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February 2015 Galaxy Update

Galaxy Updates

Welcome to the February 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

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

The new papers were related to:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

1

Cloud

2

Project

7

Tools

9

UsePublic

2

HowTo

1

RefPublic

1

UseCloud

-

Visualization

1

IsGalaxy

2

Reproducibility

2

UseLocal

6

Workbench

36

Methods

4

Shared

7

UseMain

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.

Early registration (save heaps) and abstract submission will open later in February. 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.

Training Day Topic Voting Closes TODAY

Vote now!

   Vote now!   

Voting on what topics should be offered at the GCC2015 Training Day closes today, 30 January.

Topics for the GCC2015 Training Day are selected by you, the Galaxy Community. There are nominated topics spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters.

The Training Day schedule, including instructors, will be published before early registration opens in February.

About the GCC2015 Training Day:

The 2015 Galaxy Community Conference (GCC2015) will start on 6 July with a Training Day featuring parallel tracks, each with several multi-hour workshops. There will be at least one complete track about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances.

GenomeWeb Sponsors GCC2015

We are happy to announce that GenomeWeb is a Silver Sponsor for GCC2015.

GenomeWeb
  • GenomeWeb is an independent online news organization based in New York. Since 1997, GenomeWeb has served the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. Our editorial mission is to cover the scientific and economic ecosystem spurred by the advent of high-throughput genome sequencing. We operate the largest online newsroom focused on advanced molecular research tools in order to provide our readers with exclusive news and in-depth analysis of this rapidly evolving market.

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.

19 February GalaxyAdmins Meetup

GalaxyAdmins meetup February 19

The first GalaxyAdmins meetup of 2015 will happen online on Thursday, 19 February. GalaxyAdmins is a special interest group for Galaxy community members who are responsible for Galaxy installations.

A summary of both the user and admin/developer 2014 Galaxy Community Questionnaires will be presented by Dave Clements, a Galaxy Project Update will be offered by a Galaxy Team member, and Hans-Rudolf Hotz will lead a short discussion on GalaxyAdmins direction.

Thanks to everyone for letting us know what dates and times worked best for you. This time and day of the week worked for a remarkable 91% of respondents.

January Baltimore Area Galaxy Meetup Report

January 2015 Galaxy Baltimore Meetup

The first Baltimore Area Galaxy meetup was sold out. It was the right mix of current Galaxy users, people who want to learn how to use Galaxy, and students in Biology/Computer science programs. It was good to see academics unwind with a few beers and talk about their ideas to use Galaxy. The idea behind the meetup was to build a local community of Galaxy users, and to get to know one another personally. This would in turn foster collaborations and also bring forward better feedback to the Galaxy Team as well.

The second meetup is going to be hosted in February, for which we hope to have a slightly more focussed agenda. To talk about one or a few of the topics raised during the course of the month. There is now a Baltimore newsletter (subscribe if you are interested) which goes out to the members who signed up for the first meetup. We hope to have more people in the coming months, and to grow a stronger Galaxy community in Baltimore.

Enis Afgan & Nitesh Turaga

Other Events

Analyse bioinformatique de séquences sous Galaxy   19 February GalaxyAdmins Web Meetup   QFAB Workshops RNA-Seq and ChIP-Seq Analysis with Galaxy  

http://bit.ly/gxycal

There are upcoming events in 4 countries on 3 continents. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date

Topic/Event

Venue/Location

Contact

February 9-13

Analyse bioinformatique de séquences sous Galaxy

Training offered by GTN Member
Montpellier, France

J.F. Dufayard <jean-francois.dufayard@cirad.fr>

February 16-18

Accessible and Reproducible Large-Scale Analysis with Galaxy

Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States

James Taylor

Large-Scale NGS data Analysis on Amazon Web Services Using Globus Genomic

Genomics & Sequencing Data Integration, Analysis and Visualization, part of Molecular Medicine Tri-Conference, San Francisco, California, United States

Ravi Madduri

iReport: An Integrative “omics” Reporting and Visualisation Platform

Andrew Stubbs

February 19

February 2015 GalaxyAdmins Web Meetup

Online

Hans-Rudolf Hotz, Dave Clements

March 2

RNA-Seq analysis using Galaxy

Training offered by GTN Member
QFAB, University of Queensland, St Lucia, Australia

Mark Crowe

March 3-5

Développement et intégration d’applications sous Galaxy

Training offered by GTN Member
La Chapelle Sur Erdre, France

Frederique Malipier <frederique.malipier@nantes.inra.fr>

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 <bioinformatics.core@ucdavis.edu>

March 24-27

Visualization and Visual Analytics with Galaxy

Training offered by GTN Member
Visualizing Biological Data (VIZBI) 2015, Cambridge, Massachusetts, United States

Jeremy Goecks

July 6-8

2015 Galaxy Community Conference (GCC2015)

Training offered by GTN Member
The Sainsbury Lab, Norwich, United Kingdom

Galaxy Outreach <outreach@galaxyproject.org>

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

Several new public Galaxy servers were added in January.

RiboGalaxy

RiboGalaxy
  • Link:

  • Domain/Purpose:

    • RiboGalaxy provides on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique.

  • Comments:

    • RiboGalaxy is a freely available web server for processing and analysing ribosome profiling (ribo-seq) data with the visualization functionality provided by GWIPS-viz. RiboGalaxy provides a compact suite of tools specifically tailored for the alignment and visualization of ribo-seq and corresponding mRNA-seq data. Users can take advantage of the published workflows on RiboGalaxy which reduce the multi-step alignment process to a minimum of inputs.

  • User Support:

  • Quotas:

    • Anonymous users can use RiboGalaxy. However, the upload and processing of datasets larger than 2GB and the use of advanced features such as published workflows, will require the user to be registered on RiboGalaxy.

  • Sponsor(s):

CardioVascular Research Grid (CVRG)

CardioVascular Research Grid (CVRG)

Center for Phage Technology (CPT)

Center for Phage Technology (CPT)

Galaxy Community Hubs


Ruđer Bošković Institute (RBI)

New GTN Member: Ruđer Bošković Institute

We are pleased to welcome the Ruđer Bošković Institute in Zagreb, Croatia as the newest member of Galaxy Training Network (GTN). Dobrodošli!

Several new Training Resources were added in January:

New Releases

Galaxy 2015/01/13 Distribution

width=175

Complete News Brief

Security

Several critical security vulnerabilities were recently discovered by Bartlomiej Balcerek and colleagues at the Wroclaw Centre for Networking and Supercomputing. This stable Galaxy release contains fixes for those vulnerabilities. The Galaxy Team strongly encourages Galaxy server administrators to update their Galaxy servers immediately.

IPython Integration

Thanks to the awesome work of community members Björn Grüning and Eric Rasche, Galaxy now features integration with the popular IPython project. The Galaxy-IPython project has been merged into Galaxy core and made into a generic plugin framework of interactive environments based on Docker.

Tool Form Upgrade (for Beta Testing)

In Galaxy's development branch, the basic tool from has been redesigned and modernized to address certain limitations in Galaxy's responsiveness when working with longer forms containing multiple parameter choices. This new tool form will become the default with the next release - but we are hoping tool author's and power users enable it and provide feedback during this release cycle in order to ensure it is working ideally when it becomes the default.

Get The Distribution

getgalaxy   

getgalaxy.org

galaxy-dist.readthedocs.org

bitbucket.org/galaxy/galaxy-dist

new:

$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable 

upgrade:

$ hg pull 
$ hg update latest_2015.01.13

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.

Planemo 0.2.0

Version 0.2.0 of Planemo was released in January. Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Updates included:

  • Improvements to way Planemo loads its own copy of Galaxy modules to prevent various conflicts when launching Galaxy from Planemo. (Pull Request 56)

  • Allow setting various test output options in ~/.planemo.yml and disabling JSON output.

  • More experimental Brew and Tool Shed options that should not be considered part of Planemo's stable API. See this presentation for more details.

  • Fix project_init for BSD tar (thanks to Nitesh Turaga for the bug report.)

  • Documentation fixes for tool linting command (thanks to Nicola Soranzo).

Other

New versions CloudMan, and blend4j were released in August.


Galaxy ToolShed

ToolShed Contributions

Galaxy Project ToolShed Repos

Here are new contributions for the past month.

In no particular order:

Tools

Tool Suites

Packages / Tool Dependency Definitions

Select Updates

Other News

And a Huge Thank You!

The Galaxy Team would like to thank everyone who took the time to respond to the project's call for support. These will be extremely helpful with our renewal.