March 2013 Galaxy Update
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
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.
- "RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next generation sequence reads," by Petr Novák, Pavel Neumann, Jiří Pech, Jaroslav Steinhaisl, Jiří Macas, Bioinformatics (1 February 2013)
- "A unified framework for the deployment, exposure and access of HPC applications as services in clouds," by Adam K. L. Wonga, Andrzej M. Goscinskia, Future Generation Computer Systems (February 2013)
There are now over 880 papers in the Galaxy CiteULike Group.
Who's Hiring
The Galaxy is expanding! Please help it grow.
- The Galaxy Project is hiring software engineers and post-docs! at both Emory and Penn State.
- Bioinformatics Trainter/Analyst, Morgridge Institute for Research, Madison, Wisconsin, United States
- Poste d’ingénieur bio-informaticien en métagénomique au Laboratoire d’Analyses Bioinformatiques en Génomique et Métabolisme (LABGeM)
Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.
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.
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.
Sponsorships
We are pleased to announce several new sponsorships for GCC2013:
- Ion Torrent will be the exclusive Platinum Sponsor for the event.
- EMC Isilon will be a Gold Sponsor for GCC2013.
- Illumina will be a Bronze Sponsor 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
The next GalaxyAdmins Meetup will be held March 20, 2013 and feature [Hailiang "Leon" Mei](mailto:hailiang DOT mei AT nbic DOT nl), 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
Galaxy will have a presence at both the [GMOD 2013](http://gmod.org/wiki/April 2013 GMOD Meeting) 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
Events
Galaxy Distributions
February 8, 2013 Galaxy Distribution
http://bitbucket.org/galaxy/galaxy-dist
http://galaxy-dist.readthedocs.org
new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable galaxy-dist
upgrade: $ hg pull
$ hg update release_2013.02.08
Tool Shed Contributions
- 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
- A Software Carpentry bootcamp has been scheduled in Oslo immediately after GCC2013.
- An improved Galaxy Project issues board is out
- Going to GCC2013? SocBiN / PTBI is right before; Paper and early registration deadline is 15 March
- Introduction to Galaxy 2013 Bootcamp by Nikhil Joshi, Bioinformatics Core, UC Davis Genome Center
- Galaxy Tutorials Including RNA-Seq, Variant Detection, and Genome Assembly from The Genomics Virtual Lab
- CloudBioLinux can now install genome indices from the Galaxy rsync server.
- Uploading NGS data to Amazon S3 for use in Galaxy