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2011 Galaxy Community Conference (GCC2011)

GDC becomes GCC, and moves to Europe

The 2011 Galaxy Community Conference was held 25-26 May, at the Conference Centre De Werelt in Lunteren, The Netherlands. The conference featured two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy locally, and best practices for using Galaxy to further your research. The event drew almost 150 participants from 19 countries on six continents. The conference was co-organized and hosted by the Netherlands Bioinformatics Centre (NBIC).

See the conference page for more details.

See all Galaxy Community Conferences.


Videotaping of the talks was generously supported by NBIC. Links to each talk are belo. All talks can be viewed at Vimeo.

Full Talks

Listed in the order they were given:

Title Presenter Slides Video
Introduction to Galaxy Anton Nekrutenko, Penn State University Keynote, PDF Watch
New Data Sources, New Tools Daniel Blankenberg, Penn State University Keynote, PDF Watch
Galaxy Tool Shed Greg von Kuster, Penn State University Keynote, PDF Watch
Assembly and Annotation using Galaxy Konrad Paskiewicz, University of Exeter PowerPoint, PDF Watch
Galaxy in Plant Pathology, Not Everything is NGS Data Peter Cock, James Hutton Institute PowerPoint, PDF Watch
Integrated Small Variant Detection Using Galaxy Erik Garrison, Boston College PowerPoint, PDF Watch
Efficient Tool Deployment to the Galaxy Cloud: An RNA-Seq Workflow Case Study Sebastian J. Schultheiss, FML of the Max Planck Society, Tübingen PDF Watch
Galaxy Trackster and Visual Analytics Jeremy Goecks, Emory University PDF Watch
Galaxy Deployment and API Nate Coraor, Penn State University, and Dannon Baker, Emory University PowerPoint, PDF Watch
Pathogenomics Analysis and Visualization Freddy de Bree, Central Veterinary Institute at Wageningen UR Watch
National Collaborative Platform for Genomics and Proteomics Data Analysis Hailiang Mei, NBIC PDF Watch
Using Galaxy to Provide Tools for the Analysis of Diverse Local Datasets Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research PDF Watch
Deploying Galaxy for Use with High-Throughput Screening Experiments Grainne Kerr, German Cancer Research Center and Heidelberg University PowerPoint, PDF Watch
A Galactic Experience and Extending Galaxy Sample Tracking Jelle Scholtalbers, TRON gGmbH OpenOffice, PDF Watch
Movement of Large Datasets via Integration of GridFTP and GlobusOnline with a Production Galaxy Setup at the University of Chicago Neil Bahroos and Alex Rodriquez, University of Chicago Watch
Galaxy for High Throughput Sequencing Kirt Haden, Illumina PowerPoint, PDF Watch
JAX: Exploring the Galaxy — Our Experiences Deploying and Using Galaxy Glen Beane, Jackson Laboratory PowerPoint, PDF Watch
CloudMan: Galaxy on the Cloud Enis Afgan, Emory University PDF Watch
The Genomic Hyperbrowser Geir Kjetil Sandve, University of Oslo PDF Watch
Customized Galaxy with Applications as Web Services and on the Grid for Open Source Drug Discovery Anshu Bhardwaj, Open Source Drug Discovery Consortium, Council of Scientific and Industrial Research; and Chintalapati Janaki, Center for Development of Advanced Computing (C-DAC); India PDF Watch
Enacting Taverna Workflows Through Galaxy Konstantinos Karasavvas, NBIC PDF Watch
Pushing Data to Galaxy Ido M. Tamir, Institute of Molecular Pathology, Vienna PDF Watch
Using Galaxy for the Analysis of NGS-derived Pathogen Genomes in Clinical Microbiology Anthony Underwood, Health Protection Agency, UK PowerPoint, PDF Watch

Lightning Talks

Watch all.

Listed in the order they were given:

Title Presenter Slides Video
Blue Collar Bioinformatics NGS Pipeline Roman Valls Guimerà, Science for Life Laboratory, Stockholm GitHub Watch all
starts @ 0:01:40
RunBlast Mike Cariaso, KeyGene Google Docs, PDF Watch all
starts @ 0:08:50
Free Omixon Tool to Up/Download Large Genomic Data files to Amazon Web Services Attila Berces, Omixon [PowerPoint](https://depot.galaxyproject.org/hub/attachments/events/gcc2011/FreeOmixonToolTo UpDownloadLargeGenomicDataFilesToAmazonWebServices.pptx), [PDF](https://depot.galaxyproject.org/hub/attachmentsnomicDataFilesToAmazonWebServices.pdf: unknown primary or operator) Watch all
starts @ 0:16:30
NBIC Galaxy Hackathon Report Freek de Bruijn, NBIC PowerPoint, PDF Watch all
starts @ 0:19:45
InterMine Alex Kalderimis, University of Cambridge PowerPoint, PDF Watch all
starts @ 0:27:20
A start on running Galaxy DRMAA jobs as different users Paul Smith, Illumina PowerPoint, PDF Watch all
starts @ 0:33:20
iPlant Storage Plans Matt Vaughan, Texas Advanced Computing Center Watch all
starts @ 0:37:35
Importing Clinical Annotations into Galaxy Alain Colleta, inSilico, ULB PDF Watch all
starts @ 0:45:20
Assertion Based Testing (Issue #490) Jim Johnson, University of Minnesota PowerPoint, PDF Watch all
starts @ 0:49:40
Galaxy, GridFTP, Condor, and Globus Online Ravi Maduri, University of Chicago PowerPoint, PDF Watch all
starts @ 0:54:40
Space Junk Nate Coraor, Penn State University PowerPoint, PDF Watch all
starts @ 1:01:40


Relocate the links from the current pages in Bitbucket to here.

Each breakout has its own wiki page for notes. Someone in each group was selected to take notes, either directly on the wiki page, or just in a text editor (in which case, they will show up in June).


Many thanks to Rob Hooft for taking these pictures on the first day of the meeting.


We received feedback from 73 participants.