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.
Program
Day 0: Training Day, 30 June
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 Architecture | Statistical Genome Analysis with Galaxy | Installing and Maintaining a Local Galaxy Server | Introduction to Galaxy and the Galaxy Ecosystem | Running Galaxy on the Cloud |
| 11:00 | Catered Lunch | ||||
| 12:30 | The Galaxy API | Introduction to Tool and Data Source Configuration | RNA-Seq Analysis with Galaxy | Statistical Genome Analysis with Galaxy | Running Galaxy on the Cloud |
| 14:30 | Break | ||||
| 15:00 | Advanced Tool and Data Source Configuration | Galaxy Tool Shed | Variant and SNP Analysis with Galaxy | RNA-Seq Analysis with Galaxy | ChIP-Seq Analysis with Galaxy |
| 17:00 | Finish | ||||
| Key: | General | Biologist centric | Developer & Deployer centric | ||
Escape (to the) Pub!
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
Escape (to the) Pub, Again!
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
| |||||||||||||||
| 10:40-11:10 | Break | |||||||||||||||
| 11:10-12:30 | Session 6: Extending Galaxy Moderator: Jennifer Hillman-Jackson, Penn State University | |||||||||||||||
| 11:10 | Accepted Talks | |
| 11:10 | Globus 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 | |
Lunch sponsored by EMC Isilon
Moderator: Geir Kjetil Sandve, University of Oslo
| 13:30 | Accepted Talks | |
| 13:30 | Enhancing 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 | |
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 | |
| Workflow4Metabo 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 Samuel Lampa, SNIC-UPPMAX, Dept of Pharm Biosciences | |
| ChemicalToolBoX: Cheminformatics inside the Galaxy Björn Grüning, University of Freiburg | |
| 17:20 | Closing |
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.