March 2013 Galaxy Update

Galaxy Updates

Welcome to the March 2013 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 Public Galaxy Servers

University of Costa Rica
The University of Costa Rica School of Medicine, Master in Bioinformatics and System Biology and BREL (Bioinformatics Research Laboratory) have made the Galaxy NELLY server publicly accessible. NELLY features the standard Galaxy tool set. It requires a login, but anyone can create a login. This server joins the growing list of public Galaxy servers. ## New Papers

These papers may be of interest to the Galaxy community.

There are now over 880 papers in the Galaxy CiteULike Group.

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.


2013 Galaxy Community Conference (GCC2013)

Registration, Talk/Poster Submission Open

Early registration and paper and poster abstract submission are now open for the 2013 Galaxy Community Conference (GCC2013). GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo.

2013 Galaxy Community Conference (GCC2013) Training Day

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Day for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics.

|Register early and save up to 75% off regular registration costs. Early registration is very affordable, with combined registration (Training Day + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a session becomes full, it will be closed to new registrations. Early registration closes 24 May.

Abstract submission for both oral presentations and posters is also open. Abstract submission for oral presentations closes 12 April, and poster abstract submission closes 3 May. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.


Ion Torrent by Life Technologies
EMC Isilon

We are pleased to announce several new sponsorships for GCC2013:

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

March GalaxyAdmins Web Meetup

March Galaxy Admins Web Meetup

The next GalaxyAdmins Meetup will be held March 20, 2013 and feature Hailiang "Leon" Mei, and David van Enckevort speaking on NBIC Galaxy at SURFsara's HPC cloud.

NBIC Galaxy (Andromeda) was migrated to a HPC cloud hosted by Surfsara in September 2012. In this presentation, we will present the setup of this HPC cloud and the architecture of our NBIC Galaxy. We will also share our experience on the installation of the NBIC Galaxy using the Cloudman scripts. The presentation will finish with a list of issues and our possible future plans.

See the meetup page for details.

Galaxy at GMOD 2013 and Biocuration 2013

GMOD 2013 Biocuration 2013

Galaxy will have a presence at both the GMOD 2013 and Biocuration 2013. Both are being held in Cambridge, UK in early April. If you are interested in either community, then it would be great to see you there.

GMOD is also running a community-wide survey through March 1. The survey "aims to find out how you are using GMOD, what you find useful (or otherwise), what support you need, and some information on the GMOD components you use." The survey results will be published and past surveys have been extremely useful to the project. If that's not enough motivation, you can enter to win a free genome profile from 23andMe.

Other Upcoming Events and Deadlines

ABRF 2013 QFAB Workshops RNA Technologies and Analysis Workshop
See the Galaxy Events Google Calendar for details on these and other events. ### Events
Date Topic/Event Venue/Location Contact
March 2-5 Accessible, Transparent and Reproducible Analysis With Galaxy, part of Galaxy for Core Facilities, part of ABRF 2013
Palm Springs, California, United States
Dave Clements
March 8 RNA-Seq Analysis Using Galaxy QFAB, Brisbane, Australia Mark Crowe
March 20 NBIC Galaxy at SURFsara's HPC cloud GalaxyAdmins web meetup Hailiang "Leon" Mei,David van Enckevort
March 22 Introduction to Variant Detection Using Galaxy QFAB, Brisbane, Australia Mark Crowe
March 26-28 RNA Technologies and Analysis Workshop DOE JGI User Meeting Zhong Wang, Len Pennacchio
April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 Dave Clements
April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom Dave Clements, Suzanna Lewis
May 14-16 Tutorial: Exploring and Enabling Biomedical Data Analysis with Galaxy Great Lakes Bioinformatics Conference (GLBIO) 2013, Pittsburgh, Pennsylvania, United States Anton Nekrutenko
June 6-7 Informatics on High Throughput Sequencing Data Workshop Toronto, Ontario, Cananda Francis Ouellette
June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan
June 30 - July 2 2013 Galaxy Community Conference (GCC2013) University of Oslo, Oslo, Norway Organizers
## Galaxy Distributions February 8, 2013 Galaxy Distribution
Highlights: Improvements to our release process. Release tag must be used in the hg update command to upgrade. More at Tool Shed Complex repository dependencies are introduced, streamlining core dependency use across individual tools. Also updated in the Tool Shed: multiple repository installation, dependency installation (when defined - see graphic on right for an example), and many usability enhancements and fixes. New Bedgraph-to-bigwig tool plus Filter tool updated. Workflows now include option to export an image and the core Framework now allows more unified reference genome usage and access. Ten Community Pull-Requests incorporated, plus another contribution to the tool Shed, addressing general usability, API, tools, error handling, workflows, and more. Thanks!! Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. * new: $ hg clone galaxy-dist upgrade: $ hg pull $ hg update release_2013.02.08

Tool Shed Contributions

Galaxy Tool Shed
  • viralcloud: Viral Cloud Resource (VCR) includes viral assembly & VIGOR
  • cummeRbund: CuffDiff output analysis
  • fastq_sync: Check or repair synchronization of a pair of fastq datasets
  • velvet_optimiser: Updated version of velvet optimiser wrapper with all features
  • tophat_stats_pe: Calculate mapping statistics from Tophat BAM files
  • blastxml_to_top_descr: Make table of top BLAST match descriptions
  • qualimap_suite: detect biases in sequencing and/or mapping in SAM/BAM data
  • smalt: efficiently align DNA sequencing reads with a reference genome
  • rdiff: detection of differential RNA processing from RNA Sequncing data
  • pileup_to_vcf: convert a samtools mpileup pileup to vcf
  • predictnls : Python reimplementation of predictNLS for Galaxy

Other News