May 2012 Galaxy Update

Galaxy Updates

Welcome to the May 2012 edition of 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.

GCC2012: Just 3 Months Away!

2012 Galaxy Community Conference

Training Day: We Need Your Help!

Training Day

GCC2012 Training Day needs your help! We are adding several new sessions to the GCC2012 Training Day that will cover how to use Galaxy to perform several common kinds of analysis, such as ChIP-Seq, RNA-Seq, Metagenomics, and others. However, before we can to do that, we need your input on which topics there is the most interest in!

If you are planning on or are interested in attending GCC2012, please take 2 minutes to tell us which topics you are interested in. We will use your feedback to set the Training Day schedule.

Also, if you are interested in presenting a topic, especially a "how to use Galaxy" topic, then we strongly encourage you to also nominate yourself (or, hey someone else!) on the survey as well. Please provide your feedback no later than May 11.

  Give up your input!  

Galaxy Tour de France 2012

Galaxy Tour de France 2012

We are pleased to announce the Galaxy Tour de France 2012, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in Perpignan, Lyon and Paris. Each day will feature a Galaxy for Biologists workshop in the morning, and a Galaxy for Developers workshop in the afternoon. All workshops will be taught by Galaxy Team members Nate Coroar, Anton Nekrutenko and James Taylor.

Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. See Galaxy Tour de France 2012 for details and links.

New Public Server: Nebula

Nebula Galaxy Server @ Institut Curie

Nebula is a web service provided by Institut Curie and powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data. Many thanks to Institut Curie for making Nebula publicly available.

New Papers

This paper may be of interest to the Galaxy community:

Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis, by Kun H. Liu, Matthew McCormack, Jen Sheen, Plant Methods 2012, 8:12

This open access article includes a detailed recipe describing how Galaxy was used in their analysis.

This paper was among 31 papers added to the Galaxy CiteULike group since the last Galaxy Update. The new papers were spread across 5 categories.
# Tag     # Tag
19 methods 1 howto
6 other 6 workflow
2 shared

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.

Upcoming Events and Deadlines

Galaxy Tour de France 2012 Informatics on High Throughput Sequencing Data Workshop Next-gen Sequencing in Evolutionary Biology Course ISMB 2012 2012 Galaxy Community Conference


There are May application deadlines for the Informatics on High Throughput Sequencing Data Workshop, and abstract and poster deadlines for SciPy and EuroSciPy (May 1!), SocBiN Bioinformatics 2012, and InCoB.

See the Galaxy Events Google Calendar for details on these and other events.


Date Topic/Event Venue/Location Contact
May 8-12 Staying on top of evolving best practices with Galaxy, Poster The Biology of Genomes, Cold Spring Harbor Laboratory, New York, United States Dan Blankenberg|GMOD in the Cloud, Poster Scott Cain
Integrative venomics reveals different infection strategies for parasitic wasps, poster Jeremy Goecks
May 28 - June 1 Galaxy Tour de France 2012 Perpignan, Lyon, Paris Outreach
June 6-8 Dynamically Scalable, Accessible Analysis with Galaxy Cloud Bio-IT World Asia, Singapore James Taylor
June 11-12 Informatics on High Throughput Sequencing Data Workshop Toronto, Ontario, Canada Francis Ouellette
June 11-19 Next-gen Sequencing in Evolutionary Biology Course US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States Sergei Kosakovsky Pond
July 11 Reproducible workflows for next generation sequencing analysis Nowgen, University of Manchester, United Kingdom Tom Hancocks
July 13-17 Bioinformatics Software Interoperability SIG (BSI-SIG) ISMB 2012, Long Beach, California, United States Anton Nekrutenko
July 25-27 2012 Galaxy Community Conference
Early registration is now open.
Chicago, Illinois, United States Dave Clements

Tool Shed Contributions

At least 7 new repositories were added to the Galaxy Tool Shed in April, including

  • head_and_tail, cdf_plot, venn, and matrix_visualization
  • BEAST (Bayesian Evolutionary Analysis Sampling Trees): Bayesian MCMC analysis of molecular sequences.
  • rtg_investigator: Mapping and Analysis Software for NGS Platforms Roche, Illumina and Complete Genomics; software from Real Time Genomics.
  • filter_on_md: Filter mapped reads on MD tag string in SAM files.


The most recent distribution was on March 12, 2012. Look for a new one this month.