September 2012 Galaxy Update

Welcome to the September 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:

• "Next-generation sequencing data interpretation: enhancing reproducibility and accessibility", by Nekrutenko & Taylor, Nature Reviews Genetics, 13, 667-672 (September 2012)
• "IBDsite: a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis", by Merelli, Viti, Milanesi, BMC Bioinformatics, Vol. 13, No. Suppl 14. (2011), S5
• "Data Mining as a Discovery Tool for Imprinted Genes Genomic Imprinting", by Chelsea Brideau, Paul Soloway, Methods in Molecular Biology, Vol. 925 (2012)

These papers were among 46 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 421 papers in the last ~19 months). The new papers are spread across 7 categories.

New Public Servers

Three new publicly accessible Galaxy servers were added to the Public Galaxy Servers page in August:

Server	Purpose / Community	Other Comments	Restrictions	Sponsor
IBDsite	a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis			CNR-ITB
NCBO and OPPL Galaxy	The NCBO-Galaxy tools provide Galaxy users with the functionality of the NCBO BioPortal services. OPPL-Galaxy is a set of functions that can be executed over OWL ontologies with the aim of facilitating the use of semantic activities within Galaxy Bioinformatics workflows.	See "NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform," by Giménez, et al., presented at ICBO2012; and "OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL" by Aranguren, et al.		Universidad de Murcia
PopGenIE	The Populus Genome Integrative Explorer Galaxy instance.		Storage quotas	Plant Physiology, University of Umeå

Who's Hiring

The Galaxy is expanding! Please help it grow.

• The Galaxy Project is hiring post-docs @ Penn State and Emory
• Bioinformatics & Integrative Genomics Specialist - Manager Bioinformatics Consulting Core @ Leuven, Belgium
• 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 September application, poster, and paper deadlines for

• Personal Genomes and Medical Genomics, CSHL (deadline August 31)
• ISCB-Asia/SCCG 2012 posters

September events include Galaxy workshops and talks in South Africa, 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
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
	Assembling a cassava transcriptome using Galaxy on a high performance computing cluster		Aobakwe Matshidiso
September 11-13	Facilitating Research on Heart Disease through SaaS	Bio-IT World Cloud Summit, San Francisco, California, United States	Raimond Winslow
September 11-14	Automated and reproducible analysis of NGS data (ARANGS12)	Instituto Gulbenkian de Ciência, Oeiras, Portugal	Rutger Vos, Darin London
September 27-29	Informatics Workshop	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
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 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

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.

New Galaxy-France Mailing List

A new mailing list has been launched, specifically for the French Galaxy Community:

• Liste de diffusion Galaxy France

This list is intended to communicate and share our experiences with Galaxy in France. The official language of this list is French. See the list announcement, list archive and list subscription page for more. Postings to the list will be integrated into Galaxy search.

Tool Shed Contributions

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

• sambamba_filter Flexible filtering of BAM/SAM
• ncbi_blast_plus tblastx, blastn, blastp, blastx, BLAST XML → tabular, and tblastn
• kmersvm use a Support Vector Machine (SVM) with k-mer sequence features (kmer-SVM) to identify predictive combinations of short TF binding sites which determine the tissue specificity of these genomic assays.

New Distributions

The most recent Galaxy distribution was released on July 20, 2012.

Other News

• blend4j - a Java library for interacting with the API.

• Two new tutorials from Paul-Michael Agapow:

  • Upgrading Galaxy
  • Setting up a Galaxy toolshed
• Ntino Krampis BioTechniques interview on doing bioinformatics on the cloud, including CloudMan.
• Jeremy Goecks updated his RNA-seq Analysis Exercise Galaxy Page to cover quality control through CuffDiff: paired-end data, iGenomes gtf, answer key, and bonus resources
• Slides and videos for the Iowa Initiative in Human Genetics Bioinformatics Course

• A few summaries of the recent 2012 Galaxy Community Conference (GCC2012) have been posted online:

  • Peter Li's GigaBlog post
  • Brad Chapman's day 1 and day 2 summaries.
  • Slides for all workshops and talks are now available.