Galaxy Wiki
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.
Presentations
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 |
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New Data Sources, New Tools |
Daniel Blankenberg, Penn State University |
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Galaxy Tool Shed |
Greg von Kuster, Penn State University |
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Assembly and Annotation using Galaxy |
Konrad Paskiewicz, University of Exeter |
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Galaxy in Plant Pathology, Not Everything is NGS Data |
Peter Cock, James Hutton Institute |
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Integrated Small Variant Detection Using Galaxy |
Erik Garrison, Boston College |
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Efficient Tool Deployment to the Galaxy Cloud: An RNA-Seq Workflow Case Study |
Sebastian J. Schultheiss, FML of the Max Planck Society, Tübingen |
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Galaxy Trackster and Visual Analytics |
Jeremy Goecks, Emory University |
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Galaxy Deployment and API |
Nate Coraor, Penn State University, and Dannon Baker, Emory University |
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Pathogenomics Analysis and Visualization |
Freddy de Bree, Central Veterinary Institute at Wageningen UR |
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National Collaborative Platform for Genomics and Proteomics Data Analysis |
Hailiang Mei, NBIC |
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Using Galaxy to Provide Tools for the Analysis of Diverse Local Datasets |
Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research |
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Deploying Galaxy for Use with High-Throughput Screening Experiments |
Grainne Kerr, German Cancer Research Center and Heidelberg University |
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A Galactic Experience and Extending Galaxy Sample Tracking |
Jelle Scholtalbers, TRON gGmbH |
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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 |
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Galaxy for High Throughput Sequencing |
Kirt Haden, Illumina |
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JAX: Exploring the Galaxy — Our Experiences Deploying and Using Galaxy |
Glen Beane, Jackson Laboratory |
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CloudMan: Galaxy on the Cloud |
Enis Afgan, Emory University |
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The Genomic Hyperbrowser |
Geir Kjetil Sandve, University of Oslo |
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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 |
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Enacting Taverna Workflows Through Galaxy |
Konstantinos Karasavvas, NBIC |
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Pushing Data to Galaxy |
Ido M. Tamir, Institute of Molecular Pathology, Vienna |
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Using Galaxy for the Analysis of NGS-derived Pathogen Genomes in Clinical Microbiology |
Anthony Underwood, Health Protection Agency, UK |
Lightning Talks
Listed in the order they were given:
Title |
Presenter |
Slides |
Video |
Blue Collar Bioinformatics NGS Pipeline |
Roman Valls Guimerà, Science for Life Laboratory, Stockholm |
Watch all |
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RunBlast |
Mike Cariaso, KeyGene |
Watch all |
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Free Omixon Tool to Up/Download Large Genomic Data files to Amazon Web Services |
Attila Berces, Omixon |
Watch all |
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NBIC Galaxy Hackathon Report |
Freek de Bruijn, NBIC |
Watch all |
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InterMine |
Alex Kalderimis, University of Cambridge |
Watch all |
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A start on running Galaxy DRMAA jobs as different users |
Paul Smith, Illumina |
Watch all |
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iPlant Storage Plans |
Matt Vaughan, Texas Advanced Computing Center |
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Watch all |
Importing Clinical Annotations into Galaxy |
Alain Colleta, inSilico, ULB |
Watch all |
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Assertion Based Testing (Issue #490) |
Jim Johnson, University of Minnesota |
Watch all |
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Galaxy, GridFTP, Condor, and Globus Online |
Ravi Maduri, University of Chicago |
Watch all |
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Space Junk |
Nate Coraor, Penn State University |
Watch all |
Breakouts
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).
Sample Tracking and Instrument Integration (Greg Von Kuster)
Thinking Big: !CloudMan, Grid, and Scalability (Enis Afgan)
Workflows and API (Kanwei Li)
Complex Tools and Datasources: Parameters, Datatypes and Metadata (Dan Blankenberg)
Building a Data Infrastructure: Genomic Data Management (Kelly Vincent)
Pictures
Many thanks to Rob Hooft for taking these pictures on the first day of the meeting.
Feedback
We received feedback from 73 participants.
Would you recommend future Galaxy meetings to others?
Answer |
# |
% |
Comments |
Yes |
72 |
99% |
|
Yes, but ... |
1 |
1% |
The one response was "there was a bit too much info from the field, and not enough from the core development team." |
No |
0 |
0 |
|
How useful was the meeting?
Weight |
Answer |
# |
% |
Comments |
4 |
Exceptional |
21 |
29% |
|
3 |
Above Average |
42 |
58% |
|
2 |
Average |
9 |
12% |
|
1 |
Below Average |
1 |
1% |
This might have been a misclick. The same person indicated above average organization and "Exceeded my expectations" for the meeting. No criticism was provided. |
0 |
Not at all |
0 |
0% |
|
Average weighted score: 3.14 out of 4 (just above "Above Average") |
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Was the meeting well run and organized?
Weight |
Answer |
# |
% |
Comments |
4 |
Exceptional |
28 |
38% |
|
3 |
Above Average |
40 |
55% |
|
2 |
Average |
5 |
7% |
|
1 |
Below Average |
0 |
0% |
|
0 |
Not at all |
0 |
0% |
|
Average weighted score: 3.32 out of 4 (just above "Above Average") |
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Did the meeting meet your expectations?
Weight |
Answer |
# |
% |
Comments |
2 |
Exceeded |
38 |
52% |
|
1 |
Met |
35 |
48% |
|
0 |
Fell short |
0 |
0% |
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Average weighted score: 1.52 out of 2 (halfway between "Met" and "Exceeded") |
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And a sampling of other comments in the feedback:
- I'm looking at setting up a new Galaxy instance for my research organisation and this conference answered all my questions and more about how best to go about this.
- Really nice conference, nice people
- It was awesome to meet the actual team behind all this and approach them directly with questions.
- One big realization was the fact that we're all having the same issues on the biomedical field, it's good to share those insights.
- I think the format was perfect. A good series of talks, lighting talks, and some nice discussion in the break out group.
- The meeting was well orginized!
- Just keeping on doing what you just did!
It was just awesome
Keep the great work guys ! - Thanks for all the good work, both the conference organization and galaxy itself! Keep on.
- The organisation was excellent!
- Conference was very well organization. Its amazing to see participation from so many organizations.
- Fantastic venue, relaxed atmosphere, fantastic organisation and great to interact with the community as a whole.
- I also found that the frequent opportunities to interact with other Galaxy users and developers very useful, and which was helped by having everything on the single site.
- The relaxed atmosphere encouraged interaction and discussion.
- The community aspect was most useful; the chance to talk to the devs and to other people in a similar situation to our institution.
- Good sense of community and the desire to help each other out.
And my two favorites:
- Graag gedaan!
- Avoid volcanic eruptions