March 2014 Galaxy Update

Galaxy Updates

Welcome to the March 2014 Galaxy Update, a monthly summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

New Papers

54 papers were added to the Galaxy CiteULike Group in Febrary. Some papers that may be particularly interesting to the Galaxy community:

How those papers were tagged:

# Tag    # Tag    # Tag    # Tag
3 Cloud 1 Project 6 Tools 3 UsePublic
- HowTo = RefPublic - UseCloud - Visualization
4 IsGalaxy 3 Reproducibility 3 UseLocal 14 Workbench
26 Methods 2 Shared 6 UseMain

GigaScience Galaxy Series

GigaScience Journal

The GigaScience "Galaxy: Data Intensive and Reproducible Research" series announced for the 2013 Galaxy Community Conference has just published its first papers, and is continuing to take submissions. Whilst the series considers best practice papers, discussion, as well as novel uses of Galaxy, these first papers are examples of Galaxy toolkits, with a genome diversity tool collection presented from the Miller lab at Pennsylvania State, and a set of analytical and visualisation tools for Complete Genomics sequencing data from the Stubbs lab at Erasmus Medical College. The genome diversity toolkit is their first example that integrates with their GigaGalaxy server, with SVG graphs to help visualize how input datasets, workflows and histories are related to each example analysis in the paper. BGI is continuing to cover the article processing charges until the end of this year, so for more information see their blog posting.

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to and we'll put it in the Galaxy News feed and include it in next month's update.


Galaxy Australasia Workshop 2014: 24-25 March

The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.

Galaxy Australasia Workshop 2014 (GAW2014)

The Galaxy Australasia Workshop is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne. GAW 2014 will also include poster session, keynote speakers.

Melbourne Convention Centre

Registration is open. Registration is also free, but space is limited.

The first day (Monday) will be in Clayton, next to the Australian Synchrotron. For the 2nd day (Tuesday) we will move downtown the Melbourne Convention Centre, the venue for the Computational and Simulation Sciences and eResearch.

Globus World 2014

Globus World 2014

GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld features a Biosciences/Genomics Program devoted to research data in genomics and biosciences including Globus Genomics, a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago.

Learn how to get more out of your data, and connect with other HPC administrators, research scientists, and developers who are building and using cutting-edge solutions to wrangle data.

Galaxy will have a presence at this meeting, and GCC2014 is a Silver Sponsor of GlobusWorld.

GCC2014: June 30 - July 2, Baltimore

GCC2014: June 30 - July 2

The 2014 Galaxy Community Conference (GCC2014) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States.

Registration is Open

Early registration is now open. Early registration saves more than 70% on registration costs, and Training Day registration is an additional 55% off if you register for both at the same time. This is by far the most affordable option, with early registration fees starting at less than $50 per day. When you register you can also reserve lodging at Charles Commons, a very affordable housing option in the same building as the conference.

Training Day is an opportunity to learn about all things Galaxy including using Galaxy, deploying and managing Galaxy, extending Galaxy, and Galaxy internals. There are 5 parallel tracks, each with 3 sessions, with each of those sessions two and half hours long. That's 15 sessions and over 37 hours of workshop material.

Abstract Submission is Open

Abstract submission for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May 2. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

Accepted talks and selected posters from GCC2014 are also eligible for consideration to appear in the GigaScience "Galaxy: Data Intensive and Reproducible Research" series described above.


Amazon Web Services

We are pleased to have Amazon Web Services (AWS) as the sponsor for the GCC Training Day for the third year in a row. Also please welcome BioMaryland as a Bronze Sponsor for GCC2014. BioMaryland is new to the GCC.

There are still Silver and Bronze sponsorships available. Please contact the Organizers if your organization would like to help sponsor this event.


In 2014 we are also adding non-sponsor exhibit spaces in addition to the sponsor exhibits. This will significantly increase the size of the exhibit floor. Please contact the Organizers if your organization would like to have an exhibit space at GCC2014.

Other Events

There are several other [events of interest](/events/) in the next few months. Also see the [Galaxy Events Google Calendar]( for details on other events of interest to the community.
Register now for Galaxy Australasia Workshop (GAW 2014)   GlobusWorld 2014   Bio-IT World 2014   GCC2014 early registration and abstract submission are now open
Date Topic/Event Venue/Location Contact
March 24-25 Galaxy Australasia Workshop 2014 (GAW2014) Melbourne, Australia Organisers
March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States Anton Nekrutenko, Jen Jackson
April 15-17 Biosciences/Genomics Program GlobusWorld, Chicago, Illinois, United States Globus Outreach
April 29 - May 1 W1: Integrated Research Data Management for Next Gen Sequencing Analysis Using Galaxy and Globus Online Software-as-a-Service BioIT World Ravi Madduri, Alex Paciorkowski, Vas Vasiliadis
W4: Analyzing NGS Data in Galaxy Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski
W14: Running a Local Galaxy Instance Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney
Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs Ravi Madduri
Integrated Analysis and Visualization of Large-Scale Biological Data with the Refinery Platform Nils Gehlenborg
Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy Jeremy Goecks
May 6-7 Scaling Galaxy for Big Data NGS Data after the Gold Rush, TGAC, Norwich, United Kingdom Dave Clements
May 9 Galaxy Workshop The Genome Analysis Centre (TGAC), Norwich, United Kingdom Dave Clements
May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia Enis Afgan
June 9-10 Informatics on High Throughput Sequencing Data Workshop Toronto, Canada Francis Ouellette
June 10 Initiation à l’utilisation de Galaxy Cycle "Bioinformatique par la pratique" 2014, INRA Jouy-en-Josas, France Véronique Martin, Sophie Schbath
June 11 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy
June 16 Initiation à l’utilisation de Galaxy Cycle "Bioinformatique par la pratique" 2014, INRA Jouy-en-Josas, France Véronique Martin, Sophie Schbath
June 17 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy
June 16-20 Using Galaxy for Analysis of High Throughput Sequence Data UC Davis, California, United States UC Davis Bioinformatics Training
June 28-30 Galaxy Hackathon Homewood Campus of Johns Hopkins University, Baltimore, Maryland, United States Organizers
June 30 - July 2 2014 Galaxy Community Conference (GCC2014) Organizers
September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) Hans-Rudolf Hotz and Bjoern Gruening
(second Swiss) Galaxy Workshop SyBIT Tech Day, Bern (Switzerland)
German Galaxy Developers Day Freiburg (Germany)

New Public Servers

One new public Galaxy server, PGTB was added, and the NELLY server is back.

Galaxy PGTB (Virtual Biodiversity Lab)

PGTB Galaxy

Galaxy Distributions

The most recent version of CloudMan was released in January 2014.

Feb 10, 2014 Galaxy Distribution

**Complete [News Brief](**

  • Visualization upgrades, including Trackster CSS styling
  • Multiple Tools migrated to the Tool Shed for a leaner distribution
  • Redesign of UI rendering: new icons, new font, history pane updates
  • API functionality upgrades featuring a new master admin API key and
  • Tool Shed updates a focus on repository metadata, displays, installs, and tests
  • Over 35 new community contributions added

new:       $ hg clone

upgrade:   $ hg pull 
           $ hg update release_2014.02.10

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   

The Community Log Board and Deployment Catalog Galaxy community hubs were launched in December. If you have a deployment, or experience you want to share then please publish them.

ToolShed Contributions

Galaxy ToolShed

New Repositories in the Galaxy Project ToolShed

Other News