October 2014 Galaxy Update

Galaxy Updates

Welcome to the October 2014 Galaxy Update, a 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.

Galaxy Needs Your Input!

The Galaxy Project is preparing for our next grant cycle and we are seeking your feedback and comments on on all things Galaxy. There are two questionnaires, each with a different focus, based on how you interact with Galaxy:

  1. Galaxy User Questionnaire
  2. Galaxy Admin, Tool Developer, and Galaxy Developer Questionnaire

Please take a few minutes and fill out whichever surveys apply to you. The questionnaires are structured so you can skip topics that don't apply to you, and every question is optional.

And, to thank you for your time and effort, the Galaxy Project will increase your storage quota on usegalaxy.org by 50GB, a 20% increase.

Let your voice be heard!

IRC Channel Policy Change

Galaxy IRC Channel

A proposed change for the #galaxyproject IRC channel was proposed, and then discussed, and approved on Galaxy Biostar. Starting sometime in October, posts to this channel will be made available in a searchable archive on the web.

Thanks to everyone who participated in the decision, and those at GCC2014 who suggested this.


Galaxy at ECCB'14 / JOBIM

Galaxy at ECCB'14

Galaxy had a strong presence at ECCB'14. Galaxy was featured in workshops, demos and posters. Couldn't make it? No worries, as most slides and posters are now available online.

Other Events

2014 Swiss German Galaxy Tour QFAB Workshops iReport - A tool to create flexible, scalable Galaxy tool interface, presented at the DTL Programmers Meeting Des bonnes pratiques d'intégration d'outils sous Galaxy   Galaxy Training Days  

There are upcoming events in Switzerland, Germany, Australia, Norway, France, Italy, and the United States. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date Topic/Event Venue/Location Contact
September 30 - October 2 Galaxy Training and Demo Day 2014 Swiss-German Galaxy Tour with events in Bern, Switzerland and Freiburg, Germany Hans-Rudolf Hotz and Bjoern Gruening
(second Swiss) Galaxy Workshop
German Galaxy Developers Day
October 1 Workshop: RNA-Seq analysis using Galaxy The University of Queensland, Brisbane, Queensland, Australia Mark Crowe
October 6 - 24 Intensive course in High Throughput Sequencing technologies and bioinformatics analysis University of Oslo, Oslo, Norway Lex Nederbragt, Karin Lagesen
October 10 iReport - A tool to create flexible, scalable Galaxy tool interface DTL Programmers Meeting, SURF Foundation, Utrecht, The Netherlands Saskia Hiltemann
October 29 - November 4 Computational & Comparative Genomics Course
Application Deadline: July 15
Cold Spring Harbor Laboratories (CSHL), New York, United States William Pearson, Lisa Stubbs
November 3-5 Des bonnes pratiques d'intégration d'outils sous Galaxy Station Biologique de Roscoff, France Christophe Caron
November 3-6 Galaxy training days INRA de Toulouse Midi-Pyrénées, France GenoToul Bioinformatics Team
November 18-20 Analisi dati Next Generation Sequencing con Galaxy Cagliari, Italy CRS4
November 19-20 Workshop: Extended RNA-Seq analysis The University of Queensland, Brisbane, Queensland, Australia Mark Crowe
November 26-28 RNA-Seq & ChIP-Seq analysis course using Galaxy PRABI, Lyon, France Navratil V., Oger C., Veber P., Deschamps C., Perriere G.
July 6-8 2015 Galaxy Community Conference (GCC2015) The Sainsbury Lab, Norwich, United Kingdom Galaxy Outreach

New Papers

The Galaxy CiteULike library of publications reached 1800 papers this month. 71 papers (a new record) were added to the Galaxy CiteULike Group in September, including:

The new papers were tagged in many different areas:

# Tag    # Tag    # Tag    # Tag
4 Cloud - Project 4 Tools 5 UsePublic
- HowTo 2 RefPublic - UseCloud - Visualization
5 IsGalaxy 2 Reproducibility 7 UseLocal 22 Workbench
31 Methods - Shared 5 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.

New Public Servers

Two new public Galaxy server was added to the published list in September:



GalaxEast aims at providing a large range of bioinformatics tools for the analysis of various types of Omics data. It supports reproducible computational research by providing an environment for performing and recording bioinformatics analyses.

The GalaxEast project has the following main objectives:

  • Provide the academic scientific community with an open and powerful Galaxy instance with a guaranteed availability. The platform offers access to cutting-edge and up-to-date tools for Omics data analysis with help and support.
  • Propose innovative developments and new helpful tools packaged for Galaxy (available in the GalaxEast toolshed)
  • Promote the packaging of new developments for Galaxy (through wrappers and/or toolshed packages).

GalaxEast is supported by IGBMC, CNRS, Inserm, and Université Strasbourg.

See GalaxEast: an open and powerful Galaxy instance for integrative Omics data analysis, poster presented at ECCB'14 by Stephanie Le Gras, et al. for more.


MIRPIPE - the miRNA identification pipeline

MIRPIPE focuses on quantification of microRNA based on smallRNA sequencing reads. From the home page: In opposition to present algorithms that generally rely on genomic data to identify miRNAs, MIRPIPE focuses on niche model organisms that lack such information. Among the MIRPIPE features are automatic trimming and adapter removal of raw RNA-Seq reads originating from various sequencing instruments, clustering of isomiRs, and quantification of detected miRNAs by homology search versus public or user uploaded reference databases.

See "MIRPIPE – quantification of microRNAs in niche model organisms," C. Kuenne, et al. for more. Email support and a MIRPIPE Manual are provided. MIRPIPE is sponsored by the Max Planck Institute for Heart and Lung Research.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   

Overview of Galaxy on Bio-Linux 8

The deployment details for the GalaxEast public server were posted in September. Tracey Timms-Wilson's (of the NERC Environmental 'Omics Synthesis Centre) Overview of Galaxy on Bio-Linux 8 page was also added to the Community Log Board.

The Deployment Catalog and Community Log Board Galaxy community hubs were launched in 2013. If you have a Galaxy deployment, or experience you want to share then please publish them this month.

Galaxy ToolShed

New Releases

New versions of Galaxy, CloudMan, BioBlend, and blend4j were all released in August. And so was Galaxy IPython too.

Look for a new Galaxy distribution in October.

ToolShed Contributions

Galaxy Project ToolShed Repos

Here are new contributions for the past two months.

In no particular order:



Packages / Tool Dependency Definitions


Other News