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Events/GCC2011

http://galaxy.psu.edu/gcc2011/

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

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, PDF

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

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).

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")

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")

Did the meeting meet your expectations?

Weight

Answer

#

%

Comments

2

Exceeded

38

52%

1

Met

35

48%

0

Fell short

0

0%

Average weighted score: 1.52 out of 2 (halfway between "Met" and "Exceeded")

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