August 2012 Galaxy Update

Welcome to the August 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:

• "Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change", by Miller, et al., Proceedings of the National Academy of Sciences (23 July 2012)
• "Nebula - a web-server for advanced ChIP-seq data analysis", by Boeva, et al., Bioinformatics

These papers were among 29 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 375 papers in the last ~18 months). The new papers are spread across 6 categories.

The [2012 Galaxy Community Conference (GCC2012)](/src/events/gcc2012/index.md) was held July 25-27, in Chicago. Highlights included:

• the inaugural and very well attended GCC Training Day (featuring 12 hands-on sessions on 10 different topics)
• a main program with 8 sessions, 27 talks,
• 10 lightning talks (and many more proposals)
• 6 breakout sessions,
• Ion Torrent as the Platinum Sponsor, EMC Isilon as the Gold Sponsor, and an amazing eight Host and Silver Sponsors.
• The conference dinner and reception, sponsored by Ion Torrent, from which many of us departed hoarse and/or hard of hearing.

Slides for most talks are already on the wiki, and the rest will trickle in over the next week. Videos of talks and workshops will be posted in about two weeks. Finally, with over 200 registrations, this was for the third year running, the largest Galaxy conference yet.

GCC2013 was also announced at the meeting. It will be held 30 June through 2 July in Oslo, Norway. Watch the GCC2013 page for information as it become available.

Who's Hiring

The Galaxy is expanding! Please help it grow.

• The Galaxy Project is hiring post-docs @ Emory and Penn State.
• Bioinformatics & Integrative Genomics Specialist - Manager Bioinformatics Consulting Core @ Leuven, Belgium
• Bioinformatics Analyst @ U Virginia
• [Bioinformaticians @ FDA](http://gmod.org/wiki/News/Bioinformaticians @ FDA)
• Internship @ EMBL Heidelberg building an emBASE-Galaxy Bridge

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 August application, poster, and paper deadlines for

• Extending High-Performance Computing Beyond its Traditional User Communities (deadline August 6)
• International Digital Curation Conference (deadline August 20)
• Analysis of High-Throughput Sequencing Data, EMBO Practical Course (deadline August 24)
• eScience 2012 (deadline August 24)
• Personal and Medical Genomics (deadline August 31)

August events including a Bioinformatics Short Course on Mutation Detection at the University of Iowa, and the [2012 GMOD Summer School](http://gmod.org/wiki/2012 GMOD Summer School).

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

Events

Date	Topic/Event	Venue/Location	Contact
August 1-3	Bioinformatics Short Course: Mutation Detection Using Massively Parallel Sequencing: From Data Generation to Variant Annotation	University of Iowa, Iowa City, United States	Iowa Initiative in Human Genetics
August 25-29	http://gmod.org/wiki/2012 GMOD Summer School	US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States	Dave Clements
September 3-4	Galaxy Workshop	University of Pretoria, Pretoria, South Africa	Dave Clements
September 6-7		Stellenbosch University, Stellenbosch, South Africa
September 10-11	Systems Bioinformatics Workshop	Institute for Systems Biology Seattle, Washington, United States	James Taylor
September 10-12	Transparent, accessible, reproducible analysis with Galaxy	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
October 3	(first Swiss) Galaxy Workshop	SyBIT Tech Day, Bern, Switzerland	Hans-Rudolf Hotz
October 8-12	Extending High-Performance Computing Beyond its Traditional User Communities Workshop	8th IEEE International Conference on eScience (eScience 2012), Chicago Illinois, United States	James Taylor

Swiss Galaxy Day

The 1^st Swiss Galaxy Workshop will be held October 3-4 in Bern, and is aimed at Galaxy administrators and users alike. We also welcome participants who are using other workflow management systems, and tool developers who are looking for such systems to offer their tools to a wider audience.

We would like to discuss the status of the Galaxy project, new developments, interface to other systems, extensions and best practice in reproducible research.

The workshop is part of the SyBIT Tech Day series.

Tool Shed Contributions

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

• nosql_interface query and download data from MongoDB and CouchDB NoSQL databases
• synapse_interface interface with Sage Bionetworks Synapse platform
• mtls_analysis: Analyze and compare multiple ChIP-seq experiments
• trinityrnaseq: De novo assembly of rna-seq data coupled with downstream analyses
• Toolfactory: Turn scripts into Galaxy Tools; presented at GCC2012
• protk: Identify Peptides and Proteins from tandem Mass Spec data; also presented at GCC2012
• deseq_and_sam2counts: RNA-Seq differential expression analysis on aligned reads to a transcriptome using sam2counts and DESeq; also presented at GCC2012
• freebayes: Bayesian genetic variant detection tool
• GFAP: annotate & prioritize human genetic variants identified by NGS

New Distributions

A new Galaxy distribution was released on July 20, 2012. Highlights include:

• Freebayes has moved from the Galaxy distribution to the Galaxy's Main Tool Shed
• EMBOSS version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing.
• Tool Shed now also supports specifying the third party tool dependencies to be automatically installed in new repositories
• Admin Genome Indexing is now in BETA. Download, index, and track progress right from the admin UI! That's a screen shot on the right ->
• Improved Error Handling that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details.
• TopHat2/Bowtie2 latest support includes option to 'report discordant pairs', updated tests, and more preset options.
• Trackster new parameter space visualization. BRAND NEW!! More details coming soon, but give a test drive now.

Other News

• The first GalaxyCzars conference call was held in July, and slides and video are now available online.