April 2014 Galaxy Update

Galaxy Updates

Welcome to the April 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

63 papers (a new monthly record) were added to the Galaxy CiteULike Group in March. Some papers that may be particularly interesting to the Galaxy community:

The new papers covered:

# Tag    # Tag    # Tag    # Tag
1 Cloud 2 Project 4 Tools 3 UsePublic
2 HowTo - RefPublic 1 UseCloud - Visualization
2 IsGalaxy 2 Reproducibility 3 UseLocal 19 Workbench
33 Methods 6 Shared 11 UseMain


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.

Oral Presentation Abstract Submission Closes April 4

Abstract submission for oral presentations closes April 4, which is this Friday. Poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May 2. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

**[Submit an abstract](/events/gcc2014/abstracts/) *[now](/events/gcc2014/abstracts/).***

GigaScience Journal

Accepted talks and selected posters from GCC2014 are also eligible for consideration to appear in the GigaScience "Galaxy: Data Intensive and Reproducible Research" series.

Registration is Open

Early registration is now open. Early registration saves more than 70% on registration costs, and Training Day registration is an additional 55% off if you register for both at the same time. This is by far the most affordable option, with early registration fees starting at less than $50 per day. When you register you can also reserve lodging at Charles Commons, a very affordable housing option in the same building as the conference.

Training Day is an opportunity to learn about all things Galaxy including using Galaxy, deploying and managing Galaxy, extending Galaxy, and Galaxy internals. There are 5 parallel tracks, each with 3 sessions, with each of those sessions two and half hours long. That's 15 sessions and over 37 hours of workshop material.


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.

Globus World 2014

Globus World 2014

GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld 2014 features a features a Using Globus Genomics to Accelerate Analysis Tutorial, and a full half day on Globus Genomics in the main meeting, including a keynote by Nancy Cox and these accepted talks:

  • Globus Genomics: Enabling high-throughput cloud-based analysis and management of NGS data for Translational Genomics research at Georgetown, by Yuriy Gusev,
  • Improving next-generation sequencing variants identification in cancer genes using Globus Genomics, by Toshio Yoshimatsu
  • Globus Genomics: A Medical Center's Bioinformatics Core Perspective, by Anoop Mayampurath
  • Building a Low-budget Public Resource for Large-scale Proteomic Analyses, by Rama Raghavan

Globus Genomics is a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago. And, GCC2014 is a Silver Sponsor of GlobusWorld.

UC Davis 2014 Bioinformatics Workshop

Using Galaxy for Analysis of High Throughput Sequence Data Workshop

Registration is now open for the Using Galaxy for Analysis of High Throughput Sequence Data Workshop being held at UC Davis, June 16-20, 2014 from 9-5 each day. The workshop will cover modern high throughput sequencing technologies, applications, and ancillary topics, including:

  • Illumina HiSeq / MiSeq, and PacBio RS technologies
  • Read Quality Assessment & Improvement
  • Genome assembly
  • SNP and indel discovery
  • RNA-Seq differential expression analysis
  • Experimental design
  • Hardware and software considerations
  • Cloud Computing
UC Davis

The workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools. We will cover the basics of several high throughput sequencing technologies, but will focus on Illumina and PacBio data for hands-on exercises. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data. Workshop exercises will be performed using the popular Galaxy platform (http://usegalaxy.org) on the Amazon Cloud which allows for powerful web-based data analyses. There are no prerequisites other than basic familiarity with genomic concepts.

A similar workshop, using command line interfaces to perform the analysis, is being offered September 15-19, 2014.

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.
GlobusWorld 2014   Bio-IT World 2014   NGS Data after the Gold Rush  GCC2014 early registration and abstract submission are now open 
Date Topic/Event Venue/Location Contact
April 8-9 Building a scalable Galaxy cluster for biomedical research in The Netherlands Netherlands Bioinformatics Conference (NBIC2014), Lunteren, The Netherlands David van Enckevort, Anthony Potappel
April 15-17 Biosciences/Genomics Program GlobusWorld, Chicago, Illinois, United States Globus Outreach, John Chilton
April 29 -
May 1
W1: Integrated Research Data Management for Next Gen Sequencing Analysis Using Galaxy and Globus Online Software-as-a-Service BioIT World Ravi Madduri, Alex Paciorkowski, Vas Vasiliadis
W4: Analyzing NGS Data in Galaxy Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski
W14: Running a Local Galaxy Instance Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney
Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs Ravi Madduri
Integrated Analysis and Visualization of Large-Scale Biological Data with the Refinery Platform Nils Gehlenborg
Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy Jeremy Goecks
May 6-7 Scaling Galaxy for Big Data NGS Data after the Gold Rush, TGAC, Norwich, United Kingdom Dave Clements
May 9 Galaxy Workshop The Genome Analysis Centre (TGAC), Norwich, United Kingdom Dave Clements
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 16-20 Using Galaxy for Analysis of High Throughput Sequence Data UC Davis, California, United States UC Davis Bioinformatics Training
June 28-30 Galaxy Hackathon Homewood Campus of Johns Hopkins University, Baltimore, Maryland, United States Organizers
June 30 -
July 2
2014 Galaxy Community Conference (GCC2014) Organizers

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

Three public Galaxy servers were added to the published list in March:


Biomina Galaxy

Image Analysis and Processing Toolkit

Image Analysis and Processing ToolKit
* *Links:* * [Image Analysis and Processing Toolkit Server](http://cloudimaging.net.au/) * [Project blog](http://cloudimaging.blogspot.com.au/) * *Domain/Purpose:* Image analysis and processing. * *Comments:* This service provides a novel way of carrying out image analysis, reconstruction and processing tasks using cloud based service provided on the Australian [National eResearch Collaboration Tools and Resources (NeCTAR](http://www.nectar.org.au)) infrastructure. The toolbox allows access to a wide range of useful blocks of functionalities (imaging functions) that can be connected together in workflows allowing creation of even more complex algorithms that can be re-run on different data sets, shared with others or additionally adjusted. The functions given are in the area of cellular imaging, advanced X-ray image analysis, computed tomography and 3D medical imaging and visualisation. The service is currently available [on the website](http://www.cloudimaging.net.au). * *User Support:* * [Email](mailto:admin@cloudimaging.net.au) * [Video tutorials](http://www.youtube.com/user/CloudImaging) * *Quotas:* A login is required to access the site. Logins are free and can be [requested via email](mailto:admin@cloudimaging.net.au) * *Sponsor(s):* [NeCTAR](http://www.nectar.org.au) and [CSIRO](http://www.csiro.au/)



Galaxy Distributions

The most recent release of Galaxy was February 10, 2014.

The most recent version of CloudMan was released in January 2014.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   

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

There was one new Community Log Board entry in March:

ToolShed Contributions

Galaxy ToolShed

New Repositories in the Galaxy Project ToolShed

Other News