August 2014 Galaxy Update

Galaxy Updates

Welcome to the august 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.

The Galaxy Update is going out a few days early this month because the usual release date is during GCC2014.


GCC2014: June 30 - July 2

GCC2014 Report

2014 Galaxy Community Conference (GCC2014) was held June 30 through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States. It was preceded by by the first ever GCC Hackathon.

Videos of and slides for presentations and Lightning Talks, PDFs of Posters, material for Training Day Sessions, and writeups of BoFs are now all online. There are also several meeting reports now available on the web.

Feedback has been very positive (see below for some of it), and we would like to thank absolutely everyone for making this such a successful meeting.

GCC2014 by the numbers

Measure Value      Question No Yes, but ... Yes
Total Participants 214 Would you recommend future Galaxy events to others? 2% 3% 95%
Training Day Participants 207
Hackathon Participants 40
Videos, slides, posters, exercises, ... 120+ Question Not at all Below Average Average Above Average Exceptional
Talks 26 How useful was the main meeting? 0% 0% 12% 56% 32%
Posters 30 Was the main meeting well run and organized? 0% 0% 2% 51% 47%
Lightning Talks 15
Training Day Sessions 15 Did the main meeting meet your expectations? 0% 0% 10% 55% 35%
BoFs 6


GCC2015: Norwich, United Kingdom, 6-8 July 2015

We are pleased to announce that the 2015 Galaxy Community Conference (GCC2015) will be held at The Sainsbury Laboratory in historic Norwich, United Kingdom. Norwich is a center of biological research and is home to The Sainsbury Laboratory, The John Innes Centre, The Genome Analysis Centre (TGAC), and The University of East Anglia.

GCC2015 will likely again feature a hackathon, copious training day sessions and topics, posters, birds-of-a-feather sessions, talks, lightning talks, the best darn networking opportunities, and the possible return of an onsite pub. As at past GCC's we will again strive to keep registration costs low, and to offer affordable housing options.

GCC2015 will be held 6-8th July, 2015, which is just before ISMB/ECCB 2015 in Dublin. More details will be announced through Galaxy channels as we know them.

Hope to see you in Norwich!

Galaxy @ ISMB and BOSC 2014 Slides and Posters

BOSC 2014    ISMB 2014

Slides and posters for 9 Galaxy related presentations at ISMB and BOSC 2014 this year are now available online too. There's also an interesting writeup of the Bioinfo-Core Workshop including Core on a Budget vs Enterprise and Using pipelines within a core.

Other Events

Over the rest of the few months there are many Galaxy related events in Brisbane, Rio de Janeiro, Rennes, and Melbourne. Galaxy will also be at ECCB'14/JOBIM in Strasbourg, and there is Swiss-German Galaxy Tour in the fall. See the Galaxy Events Google Calendar for details on other events of interest to the community.

QFAB Workshops T07 - Scientific Workflows for Analysing, Integrating and Scaling Bioinformatics Data: a Practical Introduction to Galaxy, Taverna and WS-PGRADE Tools integration on Galaxy   2014 Swiss German Galaxy Tour
Date Topic/Event Venue/Location Contact
August 15 Workshop: An Introduction to De Novo Genome Assembly The University of Queensland, Brisbane, Queensland, Australia Mark Crowe
August 25-27 Análise e anotação funcional de seqüências NGS usando Stingray@Galaxy Fiocruz, Rio de Janeiro, Brasil Plataforma de Bioinformática do IOC
August 29 Workshop: Variant detection using Galaxy The University of Queensland, Brisbane, Queensland, Australia Mark Crowe
September 6-10 At least one tutorial, a panel of European Public Galaxy Instances, and 5 posters European Conference on Computational Biology (ECCB'14), Strasbourg, France Presenters
September 11 Tools integration on Galaxy Galaxy User Group Grand Ouest, Rennes, France Cyril Monjeaud,Yvan Le Bras
September 19 The Great GigaScience and Galaxy (G3) Workshop The University of Melbourne, Melbourne, Australia Nick Wong, Ross Lazarus
September 30 - October 2 RNA-Seq & ChIP-Seq analysis course using Galaxy PRABI, Lyon, France Navratil V., Oger C., Veber P., Deschamps C., Perriere G.
September 30 - October 2 Galaxy Training and Demo Day Bern (Switzerland) Hans-Rudolf Hotz and Bjoern Gruening
(second Swiss) Galaxy Workshop SyBIT Tech Day, Bern (Switzerland)
German Galaxy Developers Day Freiburg (Germany)
October 1 Workshop: RNA-Seq analysis using Galaxy The University of Queensland, Brisbane, Queensland, Australia Mark Crowe
November 2-5 Introduction to Bioinformatics Analysis with Galaxy Workshop ASA, CSSA, and SSSA International Annual Meeting, Long Beach, California, United States Galaxy Outreach
SNP/Variant Analysis with Galaxy Workshop
A Gentle Introduction to Cloud Computing: Setting up your own Galaxy Server Workshop

New Papers

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

The new papers were tagged in many different areas:

# Tag    # Tag    # Tag    # Tag
3 Cloud - Project 8 Tools 6 UsePublic
1 HowTo 3 RefPublic - UseCloud - Visualization
4 IsGalaxy 2 Reproducibility 1 UseLocal 15 Workbench
26 Methods 2 Shared 8 UseMain

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to and we'll put it in the Galaxy News feed and include it in next month's update.

New Public Servers

One new public Galaxy server was added to the published list in July:



Galaxy Distributions

Security Vulnerability

A security vulnerability was recently discovered by Inge Alexander Raknes that would allow a malicious person to execute arbitrary code on a Galaxy server. The vulnerability was in a method that uses Python "pickle" functionality to decode state information from tool forms. Because pickles can be used to instantiate arbitrary Python objects, tool states could be constructed to exploit this vulnerability.

Because this vulnerability allows for arbitrary code execution, administrators are strongly encouraged to apply this fix immediately. See this posting for details on how to fix this problem.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   

There were no new Log Board or Deployment Catalog entries in July! Eek! Please don't let this happen again!

The Community Log Board and Deployment Catalog Galaxy community hubs were launched last your. If you have a Galaxy deployment, or experience you want to share then please publish them this month.

Galaxy ToolShed

ToolShed Contributions

... we didn't get there this month. Look for a double helping of tools in the September newsletter.

Other News