June 2012 Galaxy Update

Galaxy Updates

Welcome to the June 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 Public Server: GWIPS-Viz

GWIPS-Viz @ University College Cork

GWIPS-viz features tools for the analysis of protein synthesis. GWIPS-viz is part of the Genome Wide Information on Protein Synthesis using ribosome profiling project, and is in early development. At present it includes tools for motif searches and visualization:

  • MEME - Multiple Em for Motif Elicitation
  • FIMO - Find Individual Motif Occurrences
  • Sequence Logo generator for fasta (e.g. Clustal alignments)
  • CodonLogo generator for fasta (e.g. Clustal alignments)

Many thanks to the LAboratory of Post-Transcriptional control and bioInformatics (LAPTI) at University College Cork for making this Galaxy server publicly accessible.

GCC2012 is Next Month!

   Early registration ends June 11!   
2012 Galaxy Community Conference

New Papers

These papers may be of interest to the Galaxy community:

These papers were among 32 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 317 papers in the last ~15 months). The new papers were spread across 7 categories, including the new tools category.

Who's Hiring

Please Help!  Yes you!
The Galaxy is expanding! Please help it grow.

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.

Upcoming Events and Deadlines

Informatics on High Throughput Sequencing Data Workshop Galaxy: un environnement d'analyses bioinformatiques ISMB 2012   2012 Galaxy Community Conference


There are June application and early registration deadlines for GCC2012, ISMB 2012, SciPy, and the Winter School in Mathematical and Computational Biology, and an abstract deadline for ASHG 2012. It's also a big month for conferences and courses, including Arthropod Genomics, Bio-IT World Asia (James Taylor will be speaking), SocBIN, Next-gen sequencing in evolutionary biology Course at NESCent (Sergei Kosakovsky-Pond will cover Galaxy), Informatics on High Throughput Sequencing Data Workshop (Francis Ouellette will cover Galaxy), Copenhagenomics, SMBE 2012, and, ESHG 2012, to name just a few.

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


Date Topic/Event Venue/Location Contact
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
June 26 Galaxy: un environnement d'analyses bioinformatiques l'Institut de Biologie de Lille, France Sophie Gallina
July 11 Reproducible workflows for next generation sequencing analysis Nowgen, University of Manchester, United Kingdom Tom Hancocks
July 13-17 ISMB 2012 and BOSC 2012 Long Beach, California, United States Galaxy Outreach
July 25-27 2012 Galaxy Community Conference
Early registration ends June 11.
University of Illinois Chicago, United States Dave Clements

Tool Shed Contributions

These new repositories

  • deseq_hts - version 1.6.1 of the DESeq
  • fastqdump - convert SRA to FASTQ
  • iassembler - assemble Sanger and/or Roche-454 EST data into contigs

were created, and the mira_asssembler, seq_select_by_id, and java_genomics_toolkit repositories were updated in the Galaxy Tool Shed in May.

New Distribution

A new Galaxy distribution was released on May 11, 2012.

Some Highlights:

* **Emboss** tools and datatypes __have now moved from the ***Galaxy distribution** to the **[Galaxy Main Tool Shed](http://toolshed.g2.bx.psu.edu/)__**. * [Tool Integration Tests](/testing-installed-tools/), [Custom Tool Panel Configuration](/galaxy-tool-panel/#managing-the-layout-of-your-galaxy-tool-panel), and [Configurable Tool Output Locations](/admin/tools/multiple-output-files/). * Improved [Multiprocess Job Handling](/admin/config/performance/scaling/) and [Enhanced OpenID Support](http://openid.net/). * **[GATK](http://www.broadinstitute.org/gsa/wiki) version 1.4**, **[FreeBayes](http://github.com/ekg/freebayes)**, Updated **Megablast** using **[NCBI BLAST+](http://blast.ncbi.nlm.nih.gov/Blast.cgi)**, **[Trinity](http://trinityrnaseq.sourceforge.net)**, **[WormBase 2](http://www.wormbase.org)**, and **[IGB](http://bioviz.org/igb/index.html)** external display. * **[Trackster](/learn/visualization/)** upgrades include strand coloring, interval datatype support, and tabix indexing (fast!!). * Updated **User Interface**, **Workflow-API** upgrades, and Custom **UCSC Display**.

Other News

  • GalaxyCzars a discussion group for Galaxy community members who are responsible for large Galaxy installations has been started. Their first conference call will be this month.

  • Galaxy Main was down for a little over a day. Watch the Galaxy News for an explanation.