March 2012 Galaxy Update

Galaxy Updates

Welcome to the March 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.

New Papers

There were 28 papers added to the Galaxy CiteULike group since the last Galaxy Update. The new papers were spread across 5 categories.

# Tag     # Tag
15 methods 2 howto
7 other 2 workflow
3 isgalaxy

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

April 2012 GMOD Meeting   Informatics on High Throughput Sequencing Data Workshop Next-gen Sequencing in Evolutionary Biology Course ISMB 2012


There are March application deadlines for a Next-gen Sequencing in Evolutionary Biology course at NESCent; Bio-Linux, and Advanced RNA-Seq and ChIP-Seq Data Analysis courses at Hinxton; Next Generation Sequencing Data Analysis at EMBL Heidelberg; Bioinformatics and Comparative Genome Analyses in Naples; Statistical Analysis of Genomic Data at CSHL; abstract deadlines for BITS 2012 and Information Visualization in BioMedical Informatics (IVBI 2012); and early registration deadlines for the April GMOD Meeting and Copenhagenomics.

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


Date Topic/Event Venue/Location Contact
April 5-6 April 2012 GMOD Meeting
Including a Galaxy Workshop on evening of April 5. Early registration ends March 7.
Washington DC, immediately following Biocuration 2012 Dave Clements
April 24-26 Leveraging SaaS for Next-Gen Sequencing: Case Study with the Galaxy Community
Pre-Conference Workshop
Bio-IT World, Boston, Massachusetts, United States Ravi Madduri, Elizabeth Bartom
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
Application deadline is March 9
US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States Sergei Kosakovsky Pond
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
Abstract submission is now open, and Training Day topics are set.
Chicago, Illinois, United States Dave Clements

GCC2012 Update

2012 Galaxy Community Conference

Training Day

Tool Shed Contributions

At least 8 new repositories were added to the Galaxy Tool Shed in February, including

  • CREST (Clipping REveals STructure): maps somatic structural variation in cancer genomes
  • MACS 1.4 ChIP-Seq peak calling (Main has 1.3)
  • java_genomics_toolkit: NGS, especially WIG transformations (add/log/Z-score/etc) and visualization (KMeans/heatmaps)
  • mrFAST and mrsFAST: map Illumina short reads to reference assemblies; fast and memory-efficient
  • mrCaNaVaR: Read depth analysis method to characterize segmental duplications & predict absolute copy numbers
  • SCALCE: Compression of FASTQ files

Other News

New non-wiki documentation

Galaxy-Announce now the default for new users on Main

Newly registered users on Main, the Galaxy project's public server, who check "Subscribe to a mailing list" at registration time, are now subscribed to the moderated and low-volume Galaxy-Announce mailing list, instead of the high-volume, and sometimes overwhelming Galaxy-User list. This change was also made in the Galaxy source.