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||<class="th"> 9:00-9:10 ||<:> '''Welcome'''<<BR>>[[http://www.bioen.illinois.edu/people/profile.asp?vjongene|Victor Jongeneel]] <<BR>> [[http://www.illinois.edu/|University of Illinois at Urbana-Champaign (UIUC)]] || ||<class="th"> 9:00-9:10 ||<:> '''Welcome''' ||

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


Program

The 2012 Galaxy Community Conference includes two full days of accepted talks, lightning talks, breakout sessions, and networking time. The conference is 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 will be preceded by a Training Day, featuring 3 parallel tracks, each featuring four, 90 minutes workshops and covering 10 different topics. You register for the Training Day at the same time you Register for the meeting.

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

Day 1: July 26, Thursday

The main meeting will start on Thursday, July 26, and feature 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: TBA

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: TBA

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

5:15-6:15

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

9:10-10:30

Session 5
Moderator: Birgit Cain, 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: TBA

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.