan Platform
Oleksiy Karpenko, University of Illinois Chicago

11:30

Slides, Video (starts @ 18:15)
Integrating Galaxy with Globus Online: Lessons learned from the CVRG project
Bo Liu, Computation Institute, University of Chicago and Argonne National Laboratory

11:50

Slides, Video (starts @ 42:35)
Scalable data management and computable framework for large scale longitudinal studies

12:10

PDF, PPT, Video part 1 (starts @ 58:45), part 2
Nebula - A Web-Server for Advanced ChIP-Seq Data Analysis
Alban Lermine, Institut Curie

12:30-1:50

12:50-1:35

Lunch: Sponsored by EMC Isilon

1:50-3:10

Session 3
Moderator: Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research

3:10-3:40

Break

3:40-5:00

Session 4
Moderator: Ravi Madduri, Computation Institute

3:40

GPS: a real-time recommendation system for ChIP-Seq analysis
Hanfei Sun, Dana-Farber Cancer Institute

4:00

Slides, Video (starts @ 16:45)
Integration of Taverna workflows on a Galaxy-based platform for large-scale genomics analysis
Tin-Lap Lee, The Chinese University of Hong Kong

4:20

PDF, PPTX, Video part 1 (starts @ 35:30), part 2
NGS analysis for Biologists: experiences from the cloud
Karen Reddy, Johns Hopkins University

4:40

Slides, Video (starts @ 8:40)
The Galaxy Visualization Framework
Jeremy Goecks, Emory University

5:00-5:15

Break

5:15-6:15

Ion Torrent
Ion Torrent: Open, Accessible, Enabling
Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products
Ion Torrent Sponsor Presentation
PDF, PPT, Video

7pm

Haymarket Pub & Brewery
Conference Dinner @ Haymarket Pub & Brwery
Sponsored by Ion Torrent

Day 2: July 27, Friday

Time

Topic

8:00-9:00

Continental Breakfast

9:00-9:10

Welcome
Christopher Fields
University of Illinois at Urbana-Champaign

9:10-10:30

Session 5
Moderator: Birgit Crain, Complete Genomics

9:10

Slides, Video (starts @ 7:55)
High level distributed processing pipelines with Galaxy
Brad Chapman, Harvard School of Public Health

9:30

PDF, Keynote, Video (starts @ 28:30)
Proteomics tools for Galaxy
Ira Cooke, La Trobe University

9:50

PDF,PPT, Video (starts @ 48:05)
Using Galaxy for Molecular Assay Design
James Ireland, 5AM Solutions

10:10

PDF, PPTX, Video part 1 (starts @ 1:07:10), part 2, part 3
The National Center for Genome Analysis Support and Galaxy
Richard LeDuc, Indiana University

10:30-10:55

Break

10:55-12:15

Session 6
Moderator: Neil Bahroos, University of Illinois Chicago

10:55

Integration of SeqWare within Galaxy
Zhibin Lu, Ontario Institute for Cancer Research

11:15

PDF, PPSX, Video (starts at 13:40)
Window2Galaxy – Enabling Linux-Windows Hybrid Workflows
Liram Vardi, Agilent Labs

11:35

PDF, PPTX, Video (starts @ 35:15)
NBIC Galaxy to Strengthen the Bioinformatics Community in the Netherlands
David van Enckevort, Netherlands Bioinformatics Centre

11:55

PDF, PPTX, Video part 1 (starts @ 54:10), part 2
GenomeSpace
Ted Liefeld, Broad Institute

12:15-1:10

Lunch

1:10-2:50

Session 7
Moderator: Ross Lazarus, BakerIDI

1:10

Tool Shed and Changes to Galaxy Distributions
Greg von Kuster, Penn State University

1:30

Lightning Talks

PDF, PPTX, Video (starts @ 24:40)
Customizing Galaxy for a Hospital Environment
Larry Helseth, NorthShore University HealthSystem

Slides, Video (starts @ 30:30)
ObjectStore
Nate Coraor, Penn State University

PDF, PPTX, Video (starts @ 36:35)
Galaxy and Condor: Challenges with harnessing widely-distributed resources
Jaime Frey, University of Wisconsin-Madison

Link, Video (starts @ xx:yy)
Interactive metagenomic visualization in Galaxy
Brian Ondov, NBACC

Slides, Video (starts @ xx:yy)
Reusable / Scalable Workflows
Clare Sloggett, VLSCI

Slides, Video (starts @ xx:yy)
The Galaxy VM Launcher
John Chilton, University of Minnesota

Slides, Video (starts @ xx:yy)
Differential Expression with Diagnostic Plots using sam2counts and DESeq
Nikhil Joshi, UC Davis

PDF, PPT, Video
Galaxy-P
Pratik Jagtap, University of Minnesota

The Genomic Hyperbrowser: Prove Your Point
Geir Kjetil Sandve, University of Oslo

Slides, Video (starts @ 6:10)
ChemicalToolBoX
Björn Grüning, Albert-Ludwigs-University Freiburg

2:45

Video (starts @ 12:35)
Closing Remarks
Anton Nekrutenko, Penn State University, James Taylor, Emory University

2:55-3:15

Break

3:15-5:00

Session 8: Breakouts
Moderator: Dave Clements, Emory University

Breakouts are informal, open discussion sessions where participants interested in a particular topic gather to discuss that topic.

There was discussion of merging the GalaxyCzars and Automation Strategies for Data, Tools, & Config breakouts. However, this wasn't been done because the emphases of the two breakouts is distinct:

  • Automation Strategies has a narrow focus on automating deployment of genomes, tools, data libraries and such.

  • GalaxyCzars is about the breadth of issues facing those deploying and managing Galaxy installations.

5:00

2012 Galaxy Community Conference ends




Questions? Ask the organizers.