October 2012 Galaxy Update

Galaxy Updates

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:

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

Please Help!  Yes you!
The Galaxy is expanding! Please help it grow.

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

Swiss Galaxy Day Extending High-Performance Computing Beyond its Traditional User Communities Workshop  ASHG 2012


There are October application, poster, and paper deadlines for

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.


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


September 7, 2012


Other News