July 2012 Galaxy Update

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.

The [2012 Galaxy Community Conference (GCC2012)](/src/events/gcc2012/index.md) will be held July 25-27, in Chicago. [Register by July 18](/src/events/gcc2012/register/index.md) to avoid paying late registration rates. [Register well before July 18](/src/events/gcc2012/register/index.md), if you are planning on attending the [GCC2012 Training Day](/src/events/gcc2012/training-day/index.md). 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

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](http://gmod.org/wiki/News/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

Deadlines

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

• the Galaxy Workshops in South Africa (deadline: June 30) and the South African Genetics & Bioinformatics Society Conference (deadline July 1)
• Systems Bioinformatics Workshop (deadline: June 30)
• [GMOD Summer School](http://gmod.org/wiki/2012 GMOD Summer School) (deadline: July 9)
• GCC2012 (deadline: July 18)
• and eScience 2012, Beyond the Genome, BioVis, ISCB-Asia, and the CSHL Advanced Sequencing Technologies and Applications, and Computational and Comparative Genomics courses.

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 Eight presentations, one Codefest, seven posters, and counting	Long Beach, California, United States	Galaxy Outreach
July 25-27	2012 Galaxy Community Conference Registration deadline is July 18	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

1. [RGalaxy](/src/news/r-galaxy-wrap-r-functions-as-tools/index.md), a new [Bioconductor](http://bioconductor.org/) package, automatically generates XML definitions needed to wrap *any* R function as a Galaxy tool.

1. The first GalaxyCzars conference call will happen July 9 or 10. If you are interested, please help pick a time for the call.
2. Several new videos, screencasts, and tutorials were posted:

• OpenHelix Video Tip of the Week: Visualizing the Galaxy
• Using PhyloTastic Tools inside Galaxy, by Rutger Vos
• Getting Started with the CloudMan Platform Using BioCloudCentral, by Enis Afgan
• Using Galaxy for NGS Analysis, by [Luce Skrabanek](mailto:las2017 AT med DOT cornell DOT edu)
• RNA-Seq Course v1.0 documentation, by UC Davis Bioinformatics Professional Training Program
• Cloud Computing for Bioinformatics (using AWS and Galaxy, but not using CloudMan), by UC Davis Bioinformatics Professional Training Program
• Genomic Resequencing Variant Detection and Interpretation in a Diagnostic Context Hands on workshop: Next generation sequence data analysis, by Hailiang (Leon) Mei, Jeroen Laros

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

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