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

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.


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.

Time Main Room C Meeting Room F Meeting Room E
8:00 Continental Breakfast, Registration Open
9:00 WS1: Integrating Tools & Data Sources WS2: Introduction to Galaxy WS3: Galaxy CloudMan
10:30 Break
11:00 WS4: Galaxy Code Architecture WS5: Installing Your Own Galaxy WS6: Galaxy API
12:30 Lunch Break
2:00 WS7: Galaxy Tool Shed WS8: Variant and SNP Analysis with Galaxy WS1: Integrating Tools & Data Sources
3:30 Break
4:00 WS9: RNA-Seq Analysis with Galaxy
Curtis Hendrickson, David Crossman & Jeremy Goecks
WS10: Ion Torrent – Open Source Sequencing
Matt Dyer, Associate Director, Ion Torrent, Bioinformatics & Community
WS6: Galaxy API
5:30 Finish

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
Slides, Video (start @ 7:10)
State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
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
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
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
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
Slides, Video (starts @ 42:35)
Scalable data management and computable framework for large scale longitudinal studies
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 Lunch: Sponsored by EMC Isilon
Implications of a Galaxy Community Cloud in Clinical Genomics
Sanjay Joshi, Chief Technical Officer (CTO), Life Sciences, EMC Isilon
EMC Isilon Sponsor Presentation
1:50-3:10 Session 3:
Moderator: Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research
1:50 Establishing a National Genomics Virtual Laboratory with Galaxy CloudMan
Slides, Source, Video part 1 (starts at 22:00), part 2
Keeping Track of Life Science Data
Björn Grüning, Albert-Ludwigs-University Freiburg
PPT, PDF, Video (starts at 3:00)
Easier Workflows & Tool Comparison with Oqtans+
Slides, Video (starts @ 19:25)
CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences
Gregory Minevich, Columbia University
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
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
PDF, PPTX, Video part 1 (starts @ 35:30), part 2
NGS analysis for Biologists: experiences from the cloud
Karen Reddy, Johns Hopkins University
Slides, Video (starts @ 8:40)
The Galaxy Visualization Framework
Jeremy Goecks, Emory University
5:00-5:15 Break
5:15-6:15 Ion Torrent: Open, Accessible, Enabling
Mike Lelivelt, Ion Torrent, Director of Bioinformatics and Software Products
Ion Torrent Sponsor Presentation
PDF, PPT, Video
7pm 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
Slides, Video (starts @ 7:55)
High level distributed processing pipelines with Galaxy
Brad Chapman, Harvard School of Public Health
PDF, Keynote, Video (starts @ 28:30)
Proteomics tools for Galaxy
Ira Cooke, La Trobe University
PDF, PPT, Video (starts @ 48:05)
Using Galaxy for Molecular Assay Design
James Ireland, 5AM Solutions
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
PDF, PPSX, Video (starts at 13:40)
Window2Galaxy – Enabling Linux-Windows Hybrid Workflows
Liram Vardi, Agilent Labs
PDF, PPTX, Video (starts @ 35:15)
NBIC Galaxy to Strengthen the Bioinformatics Community in the Netherlands
David van Enckevort, Netherlands Bioinformatics Centre
PDF, PPTX, Video part 1 (starts @ 54:10), part 2
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)
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
Pratik Jagtap, University of Minnesota
The Genomic Hyperbrowser: Prove Your Point
Geir Kjetil Sandve, University of Oslo
Slides, Video (starts @ 6:10)
Björn Grüning, Albert-Ludwigs-University Freiburg
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
5:00 2012 Galaxy Community Conference ends

Questions? Ask the organizers.