The 2013 Galaxy Community Conference will start with a Training Day on 30 June, followed by two full days of accepted talks, keynotes, lightning talks, poster sessions, birds-of-a-feather sessions, and networking time.

As in past years, talks will cover a wide range of biology, bioinformatics, and informatics. However, unlike in previous years, talks will be grouped and scheduled in sessions focusing on particular topics.


Day 0: Training Day, 30 June

Training Day

The GCC2013 Training Day will be Sunday, 30 June, and feature fourfive parallel tracks, each with three workshops, each of which are two hours long, for a total of twelvefifteen sessions on twelve different topics. Sessions are evenly split between topics aimed at biological research, topics aimed at Galaxy deployers and developers, and those that are geared twoards both audiences. The topics were nominated and selected by the Galaxy Community in early 2013. The increased number of parallel tracks and topics was driven by unexpected demand.

Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along.

Day 0: Learning Galaxy

Time CAML Rm 3348 C Rm 3347 Logo Rm 2438 Python Rm 2269 Prolog Rm 2465
8:00 Registration Opens and Catered Breakfast
9:00 Galaxy Code and Storage ArchitectureStatistical Genome Analysis with GalaxyInstalling and Maintaining a Local Galaxy ServerIntroduction to Galaxy and the Galaxy EcosystemRunning Galaxy on the Cloud
11:00 Catered Lunch
12:30 The Galaxy APIIntroduction to Tool and Data Source ConfigurationRNA-Seq Analysis with GalaxyStatistical Genome Analysis with GalaxyRunning Galaxy on the Cloud
14:30 Break
15:00 Advanced Tool and Data Source ConfigurationGalaxy Tool ShedVariant and SNP Analysis with GalaxyRNA-Seq Analysis with GalaxyChIP-Seq Analysis with Galaxy
Key:   General Biologist centric Developer & Deployer centric

Escape (to the) Pub!

Escape Pub
Bar @ Escape

The Escape Pub, in the Ole Johan Dahls House (the conference venue), has been reserved on Sunday and Monday evening until 21:00. It's normally a student pub, and has what are quite possibly the least expensive beverages in Oslo. If you are looking for a place to relax (or a particularly convivial evening Birds of a Feather session), then please do drop in.

Day 1: Main Meeting, 1 July

The first day of the conference will feature accepted talks and posters with a biology and bioinformatics emphasis. The first day will include a lightning talk session.

Day 1: Using Galaxy for genomics research

Time Topic
8:00 Registration Opens and Catered Breakfast
9:00-9:20 Welcome
Nils Christophersen, Dept. of Informatics, University of Oslo

Ole Petter Ottersen, Rector (President), University of Oslo

9:20-10:50 Session 1: Reproducible science
Moderator: Nils Christophersen, Dept. of Informatics, University of Oslo
9:20 Keynote:Computational Reproducibility is Crucial for Scientific Software Platforms
10:10 Accepted Talks
10:10 Reproducible research and the 90/10 rule: Improving the ratio of light script to dark script matter in your Galaxy
10:30 Reproducible and automated processing in high-throughput NGS facilities
10:50-11:15 Break
11:15-12:35 Session 2: Genome analysis
Moderator: Victoria Dominguez, ABgenomica
11:15 Accepted Talks
11:15 A Galaxy of learning: Bioinformatics tutorials based on Galaxy
Simon Gladman, Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative
11:35 The Genomic HyperBrowser: a Galaxy-based web server for analysis of genomic tracks
Eivind Hovig and Geir Kjetil Sandve, University of Oslo
11:55 modENCODE Galaxy: Uniform ChIP-Seq Processing Tools for modENCODE and ENCODE Data         
Quang M Trinh, Ontario Institute for Cancer Research
12:15 The Galaxy SlipStream Appliance: Galaxy Made Easy
Anushka Brownley
Product Manager and Scientific Consultant, BioTeam
Gold Sponsor Presentation
12:35-13:30 Lunch
Lunch sponsored by BioTeam
13:30-14:55 Session 3: Application-specific workflow
Moderator: Mohammad Heydarian, Johns Hopkins University
13:30 Accepted Talks
13:30Single-cell genomics pipeline: from raw reads to phylogenomics using Galaxy
Lionel Guy, Department for Cell and Molecular Biology and SciLifeLab, Uppsala University
13:50 A layered genotyping-by-sequencing pipeline using Galaxy
14:05 The Linked2Safety's Galaxy Based Data Analysis Space
Aristos Aristodimou, Department of Computer Science, University of Cyprus
14:20 Galaxy as an Integration and Workflow Platform for a Cloud Enabled Bio-medical Image Analysis and Image Processing Toolkit
Piotr Szul, CSIRO Commonwealth Scientific and Industrial Research Organisation
14:35 Representation and statistical analysis of 3D chromatin data in a Galaxy framework
Jonas Paulsen, Oslo University Hospital, Section for Medical Informatics, The Norwegian Radium Hospital
14:55-16:10 Break and Poster Session 1 (odd numbered posters)
16:10-17:30 Session 4
Moderator: Ross Lazarus, BakerIDI
15:50 Ion Torrent Semiconductor Sequencing Update
Mike Lelivelt, Ph.D.
Director of Bioinformatics and Software Products, Ion Torrent, part of Life Technologies
Platinum Sponsor Presentation
 Ion Torrent
16:30 Lightning Talks, Session 1
Medilaxy: A Galaxy Platform For Medical Image Analysis
Marco Carnini, Johannes Gutenberg University
Establishing a genomics analysis workbench
Enis Afgan, Victorian Life Sciences Computation Initiative, University of Melbourne
LiSIs: a Galaxy-based platform for Life Science Informatics Research
Christos Kannas, University of Cyprus
Software Carpentry - Helping scientists build better software since 1998
Lex Nederbragt, University of Oslo
Galaxy Integration into an External Information System
Alban Lermine, Institut Curie
Implementing Next Generation Web Server in Galaxy
Wai Yi Leung, Leiden University Medical Centre
Galaxy Scratchbook: How to view, customize, and layout multiple visualizations
Aysam Guerler, Emory University
Unraveling the code of our Galaxy
Pieter Lukasse
17:30 Finish

Escape (to the) Pub, Again!

Escape Pub
Bar @ Escape

The Escape Pub, in the Ole Johan Dahls House (the conference venue), has been reserved on Sunday and Monday evening until 21:00. It's normally a student pub, and has what are quite possibly the least expensive beverages in Oslo. If you are looking for a place to relax (or a particularly convivial evening Birds of a Feather session), then please do drop in.

Day 2: Main Meeting, 2 July

The second and final day of the conference will feature accepted talks and posters with a bioinformatics and informatics emphasis. The second day will have a lightning talk session, and the conference dinner

Day 2: Extending and customizing the Galaxy system

Time Topic
8:00 Registration Opens and Catered Breakfast
9:00-9:10 Welcome
9:10-10:40 Session 5: Interacting with Galaxy
Moderator: Karen Reddy, Johns Hopkins
9:10 State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project
9:40 Accepted Talks
9:40BioBlend - automating bioinformatics with Galaxy and CloudMan
Clare Sloggett, Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne
10:00 Extension of Galaxy to Utilize Web Services and A Semantic Suggestion Engine
Jessica C. Kissinger, University of Georgia
10:20 GTrack 1.0: Unified data format providing customizable representation and high-speed analysis performance within Galaxy
Sveinung Gundersen, Department of Tumor Biology, The Norwegian Radium Hospital
10:40-11:10 Break
11:10-12:30 Session 6: Extending Galaxy
Moderator: Jennifer Hillman-Jackson, Penn State University
11:10 Accepted Talks
11:10Globus Genomics - An Integrated End to End Sequencing Analysis Platform Powered by Globus Online and Galaxy
Ravi Madduri, Argonne National Laboratory
11:30 Galaxy-P: Beyond Proteomics
John Chilton, University of Minnesota Supercomputing Institute
11:50 DevOps Ignition to reach Galaxy continuous integration
Olivier Inizan and Mikael Loaec, Unité de Recherches en Génomique-Info, INRA
12:10 The Clinical Galaxy: A validated platform initiative
Sanjay Joshi
Chief Technical Officer (CTO), Life Sciences, EMC Isilon
Gold Sponsor Presentation
12:30-13:30 Lunch
Lunch sponsored by EMC Isilon 13:30-14:35 Session 7: Exploiting Galaxy
Moderator: Geir Kjetil Sandve, University of Oslo
13:30 Accepted Talks
13:30Enhancing the Galaxy Tool Shed
Greg Von Kuster, Penn State University
13:50 How to Create Your Own Web-based, Interactive Visualizations for Galaxy
Carl Eberhard, Emory University
14:05 Managing Galaxy's Built-in Data
Daniel Blankenberg, Penn State University
14:20 Contributing to Galaxy
Dannon Baker, Emory University
14:35-15:50 Break and Poster Session 2 (even numbered posters) 15:50-17:30 Session 8
Moderator: Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research
15:50 Lightning Talks, Session 2
How to set up a Galaxy service you can count upon
Vladimir Daric, CNRS, Université Paris Sud
GenesCloud : Bioinformatics cloud computing infrastructure
Victoria Dominguez, ABgenomica
Andromeda: NBIC Galaxy at Surfsara's HPC cloud
Leon Mei, NBIC
Gildas Le Corguille, UPMC-CNRS
GLM for testing differential expression and GSEA in Galaxy
Ross Lazarus, Baker IDI Heart and Diabetes Institute
Analysis of DNA methylation data using galaxy
Pavan Videm, University of Freiburg
Galaxy on an elastic HPC cluster at AWS
Srinivas Maddhi, Iowa Institute Of Human Genetics
Running Galaxy workflows using the CLC Main Workbench
Marc Logghe, Ablynx NV
Proteogenomics with Galaxy
Ira Cooke, LSCC / La Trobe
"Lightweight" HPC Client: Leveraging Galaxy Tool configs
ChemicalToolBoX: Cheminformatics inside the Galaxy
Björn Grüning, University of Freiburg
17:20 Closing
17:30 Finish 18:00
Conference Dinner @ Sporten
Sponsored by Ion Torrent

Please join us for this closing night event at Sporten, a banquet hall built in 1896 and overlooking Oslo.

Birds of a Feather (BoF) Gatherings

There is no better place than a Galaxy Community Conference to meet and learn from others doing high-throughput biology. GCC2013 will include Birds of a Feather (BoF) meetups throught the event. Birds of a Feather meetups are informal gatherings where participants group together based on common interests. BoFs can range from preplanned and pre-announced to just pre-announced to completely spontaneous. Pre-announcing a BoF has the advantage that conference participants can be notified of them ahead of time, and people can plan ahead to attend.

If you have an idea for a BoF, then you are strongly encouraged to start one.