February 2012 Galaxy Update

Welcome to the inaugural edition of Galaxy Update, a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates will complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

New Papers

New papers of note for the Galaxy community:

• Daniel MacLean & Sophien Kamoun, "Big data in small places." Nature Biotechnology
• Thomas Hentrich, Julia M. Schulze, Eldon Emberly, and Michael S. Kobor, "CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures." Bioinformatics
• Jeremy Goecks, Kanwei Li, Dave Clements, The Galaxy Team, James Taylor, "The Galaxy Track Browser: Transforming the genome browser from visualization tool to analysis tool." Biological Data Visualization (BioVis), 2011 IEEE Symposium on

Plus 27 other papers that use, reference, or are about Galaxy.

New Public Server: MGTAXA

MGTAXA, a free Galaxy server at JCVI for metagenomic taxonomy prediction was added to the list of Public Galaxy Servers in January. Many thanks to JCVI and the MGTAXA team for making this publicly available.

Who's Hiring

• [Galaxy is Hiring](/src/news/Galaxy is Hiring/index.md)

  • system administrators at Penn State
  • software engineers and post-docs at Emory
• Bioinformatics Support Provider with Galaxy experience @ Wellcome Trust Centre for Cell Biology, University of Edinburgh

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll include it in next month's update.

     

Upcoming Events and Deadlines

Deadlines

There are upcoming deadlines for ISMB 2012 (workshops), DILS (abstracts), PSB (sessions), VizBI (posters), and a Bio-Linux Course (application). See the Galaxy Events Google Calendar for details on these and other events.

Abstract submission for the 2012 Galaxy Community Conference (GCC2012) will open February 13.

Events

GCC2012 Sponsors

Plans for the 2012 Galaxy Community Conference (GCC2012) are coming along nicely. It will be held July 25-27, in Chicago. As in the past, the conference will feature two full days of presentations and discussions. A whole day of training sessions has also been added this year.

Also new in 2012 are conference sponsors. We are very pleased to have welcomed these GCC2012 sponsors in the past month:

Platinum: Ion Torrent

Gold: EMC Isilon

Silver: Roy J. Carver Biotechnology Center at University of Illinois Urbana-Champaign
The Institute for Genomic Biology at University of Illinois Urbana-Champaign
National Center for Supercomputing Applications (NCSA)

There are still Gold, Silver and Bronze level sponsorships available. Look for more announcements in the coming months.

New Distributions

There were two Galaxy distributions in January, The latest on [January 27](/src/news/Jan272012 Distribution News Brief/index.md). Some highlights from the releases:

• Important metadata and Python 2.5 support corrections
• SAMtools upgraded for version 0.1.18. Mpileup added.
• Dynamic filtering, easy color options, and quicker indexing enhance Trackster
• Set up your Galaxy instance to run cluster jobs as the real user, not the Galaxy owner
• Improvements to metadata handling and searching in the Tool Shed
• Improved solutions for schema access, jobs management, & workflow imports and inputs.
• New datatypes (Eland, XML), multiple tool enhancements, and bug fixes.
• New Object Store data integration layer introduced
• RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, & CuffCompare to 1.3.0.
• Tool Shed installation features and many new community tool additions
• Trackster performance upgrades and new drag & drop composite track creation

See the [January 27, 2012 release](/src/news/Jan272012 Distribution News Brief/index.md) for details on how to get the latest version of Galaxy.