October 2012 Galaxy Update

Welcome to the October 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:

• Turning pipe dreams into reality by Peter Li, Jeremy Goecks, Tin L. Lee, Genome Biology, Vol. 13, No. 8. (2012), 318.
• Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome, by Belinda M. Giardine, Cathy Riemer, Richard Burhans, Aakrosh Ratan, Webb Miller; in Current Protocols in Bioinformatics 39:15.2.1-15.2.27
• Galaxy Workflow Integration on Garuda Grid, by K. Karuna, N. Mangala, C. Janaki, S. Shashi, and C. Subrata; in Enabling Technologies: Infrastructure for Collaborative Enterprises (WETICE), 2012 IEEE 21st International Workshop on (June 2012), pp. 194-196

These papers were among 35 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 456 papers in the last ~20 months). The new papers are spread across 8 categories.

New Public Server: CBIIT

The CUHK-BGI Innovation Institution of Trans-Omics (CBIIT) has now made its Galaxy server publicly available. The CBIIT Galaxy Server has the standard Galaxy tool set plus SOAPdenovo and SOAPsnp for de novo assembly and SNP calling.

The CBIIT Galaxy Server joins the 20+ other publicly accessible servers on Public Galaxy Servers list.

Who's Hiring

The Galaxy is expanding! Please help it grow.

• The Galaxy Project is hiring post-docs @ Penn State and Emory
• offre CDD INRA Versailles - developpement chaine de traitements RnaSeq sous Galaxy - France Genomique

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 October application, poster, and paper deadlines for

• Rocky 2012 (deadline October 4)
• BeNeLux Bioinformatics Conference 2012 (deadline October 22)

October events include the (first Swiss) Galaxy Workshop; InCoB 2012; IEEE Conference on eScience (eScience 2012, which includes the Extending High-Performance Computing Beyond its Traditional User Communities workshop); Bio-IT World Europe; BioVis: IEEE Symposium on Biological Data Visualization; Advanced NGS Course: RNA-seq data analysis (NBIC); Advanced Sequencing Technologies & Applications Course (CSHL); the Northeast and Midwest Core directors meetings; and eResearch Australasia 2012, the Automated and reproducible analysis of NGS data (ARANGS12), Beyond the Genome 2012, and ICG Americas 2012.

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

Events

Date	Topic/Event	Venue/Location	Contact
October 3	(first Swiss) Galaxy Workshop	SyBIT Tech Day, Bern, Switzerland	Hans-Rudolf Hotz
October 8-12	Lessons from Galaxy, a Web-based Platform for High-throughput Genomic Analyses	Extending High-Performance Computing Beyond its Traditional User Communities Workshop, part of 8th IEEE International Conference on eScience (eScience 2012), Chicago Illinois, United States	Jeremy Goecks
October 9-11	Tavaxy: A Workflow System with Taverna and Galaxy Capabilities and Cloud Computing Support	Bio-IT World Europe, Vienna, Austria	Mohamed Abouelhoda
October 15-17	Advanced NGS Course: RNA-seq data analysis	Amsterdam Medical Centre (AMC), The Netherlands	Patrick Koks
October 18-30	Advanced Sequencing Technologies and Applications Course	Cold Spring Harbor Laboratory, New York, United States	Anton Nekrutenko
October 31 - November 6	Computaional & Comparative Genomics Course	Cold Spring Harbor Laboratory, New York, United States	William Pearson, James Taylor
October 28 - November 2	Genomic Virtual Laboratory Workshop	eResearch Australasia, Sydney, Australia	Enis Afgan
November 6-10	Galaxy 101: Data Integration, Analysis and Sharing	American Society of Human Genetics (ASHG), San Francisco, California, United States	Jennifer Jackson, Jeremy Goecks
	Working with High-Throughput Data and Data Visualization
November 12-14	The Genome Access Course	Cold Spring Harbor Laboratory, New York, United States	Assaf Gordon
November 13-15	Analyse des données RNA-seq et ChIP-seq (séquençage haut-débit), à l'aide d'outils orientés vers un public de biologistes	PRABI (Pôle Rhône-Alpes de Bioinformatique), Doua de l'Université Claude Bernard - Lyon, Lyon, France	Guy Perrière
June 30 - July 2	2013 Galaxy Community Conference (GCC2013)	University of Oslo, Oslo, Norway	Galaxy Outreach

Tool Shed Contributions

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

• htseq_count: Count aligned reads (SAM/BAM) that overlap genomic features (GFF)
• DNAClust: tools for Phylogenetic clustering
• fastq_groomer_parallel: a multithreaded implementation of FASTQ Groomer

New Distributions

There were two new Galaxy distributions in September:

September 20, 2012

Highlights

• A new Galaxy tool that writes other new Galaxy tools? The Tool Factory is in the Galaxy's Main Tool Shed (toolfactory). Try it now
• Learn how to display multiple versions of a tool in the Galaxy tool panel.
• CloudLaunch Overhaul includes Boto 2.5.2 and simplified instance selection and key generation.
• Release also includes more Tool Shed updates, Framework and API updates, plus Security and Bug fixes.

September 7, 2012

Highlights:

• NCBI BLAST+ has moved from the Galaxy distribution to the Galaxy's Main Tool Shed.
• Tool Shed is now running Mercurial version 2.2.3. Many updates and refinements including UI/metadata changes - read the full report!
• Streamline local setup with the Reference Genome rsync Server: same builds and indexes as on the public Galaxy Main instance.
• More updates to Output and Error Handling including updated documentation and enhancements to exit code checks.
• TopHat2 / Bowtie2 latest support includes Tophat2 fusions output, Bowtie2 sorted BAMs, and a new RNA-seq Tutorial.
• Trackster updates include improved support for bigWig / bigBed, new support for bedGraph, and a new search feature for GFF / GTF / BED datasets.
• Plus many other Workflow, API, Source, UI features and a summary of recent Galaxy Update highlights.

Other News

• Rutger Vos shows how to add a phylotastic service to Galaxy and use phylotastic tools inside Galaxy
• ENCODE Virtual Machine and Cloud Resource is now available.
• Galaxy tutorial from [2012 GMOD Summer School](http://gmod.org/wiki/2012 GMOD Summer School) is now available on the [http://gmod.org/wiki/|GMOD wiki](http://gmod.org/wiki/|GMOD wiki).
• ISCB Wikipedia Competition launched and the Galaxy Wikipedia page is eligible.