February 2014 Galaxy Update

Galaxy Updates

Welcome to the February 2014 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

42 papers were added to the Galaxy CiteULike Group in January. Some papers that may be particularly interesting to the Galaxy community:

How those papers were tagged:

# Tag    # Tag    # Tag    # Tag
8 Cloud - Project 6 Tools - UsePublic
- HowTo 1 RefPublic - UseCloud - Visualization
5 IsGalaxy 1 Reproducibility 4 UseLocal 18 Workbench
15 Methods 3 Shared 4 UseMain

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.


GCC2014: June 30 - July 2, Baltimore

GCC2014: June 30 - July 2

The 2014 Galaxy Community Conference (GCC2014) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States.

Registration opens February 10

Early registration will open February 10. The Training Day schedule will also be posted at that time. The organizers are currently contacting potential instructors and building the schedule. Thanks to everyone who took the time to nominate and vote on Training Day topics.

Training Day is an opportunity to learn about all things Galaxy including using Galaxy, deploying and managing Galaxy, extending Galaxy, and Galaxy internals. There will be 4 parallel tracks, each with 3 sessions, with each of those sessions two and half hours long. That's 12 sessions and 30 hours of workshop material.



We are pleased to have GenomeWeb as a Silver Sponsor for GCC2014. This is the first GCC that GenomeWeb has sponsored. Please welcome them.

There are still Silver and Bronze sponsorships available. Please contact the Organizers if your organization would like to help sponsor this event.


In 2014 we are also adding non-sponsor exhibit spaces in addition to the sponsor exhibits. This will significantly increase the size of the exhibit floor. Please contact the Organizers if your organization would like to have an exhibit space at GCC2014.

Galaxy Australasia Workshop 2014 (GAW 2014)

The 1st Galaxy Australasia Workshop 2014 (GAW 2014) will be held in Melbourne, Australia on 24 and 25th March 2014.

Galaxy Australasia Workshop 2014 (GAW2014)

The Galaxy Australasia Workshop is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch in Melbourne. GAW 2014 will also include poster session, keynote speakers.

Melbourne Convention Centre

Registration is open. Registration is also free, but space is limited.

Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit an abstract and brief one-paragraph bio by February 15th, 2014. Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance.

GAW 2014 will be held in Melbourne, Australia on 24 and 25th March 2014. The first day (Monday) will be in Clayton, next to the Australian Synchrotron. For the 2nd day (Tuesday) we will move downtown the Melbourne Convention Centre, the venue for the Computational and Simulation Sciences and eResearch.

GMOD Malaysia 2014

GMOD Malaysia 2014

February 26-28, 2014, Kuala Lumpur, Malaysia.

GMOD Malaysia 2014 offers an introduction to, and training in, the bioinformatics software offered by the Generic Model Organism Database project (http://gmod.org). Over three days, participants will learn about GMOD's free, open-source tools for visualising, storing, and disseminating genetic and genomic data. These include: '''Galaxy''', the GBrowse and JBrowse genome browsers, InterMine data warehouse (a frequent Galaxy data source), MAKER and MAKER-P genome annotation pipelines, Tripal website generator and database interface and the Chado database schema

Instruction is by experienced instructors and developers with deep knowledge of the tools and their applications. By the end of the course, participants will have hands-on experience of setting up and using core components needed for a modern genomics project.

GMOD Malaysia is being held after the Plant Genomics Congress, and will have a plant-specific emphasis.More information and application form on the Workshop home page.

Application deadline: 12 February 2014

GMOD Malaysia 2014

GMOD Malaysia 2014 is made possible by the generous support of the National Evolutionary Synthesis Center (NESCent) and the NESCent Ambassador program. NESCent promotes the synthesis of information, concepts and knowledge to address significant, emerging, or novel questions in evolutionary science and its applications. NESCent supports research and education across disciplinary, institutional, geographic, and demographic boundaries. The NESCent Ambassador Program is NESCent’s primary international outreach program, and is supported by a three-year grant from the NSF.

Other Events

There are several other [events of interest](/events/) in the next few months. Also see the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on other events of interest to the community.
Analyse Bioinformatique de séquences pour l'amélioration des plantes RNA-Seq & ChIP-Seq analysis course using Galaxy GMOD Malaysia 2014  Introduction to NGS Bioinformatics
Date Topic/Event Venue/Location Contact
February 5-6 Mosquito Informatics EBI, Hinxton, United Kingdom Dan Lawson
February 10-14 Analyse Bioinformatique de séquences pour l'amélioration des plantes Campus la Gaillarde, Montpellier, France Yolande OLIVIER
February 11-13 RNA-Seq & ChIP-Seq analysis course using Galaxy PRABI, Lyon, France Navratil V., Oger C., Veber P., Deschamps C., Perriere G.
February 12-15 Advances in Genome Biology and Technology (AGBT) Marco Island, Florida, United States Anton Nekrutenko
February 26-28 GMOD Malaysia 2014 Kuala Lumpur, Malaysia Amelia Ireland, Dave Clements
February 27 Introduction to NGS Bioinformatics Nowgen Centre, Manchester, United Kingdom Jan Taylor
March 24-25 Galaxy Australasia Workshop 2014 (GAW2014) Melbourne, Australia Organisers
March 26-30 Galaxy toolset for Drosophila genomics
and one-on-one help in the Flybase Demonstrations Room
Drosophila Research Conference, San Diego, California, United States Anton Nekrutenko, Jen Jackson
May 27 Enabling Data Analysis with Galaxy CloudMan workshop MIPRO 2014, Opatija, Croatia Enis Afgan
June 9-10 Informatics on High Throughput Sequencing Data Workshop Toronto, Canada Francis Ouellette
June 10 Initiation à l’utilisation de Galaxy Cycle "Bioinformatique par la pratique" 2014, INRA Jouy-en-Josas, France Véronique Martin, Sophie Schbath
June 11 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy
June 16 Initiation à l’utilisation de Galaxy Cycle "Bioinformatique par la pratique" 2014, INRA Jouy-en-Josas, France Véronique Martin, Sophie Schbath
June 17 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy

New Public Servers

Several new servers were added to the list of publicly accessible Galaxy servers last month.

Genomics Virtual Lab

Genomics Virtual Lab

CTMM-TraIT Demo Galaxy

CTMM-TraIT Demo Galaxy


QBRC Galaxy

Galaxy Distributions

The most recent Galaxy Distribution was November 04, 2013.


January 2014 CloudMan Release

An update to Galaxy CloudMan was released in January. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.

This update brings a large number of updates and new features. See the release announcement for the list. For more details on the new features, see the the CHANGELOG and for even more details see, all 103 commit messages from 4 contributors.

Galaxy Community Log Board
Galaxy Deployment Catalog

   Share your experience now   
All the cool researchers are doing it!

Galaxy Community Hubs

The Community Log Board and Deployment Catalog Galaxy community hubs were launched in December. January saw several additions:

New Galaxy Deployment Catalog entries:

  • CSIRO Galaxy Service
  • UIUC-Galaxy

bringing the number of deployment descriptions to 10.

New Community Log Board entries

bringing the number of log entries to 12.

ToolShed Contributions

Galaxy ToolShed

New Repositories in the Galaxy Project ToolShed

  • FastQC
  • prims_metabolomics: Metabolomics module of Plant Research International's Mass Spectrometry (PRIMS)
  • diffbind: Differential Binding Analysis of ChIP-Seq peak data (web site)
  • The devteam created 60 new repos for: bowtie2, ccat, clustalw, dwt_cor_ava_perclass, dwt_cor_avb_all, dwt_ivc_all, dwt_var_perclass, dwt_var_perfeature, express, fastq_combiner, fastq_filter, fastq_groomer, fastq_manipulation, fastq_masker_by_quality, fastq_paired_end_deinterlacer, fastq_paired_end_interlacer, fastq_paired_end_joiner, fastq_paired_end_splitter, fastq_stats, fastq_to_tabular, fastq_trimmer, fastq_trimmer_by_quality, fastqc, fastqtofasta, filter_transcripts_via_tracking, find_diag_hits, freebayes_wrapper, gi2taxonomy, gmaj, lca_wrapper, macs, package_bowtie_0_12_7, package_bowtie2_2_1_0, package_ccat_3_0, package_clustalw_2_1, package_express_1_1_1, package_fastqc_0_10_1, package_galaxy_utils_1_0, package_ghostscript_9_10, package_macs_1_3_7_1, package_r_2_15_0, package_readline_6_2, package_sicer_1_1, package_taxonomy_1_0_0, package_tophat_1_4_0, package_tophat2_2_0_9, package_weblogo_3_3, poisson2test, sicer, t2ps, t2t_report, tabular_to_fastq, tophat, tophat_fusion_post, tophat2, vcf_annotate, vcf_extract, vcf_filter, vcf_intersect, and weblogo3

Johns Hopkins University

Penn State University

George Washington University

Galaxy is now at Johns Hopkins and GWU (and Penn State!)

In case you haven't heard, the former Emory University contingent of the Galaxy Team went north this month to Baltimore - it's warmer there (at least this week), where James Taylor is now an Associate Professor in the Johns Hopkins Biology and Computer Science Departments. Jeremy Goecks, also formerly of the Emory University contingent is now an Assistant Professor of Computational Biology at George Washington University in the Washington DC area.

None of these moves should be particularly noticeable to the Galaxy community. We didn't lose anyone in these transitions, and in fact we are still hiring, but now at three universities instead of two.

Other News