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
- Peter Li, Jeremy Goecks and Tin Lap Lee's Meeting report in Genome Biology.
- Peter Li's GigaBlog post
- Brad Chapman's day 1 and day 2 summaries.
Day 0: July 25, Wednesday, 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 | 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 |
| 9:10 | State of the Galaxy Anton Nekrutenko and James Taylor, Galaxy Project |
| 9:40 | 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 | Connecting Galaxy to a Data Repository Richard Park, Boston University & Center for Biomedical Informatics at Harvard Medical School |
| 10:20 | 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 | Integrating Galaxy with Globus Online: Lessons learned from the CVRG project Bo Liu, Computation Institute, University of Chicago and Argonne National Laboratory |
| 11:50 | Scalable data management and computable framework for large scale longitudinal studies |
| 12:10 | 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](Events/GCC2012/Abstracts#Implications of a Galaxy Community Cloud in Clinical Genomics) Sanjay Joshi, Chief Technical Officer (CTO), Life Sciences, EMC Isilon EMC Isilon Sponsor Presentation Video | |
| 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 |
| 2:10 | Keeping Track of Life Science Data Björn Grüning, Albert-Ludwigs-University Freiburg |
| 2:30 | Easier Workflows & Tool Comparison with Oqtans+ |
| 2:50 | 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 |
| 4:00 | 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 | NGS analysis for Biologists: experiences from the cloud Karen Reddy, Johns Hopkins University |
| 4:40 | The Galaxy Visualization Framework Jeremy Goecks, Emory University |
| 5:00-5:15 | Break |
| 5:15-6:15 | Ion Torrent: [Open, Accessible, Enabling](Events/GCC2012/Abstracts#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 |
| 9:10 | High level distributed processing pipelines with Galaxy Brad Chapman, Harvard School of Public Health |
| 9:30 | Proteomics tools for Galaxy Ira Cooke, La Trobe University |
| 9:50 | Using Galaxy for Molecular Assay Design James Ireland, 5AM Solutions |
| 10:10 | 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 | Window2Galaxy – Enabling Linux-Windows Hybrid Workflows Liram Vardi, Agilent Labs |
| 11:35 | NBIC Galaxy to Strengthen the Bioinformatics Community in the Netherlands David van Enckevort, Netherlands Bioinformatics Centre |
| 11:55 | 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 |
| Customizing Galaxy for a Hospital Environment Larry Helseth, NorthShore University HealthSystem | |
| ObjectStore Nate Coraor, Penn State University | |
| Galaxy and Condor: Challenges with harnessing widely-distributed resources Jaime Frey, University of Wisconsin-Madison | |
| Interactive metagenomic visualization in Galaxy Brian Ondov, NBACC | |
| Reusable / Scalable Workflows Clare Sloggett, VLSCI | |
| The Galaxy VM Launcher John Chilton, University of Minnesota | |
| Differential Expression with Diagnostic Plots using sam2counts and DESeq Nikhil Joshi, UC Davis | |
| Galaxy-P Pratik Jagtap, University of Minnesota | |
| The Genomic Hyperbrowser: Prove Your Point Geir Kjetil Sandve, University of Oslo | |
| ChemicalToolBox Björn Grüning, Albert-Ludwigs-University Freiburg | |
| 2:45 | Video (starts @ 12:35) Closing RemarksAnton 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 |
| 5:00 | 2012 Galaxy Community Conference ends |