The 1000^th Galaxy-related paper was added to the Galaxy CiteULike group today. That paper was:

• "HvLUX1 is a candidate gene underlying the early maturity 10 locus in barley: phylogeny, diversity, and interactions with the circadian clock and photoperiodic pathways" by Chiara Campoli, Artem Pankin, Benedikt Drosse, Cristina M. Casao, Seth J. Davis, Maria von Korff; New Phytologist (1 June 2013)

The authors used the Wageningen University public Galaxy server, and the paper includes a full explanation of their analysis methods.  To top it all off, the paper is open access.  It was given the methods and usepublic tags.

Each paper in the group is tagged to indicate how it is related to Galaxy.  The first 1000 papers are tagged with:

The Galaxy CiteULike group was launched 18 months ago.  It continues to grow rapidly.

Dave Clements

* These tags were added in 2013 and very few papers before 2013 have been back-curated with them.  All the tags are explained on the CiteULike page. Posted to the Galaxy News on 2013-06-06

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Register for GCC2013 by 14 June and avoid the 100% late surcharges.  Registration is still a bargain with combined registration (Training Day + main meeting) starting at ~ €165 for post-docs and students (that just €55 per day). Register now to assure your spot in the Training Day workshops you want to attend.  Once a Training Day session becomes full, it will be closed to new registrations. 

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, and lightning talks, all about high-throughput biology and the tools that support it. The conference also includes a Training Day with in-depth topic coverage of twelve different topics in 15 sessions across 5 tracks.

The program features 25 oral presentations, 2 lightning talk sessions, two poster sessions, and an ever growing number of Birds-of-a-Feather gatherings.

If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then this conference is for you.

GCC2013 Organizing Committee

PS: And please help get the word out!

Posted to the Galaxy News on 2013-06-04

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• Visualization tool updates to Scatterplot and Trackster.

• Job distribution, error tracking/management, and reporting function improvements to Admin & Core.

• Multiple Tool updates, History and Dataset upgrades, and other related UI enhancements.

• New features and fixes added to the Tool Shed and related components.

• Python 2.5 Support officially ended.

• Plus newly merged Pull Requests and links to tickets covering key Bug Fixes.

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org

new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable  upgrade: $ hg pull  $ hg update release_2013.06.03

Thanks for using Galaxy,

The Galaxy Team

Posted to the Galaxy News on 2013-06-03

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The June 2013 Galaxy Update is now available. 

Highlights:

• Register for GCC2013 by 7 June 14 June to avoid late registration rates

• Two new public servers ODoSE and CBiB

• 39 new papers

• Open Positions at four different institutions

• Other Upcoming Events

• Duplicate Accounts on Main

• Tool Shed Contributions

• Other News

If you have anything you would like to see in the July Galaxy Update, please let us know.

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-05-31

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Directly following GCC2013, there is a unique possibility to attend a two-day Software Carpentry Boot Camp at the University of Oslo (in a building close to where the GCC is held). Software Carpentry Boot Camps aim to to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day boot camp, short tutorials will alternate with hands-on practical exercises.

The course is aimed at postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.

Content: The syllabus for this boot camp will include:

• using the shell to do more in less time
• using version control to manage and share information
• basic Python programming
• how (and how much) to test programs

Visit the Boot Camp Page for more information, and registration.

Lex Nederbragt

Posted to the Galaxy News on 2013-05-31

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Early registration saves up to 75% off regular registration costs, and is downright affordable, with combined registration (Training Day + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend.  Once a Training Day session becomes full, it will be closed to new registrations.  Early registration closes 24 May. 

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, and lightning talks, all about high-throughput biology and the tools that support it. The conference also includes a Training Day with in-depth topic coverage of twelve different topics in 15 sessions across 5 tracks.

An early program is available featuring 25 oral presentations, lightning talks and poster sessions, and the just added Birds-of-a-Feather gatherings.

If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then this conference is for you.

GCC2013 Organizing Committee

PS: And please help get the word out!

Posted to the Galaxy News on 2013-05-20

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The terms of use for the Galaxy Project's free Galaxy server, http://usegalaxy.org (a.k.a. Main) specify 

In the past we have dealt with multiple accounts on an ad-hoc basis.  Moving forward we will use an automated system to detect, disable, and eventually delete duplicate accounts.  If the automated system determines that your account is a duplicate, your account will be disabled and you will receive an email asking you if this is the account you wish to keep.  If it is, please follow the directions in the email and your access to that account will be restored.

If your account is suspended and you believe that you are not in violation of Main's terms of use, then please contact <terms_and_conditions AT galaxyproject DOT org>.

Thanks,

The Galaxy Team

Posted to the Galaxy News on 2013-05-15

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The next meeting of the GalaxyAdmins Group will be held on May 15, 2013, at 10 AM Central US time. 

Andrew Warren of the Cyberinfrastructure Division of the Virginia Bioinformatics Institute at Virginia Tech will talk about their Galaxy deployment at Pathogen Portal, a highly customized Galaxy installation, and also about the group's objectives and future plans.

Dannon Baker will bring the group up to speed on what's happening in the Galaxy project.

We use the Blackboard Collaborate Web Conferencing system for the meetup. Downloading the required applets in advance and using a headphone with microphone to prevent audio feedback during the call is recommended.

GalaxyAdmins is a discussion group for Galaxy community members who are responsible for large Galaxy installations. 

Dave Clements

Posted to the Galaxy News on 2013-05-08

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The May 2013 Galaxy Update is now available. 

Highlights:

• the GCC2013 early registration deadline is 24 May.

• 39 new papers

• Open Positions at five different institutions

• Other Upcoming Events

• Galaxy Distributions

• Tool Shed Contributions

• Other News

If you have anything you would like to see in the June Galaxy Update, please let us know.

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-05-06

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A new paper, "BioBlend: automating pipeline analyses within Galaxy and CloudMan," by Clare Sloggett, Nuwan Goonasekera and Enis Afgan has just been published in Bioinformatics. BioBlend is

Documentation is available at ReadTheDocs.  BioBlend can be installed with PyPI, and the source code is at GitHub.

Dave Clements

Posted to the Galaxy News on 2013-05-02

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A new UK-China collaboration in environmental metabolomics between the University of Birmingham, BGI and GigaScience has received funding from the UK’s Natural Environment Research Council (NERC).

The first metabolomics project will send a developer from the University of Birmingham’s School of Biosciences, to Hong Kong to work with GigaScience personnel on extending Galaxy for use in metabolomics data analyses.

"Metabolomics involves the detection and quantification of small molecules (metabolites) in living organisms and can provide an indication of their cellular condition and health. The toxicological responses of organisms to pollutants can be studied using environmental metabolomics, enabling researchers to discover diagnostic markers for monitoring and risk assessment of our environment. Research at Birmingham focuses extensively on the metabolic responses of the freshwater model organism, Daphnia, to both pollutants and engineered nanomaterials."

See the official announcement for more details.

Peter Li
GigaScience

Posted to the Galaxy News on 2013-04-22

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Galaxy will have a significant presence at the 61st ASMS Conference on Mass Spectrometry and Allied Topics being held in Minneapolis, Minnesota, June 9-13.  Galaxy related content includes the Galaxy Framework as a Solution for MS-based Informatics workshop and at least 9 posters either directly about or using Galaxy.

If you do research in proteomics than please consider attending.

Dave Clements

Posted to the Galaxy News on 2013-04-19

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