July 2012 Galaxy Update

Galaxy Updates

Welcome to the July 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 These papers may be of interest to the Galaxy community: "Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy", by Enis Afgan, Brad Chapman, Margita Jadan, Vedran Franke, James Taylor, Current Protocols in Bioinformatics. 2012 June: Unit 11.9. "Using Galaxy to Perform Large-Scale Interactive Data Analyses", by Jennifer Hillman-Jackson, Dave Clements, Daniel Blankenberg, James Taylor, Anton Nekrutenko, Galaxy Team, Current Protocols in Bioinformatics. 2012 June: Unit 10.5. These papers were among 31 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 348 papers in the last ~16 months). The new papers are spread across 8 categories.


## GCC2012 is July 25-27! 2012 Galaxy Community Conference


The 2012 Galaxy Community Conference (GCC2012) will be held July 25-27, in Chicago. Register by July 18 to avoid paying late registration rates. Register well before July 18, if you are planning on attending the GCC2012 Training Day. Training Day has limited space and will likely sell out before the entire conference does.

The program for all 3 days is now available. This includes 12 Training Day sessions on 10 different topics, and over 25 presentations by Galaxy Community and Galaxy Team members.

Who's Hiring

Please Help!  Yes you!
The Galaxy is expanding! Please help it grow. The Galaxy Project is hiring post-docs and software engineers @ Emory and Penn State. Bioinformatics Specialist opening in St. Paul, Minnesota; Galaxy experience required. Internship @ EMBL Heidelberg building an emBASE-Galaxy Bridge Bioinformatics Analyst @ U Virginia * Bioinformaticians @ FDA 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
Atelier Galaxy   ISMB 2012   2012 Galaxy Community Conference   2012 GMOD Summer School   South African Genetics and Bioinformatics Society Conference

Deadlines

There are July (and June 30!) application and registration deadlines for

It's also a big month for conferences including Evolution, ISMB and BOSC 2012, and of course GCC2012.

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

Events

Date Topic/Event Venue/Location Contact
July 5-6 Atelier Galaxy Le Centre de Génomique Fonctionnelle Bordeaux Anton Nekrutenko
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 University of Illinois Chicago, United States Dave Clements
August 25-29 2012 GMOD Summer School
Application deadline is July 9
US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States Dave Clements
September 3-4 Galaxy Workshop
Application deadline is June 30
University of Pretoria, Pretoria, South Africa Dave Clements
September 6-7 Stellenbosch University, Stellenbosch, South Africa
September 10-11 Systems Bioinformatics Workshop
Early registration deadline is June 30
Institute for Systems Biology
Seattle, Washington, United States
James Taylor
September 10-12 Transparent, accessible, reproducible analysis with Galaxy
Early registration deadline is July 1
South African Genetics & Bioinformatics Society Conference
University of Stellenbosch, Stellenbosch, South Africa
Dave Clements
September 27-29 Beyond the Genome 2012 Harvard Medical School, Boston, Massachusetts James Taylor

Tool Shed Contributions

Several new repositories were added to the Galaxy Tool Shed in June.

  • CGA Tools - Complete Genomics' CGA Tools is now available.
  • qiime1_3_0 - Extension of jjohnson's qiime repository, intended as an extension of that work. Only tools verified working in Galaxy with Qiime 1.3.0 documentation included.
  • upload_local_file - Add data to histories without having to upload them through the network.
  • svdetect - Detect genomic structural variations from paired-end and mate-pair sequencing data
  • pcr_markers - Tools for design of PCR-based Markers from Variant Data
  • sickle - A windowed adaptive trimming tool for FASTQ files using quality
  • scythe - A very simple adapter trimmer
  • protk - Identify Peptides and Proteins from tandem Mass Spec data

New Distributions

The most recent Galaxy distribution was released on May 11, 2012.

A new version of CloudMan was Released in June.

Other News

RGalaxy: Wrap R functions as Galaxy Tools

  1. RGalaxy, a new Bioconductor package, automatically generates XML definitions needed to wrap any R function as a Galaxy tool.

  2. The first GalaxyCzars conference call will happen July 9 or 10. If you are interested, please help pick a time for the call.

  3. Several new videos, screencasts, and tutorials were posted:

  4. Several new and updated genomes were added to Galaxy Main in June:

    • bosTau4, bosTau6, bosTauMd3, canFam2, ce10, gorGor3, mm9, mm10, panTro3, rn4,