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Events/GCC2013/Program

Program

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 four five parallel tracks, each with three workshops, each of which are two hours long, for a total of twelve fifteen 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

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


Opening
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
 

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 HeydarianJohns Hopkins University 

13:30

Accepted Talks

13:30

Single-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 University

9:10

 State of the Galaxy
Anton Nekrutenko and James Taylor, Galaxy Project

9:40

Accepted Talks

9:40

 BioBlend - 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

11:10

 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

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

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

17:30

Finish

18:00

Sporten
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

Events/GCC2013/BoF

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.

Questions? Contact the Organizers.