The March 2015 Galaxy News

Galaxy Updates

Welcome to the March 2015 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.

New Papers

82 new papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in February. Some highlights:

The new papers were tagged with:

# Tag    # Tag    # Tag    # Tag
4 Cloud 3 Project 1 Tools 13 UsePublic
2 HowTo 7 RefPublic - UseCloud - Visualization
2 IsGalaxy 6 Reproducibility 2 UseLocal 20 Workbench
42 Methods 1 Shared 8 UseMain


Watch the video

UseGalaxy.org Update

A refresh of UseGalaxy.org has started. It includes

  • New versions of Bowtie2, bwa-mem, Picard, BAMTools, FastQC, ....
  • New look and feel for tool forms
  • New Scratchbook features
  • New Charts functionality

All of these are described in the new Galaxy Screencast GXYCast1: 2015. Look for more updates coming soon.


Events

GCC2015: 6-8 July, Norwich UK

Sponsor GCC2015

The 2015 Galaxy Community Conference (GCC2015) is the Galaxy community's annual gathering of users, developers, and administrators. Previous GCC's have drawn over 200 participants, and we expect that to happen again in 2015. GCC2015 is being hosted by The Sainsbury Lab in Norwich, UK, immediately before BOSC and ISMB/ECCB in Dublin.

There are a lot of events going on at GCC2015, including:

Code Hackathon

An intense two-day hands-on collaboration to develop working code that is useful to the Galaxy community. If you know how to code, and want to contribute to one of the most successful open source projects in the life sciences, then please consider attending. See the Code Hackathon home page for more.

Data Wrangling Hackathon

An intense two-day hands-on collaboration to develop cutting edge analysis pipelines that are useful to the Galaxy community. If you know data analysis, we would love to have you here to help us beat back those seemingly unsurmountable analysis challenges. See the Data Wrangling Hackathon home page for more.

Training SunDay

Something new for GCC2015 is Training SunDay, an additional day of training offered the day before its older sibling Training Day, and featuring a single track with the most in-demand topics. You can attend both Training Days, or just one. Training SunDay features these three topics:

These three topics are also offered on Monday as well. You can register for one or both Training Days.


Training Day Schedules set

Training (Mon)Day

The schedule for Training Day, Monday, 6 July is available. Training Day featuring five parallel tracks, each with three, two and a half hour workshops. There are topics on using Galaxy, interacting with it programmatically, and deploying, administering, and extending Galaxy. No matter what you do with Galaxy, there are workshops for you.

Early Registration opens in March

Early registration (save heaps) will open in March. Early registration is very affordable and starts at less than £40 per day for students and postdocs. If you work in data-intensive life science research, then it is hard find a meeting more relevant than GCC2015. We look forward to seeing you there.

Abstract Submission is Now Open

Abstract submission for Oral and Poster Presentations at the 2015 Galaxy Community Conference (GCC2015) is now open.

Abstract submission for oral presentations closes 10 April, while poster submission closes 1 May. Poster authors will be notified of acceptance status within two weeks of submission, while oral presentation authors will be notified no later than 24 April. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

GigaScience Journal

We are pleased to announce that again in 2015, any oral or poster presentation will also be eligible for consideration for publication in the GigaScience "Galaxy: Data Intensive and Reproducible Research" series (first announced for GCC2013). GigaScience is pleased to offer a 15% discount on article publishing charges for accepted papers from GCC2015.


BioTeam

GCC2015 Sponsorships

We are pleased to announce that BioTeam will again be a Gold Sponsor for this annual event. This is the third year in a row that BioTeam has been a GCC Gold Sponsor.

Call for Sponsors

The 2015 Galaxy Community Conference (GCC2015) is now accepting Sponsorships. Your organisation can play a prominent part in the Galaxy community by sponsoring GCC2015. Sponsorship is an excellent way to raise your organization’s visibility.

Several sponsorship levels are available, including two levels of premier sponsorships that include presentations. Premium sponsorships are limited, however, so you are encouraged to act soon.

Please let the organisers (gcc2015-org AT lists DOT galaxyproject DOT org) know if you are interested in helping make this event a success.



RNA-Seq and ChIP-Seq Analysis with Galaxy

RNA-Seq and ChIP-Seq Analysis with Galaxy, UC Davis, March 23-26

A hands-on, 4 day workshop on RNA-Seq and ChIP-Seq Analysis with Galaxy will be held at the UC Davis Bioinformatics Core in Davis, California, United States, March 23-26. There are just a few slots left.

February GalaxyAdmins Meetup

GalaxyAdmins meetup February 19

Video and slides from the first GalaxyAdmins meetup of 2015 are now available online.

Hans-Rudolf Hotz also lead a short discussion on GalaxyAdmins direction.

GalaxyAdmins is a special interest group for Galaxy community members who are responsible for Galaxy installations. Our next meetup will be in April.

Fall 2014 Questionnaire Summaries

A summary of both the user and admin/developer 2014 Galaxy Community Questionnaires was presented by Dave Clements. A summary of the admin/devel questionnaire is now available online.

Gravity

Nate Coraor introduced Gravity, a process manager (supervisor) for Galaxy servers.

Other Events

Ruđer Bošković Institute (RBI) QFAB Workshops Développement et intégration d’applications sous Galaxy RNA-Seq and ChIP-Seq Analysis with Galaxy  

There are upcoming events in 7 countries on 4 continents. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date Topic/Event Venue/Location Contact
March 2 RNA-Seq analysis using Galaxy
Training offered by GTN Member
QFAB, University of Queensland, St Lucia, Australia
Mark Crowe
March 2-3 Workshop on Bioinformatics Methods in Genomics
Training offered by GTN Member
RBI, Zagreb, Croatia
Enis Afgan
March 3-5 Développement et intégration d’applications sous Galaxy
Training offered by GTN Member
La Chapelle Sur Erdre, France
Frederique Malipier
March 3-5 COST Basic training on NGS data analysis Course University of Latvia, Riga Latvian Genome Centre
March 23-26 RNA-Seq and ChIP-Seq Analysis with Galaxy
Training offered by GTN Member
UC Davis Bioinformatics Core, Davis, California, United States
UC Davis Bioinformatics
April 14-15 GlobusWorld 2015 Chicago, Illinois, United States Globus Outreach
April 20-21 Workshop: Extended RNA-Seq analysis
Training offered by GTN Member
QFAB, University of Queensland, St Lucia, Australia
Mark Crowe
April 21 Large-Scale NGS Analysis Using Globus Genomics: Challenges and User Success Stories Bio-IT World 2015, Boston, Massachusetts, United States Ravi Madduri
Workshop: Large Scale NGS Analysis Using Globus Genomics Paul Davé, Ravi Madduri, Alex Rodriguez, Dinanath Sulakhe
Extending Galaxy with External Microbiome Databases Bob Brown
April 23 Visualization Tools for the Refinery Platform Nils Gehlenborg
April 27 - May 3 High-throughput Biology: From Sequence to Networks 2015
Training offered by GTN Member
New York City, New York, United States
Francis Ouellette
April 28 Galaxy Workshop Tokyo 2015 RCAST, The University of Tokyo, Japan Ryota Yamanaka
July 6-8 2015 Galaxy Community Conference (GCC2015)
Training offered by GTN Member
The Sainsbury Lab, Norwich, United Kingdom
Galaxy Outreach
Designates a training event offered by GTN Member Designates a training event offered by GTN member(s)

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

One new public Galaxy servers was added in February:

Whale Shark

Whale Shark Galaxy @ The Georgia Aquarium

Galaxy Community Hubs


Two new Community Log Board entires were added in February:


Galaxy GitHub

Galaxy has moved its source from Bitbucket to GitHub. The development of Galaxy takes place there from now on.

However, the Bitbucket repositories are still the official source for deployment until we polish the process.

More information available in Develop/SourceCode.

Releases

Galaxy 2015-01-13 Distribution

The most recent Galaxy release was the 2015-01-13 distribution. This addressed several critical security vulnerabilities, added IPython integration, and included a Tool Form Upgrade for Beta Testing.

Planemo 0.5.0

There were several releases of Planemo in February. Among many other new features, it is now install-able from PyPI and contains a new command to assist in bootstrapping new tools.

BioBlend

BioBlend v0.5.2 was released in October. BioBlend is a python library for interacting with CloudMan and the Galaxy API. In January the BioBlend source was moved to the galaxyproject Github account.

CloudMan and blend4j

New versions of CloudMan, and blend4j were released in August.



Galaxy ToolShed

ToolShed Contributions

Galaxy Project ToolShed Repos

There was no shortage of new ToolShed repositories in February, but there was a shortage of time to describe them. Look for a double batch of new tools next month.


Other News