Locked History Actions

News/Archive/2013

2013 News Item Archive

News items that have were posted to the Galaxy News page/feed in 2013.

See also

Galaxy Day

The 2013 Galaxy Day event took place at Institut Curie in Paris, 4 december. Program and presentations are available online.

The Galaxy Day began with the presentation of the French Galaxy working group.

Three session were then scheduled.

In the first session, 2 presentations related the virtualization of galaxy instances. Virtualization can be a convenient way to (i) simplify storage and data sharing (Marius Van den Beek <m DOT vandenbeek AT gmail DOT com>, Drosophila Genetics and Epigenetics Lab, Université Paris VI) and (ii) to set up a scalable environment for training (Franck Samson <Franck DOT Samson AT jouy DOT inra DOT fr>, Unité Mig/Plateforme Migale INRA).

This first session was also the time to give feedback on instance installation and maintenance: In the context of a small lab (David Roquis, Laboratoire Ecologie et Evolution des Interaction, Université de Perpignan) and in the context of a big institute (Olivia Doppelt-Azeroual, Institut Pasteur).

The second session contained three types of presentations: (i) general galaxy activities around platform (GUGGO group represented by Cyril Monjeaud <Cyril DOT Monjeaud AT irisa DOT fr> and Yvan Le Bras <Yvan DOT le_bras AT irisa DOT fr>, and PRABI platform represented by Vincent Navratil) ; (ii) administrator and user advices to maintain and use a Galaxy service (Vladimir Daric from IGM, and Sébastien Carrere <Sebastien DOT Carrere AT toulouse DOT inra DOT fr> representing the CATI BBRIC) ; (iii) and an administrator tool proposition from Alban Lerminne (Institut Curie) to manage Galaxy datasets in standard user unix accounts.

The third session contained three lightning talks about global feedback from different communities (David Benaben from CBIB, Claire Toffano-Nioche from IGM, and Franck Giacomoni from INRA representing a metabolomics research community).

Olivier Inizan and Jean-François Dufayard

Posted to the Galaxy News on 2013-12-17

Galaxy Community Log Board

The Galaxy Community Log Board is a place to share how you addressed a particular task in your Galaxy deployment. Log entries describe specific solutions to particular tasks, such as the details of what steps were taken to deploy Galaxy on particular platforms, or specific stumbling blocks when configuring Galaxy. Solutions can be described on this wiki, or just some metadata and a link to the description elsewhere. Log entries are an easy way to help others (and learn from others) by sharing what you've already done. If you have figured out or documented how to do something, then this is the ideal forum for sharing that information with the community.

   Share your experience now   

C'mon, it will make you feel good!

The Galaxy Community Log Board describes how things can be done, and it complements the (also recently announced) Galaxy Deployments Catalog, which describes different Galaxy installations. Both the Log Board and the Deployments Catalog came out of discussions at the GCC2013 GalaxyAdmins Birds-of-a-Feather gathering. Thanks to everyone who attended that BoF.

Dave Clements

Posted to the Galaxy News on 2013-12-06

Galaxy Deployment Catalog

We are pleased to announce the Galaxy Deployment Catalog, a place to describe individual Galaxy deployments, and to learn how others in the community are implementing Galaxy in production environments.

If you have a Galaxy deployment then please take a few minutes to describe your instance to the community. There are two ways to do this.

Use the Wiki Template:

  • Go to the "Using the Wiki" section of the catalog home page, enter a CamelCase name for your deployment, click "Create ...," and then edit, preview, and save the page. Voilà, an entry for your deployment now exists in the catalog.

Use the Online Form

  • Fill out this online form. In a week or two, a deployment catalog page will be programmatically created and you will receive an email.

The wiki method requires a wiki login, but gives you control over how the page appears. The online form is easier.

Thanks a bunch, and please let us know if you have any questions.

Dave Clements

Posted to the Galaxy News on 2013-12-04

GCC2014 Training Day

Training Day topics are nominated by you, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see

Nominated topics will be published on the Training Day page as they come in. Nominations close December 20. Topics will be compiled into a uniform list by the GCC2014 Organizing Committee, and topics will be voted on by the Galaxy Community January 6-17.

Topics will then be selected and scheduled based on topic interest, and the organizers' ability to confirm instructors for each session.  Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens.

GCC2014 Organizing Committee

Posted to the Galaxy News on 2013-12-02

December 2013 Galaxy Update

The December 2013 Galaxy Update is out:

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-12-02

usegalaxy.org
usegalaxy.org
Complete News Brief

Highlights:

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_2013.11.04

Thanks for using Galaxy!

The Galaxy Team

Posted to the Galaxy News on 2013-11-04

November 2013 Galaxy Update

The November 2013 Galaxy Update is out:

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-10-31

Registration is now open for Bioinformatics Bootcamps in December!

Introduction to Galaxy Boot Camp @ UC Davis Bioinformatics Core
 Galaxy

We’re excited to announce our next offering of Bioinformatics Bootcamps, which will be held on the UC Davis campus December 10-13.

These focused one-day courses are perfect for the student, postdoc, faculty, or industry professional looking to get up to speed quickly on the latest technologies and techniques in bioinformatics. Students will work on their own laptops and have continued access to software and example data used in the exercises through our public Amazon Web Services virtual machine. The first three bootcamps will use the Galaxy platform, and the final bootcamp will use both Galaxy and the command-line. The Alignment and Assembly bootcamps (Dec. 11th & 12th) require you to know Galaxy, so if you are unfamiliar with Galaxy, you should also take the Introduction bootcamp on Dec. 10th.

Daily instruction will run from 9am until 5pm. Lunch, light breakfast, and snacks will be provided. Enrollment for each bootcamp will be capped at 24 students. Please enroll early to be assured of a seat, as these bootcamps usually fill up quickly! More information, including full descriptions of each bootcamp is available online. The cost for each bootcamp is $200 (academic/government) or $250 (non-academic/industry).

UC Davis

If you have any questions, please don’t hesitate to contact us:

We hope to see you in December!

The UC Davis Bioinformatics Core Team

Posted to the Galaxy News on 2013-10-18

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.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference will also includes a Training Day offering in-depth topic coverage, across several concurrent sessions.  See the GCC2013 web site for an idea of what happens at a Galaxy Community Conference.

GCC2014 Organizing Committee

Posted to the Galaxy News on 2013-10-02

Appel à contributions

Le Groupe de Travail Galaxy-IFB organise une journée d'animation autour de la plateforme Galaxy le mercredi 4 décembre à Paris (@Institut Curie - 9H30-17H00).

Cette journée a pour principal objectif d'exposer les retours d'expérience de laboratoires ou plateformes, sous la forme de présentations de 20 minutes, autour de la plateforme Galaxy.

Ces présentations peuvent aussi bien cibler des retours d'expérience autour d'une installation et mise en production d'une plateforme, que des nouveaux usages/domaines, ou encore des développements technologiques.

Si vous souhaitez soumettre une présentation, merci d'envoyer un résumé en anglais de 15/20 lignes maximum à ifb.galaxy@sb-roscoff.fr avant le 10 octobre, avec pour sujet [Galaxy Day].

En vous remerciant.

Les membres du Groupe Galaxy IFB,

URGI, GenoToul, MIGALE, PFEM, SouthGreen, Institut Curie, ABiMS


URGI GenoToul MIGALE PFEM SouthGreen Institut Curie ABiMS


Call for contributions

The IFB (French Bioinformatic Institute) Galaxy working group is organizing a seminar around the Galaxy platform which will takes place in Paris on December 4 (@Institut Curie - 9h30-17h).

The main aim of this meeting is to share experiences from laboratories and platforms working daily with Galaxy. 20 minutes talks will be offered to present insights about installations and releases of Galaxy platforms, new usages / domains, or technological developments.

If you want to submit your work, please send a 15/20 lines resume (in English) at ifb.galaxy@sb-roscoff.fr, before the 10th of October (mail subject should start with [Galaxy Day]).

We hope to hear from you soon,

The IFB Galaxy group,

URGI, GenoToul, MIGALE, PFEM, SouthGreen, Institut Curie, ABiMS

Posted to the Galaxy News on 2013-10-02

October 2013 Galaxy Update

The October 2013 Galaxy Update is out:

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-09-30

Analyzing NGS Data with Galaxy

Free Training Event in Boston: Analyzing NGS Data with Galaxy

Based on popular demand, we are pleased to announce another Galaxy training event for this year.  BioTeam and the Galaxy Team are offering a training session that will focus on analyzing NGS Data using Galaxy.  In addition to learning about the NGS related Galaxy features, you will also learn about what it takes to host your own Galaxy instance.  This event is kindly hosted by Dana-Farber Cancer Institute.  For more information about this training please visit the event website.


 Date:

Tuesday October 22nd, 2013

Time:

9:00am – 12:00pm

Location

Dana Farber Cancer Institute, Boston, MA, USA

Cost:

Free

Space is limited so please register for this free event soon.

   REGISTER NOW      

Once you register, please keep the email confirmation for your records.  If you have any questions please email anushka@bioteam.net.

Anushka Brownley
BioTeam
SlipStream Appliance Galaxy Edition
SlipStream Appliance White Paper

Posted to the Galaxy News on 2013-09-30

University of Pretoria

University of Cape Town

2013 South Africa Galaxy Workshop Tour

African Centre for Gene Technologies

A South Africa Galaxy Workshop Tour will visit Pretoria on 14-18 October and Cape Town on 21-25 October. Each leg spans five days. The first four days cover using Galaxy and participants will learn how to integrate data, and perform simple and complex analysis within Galaxy. It will also cover data visualization and visual analytics, and how to share and reuse your bioinformatic analyses, all from within Galaxy. The last day will cover deploying and running a Galaxy server.

The workshops are free and open to all researchers, but admission is competitive and will be based on the strength of your application. Applications are due 17 September.

The Pretoria event is hosted by African Centre for Gene Technologies in collaboration with the University of Pretoria’s IRT for Genomics.

The Cape Town event is hosted by the African Centre for Gene Technologies in collaboration with the University of Cape Town’s Computational Biology Group.

If you are interested, then please apply by 17 September!

Dave Clements

Posted to the Galaxy News on 2013-09-09

Opening in Drosophila Genetics and Epigenetics

A 2 and half years position in Computational Biology is available at the laboratory of Drosophila Genetics and Epigenetics (CNRS UMR 7622 – University Pierre-et-Marie-Curie, Paris) in relation with a consortium of four laboratories funded by the ANR (Plastisipi project).

Key words: Software development for NGS analysis, Galaxy integration, Small RNA biogenesis and mechanisms of action, siRNAs, piRNAs, miRNAs.

We are looking for a dynamic candidate with a wide knowledge in computer sciences and statistics. She/He will develop statistical and mathematical procedures to analyze NGS sequencing datasets and implement them in a Galaxy Framework dedicated to the consortium.

Scientific project': The Plastisipi project is aimed at studying how modulation of the piRNA silencing pathway may regulate Transposable Element repression along Drosophila germ cell differentiation, allowing an appropriate balance between genome protection and genome plasticity. Another exciting aspect of the project is to study the role of tRNAs – or tRNAs derived Fragments (tRFs) – in piRNA biogenesis.

Job description: The successful candidate will participate in 1- managing and mining the sequencing datasets generated by Plastisipi to profile piRNAs, tRFs and mRNAs; 2- developing new visualization tools; 3- developing new algorithms to analyze the piRNA signatures at genome-wide level as well as their statistical significance. Depending on the candidate profile, there is also an opportunity to work through a core computing science approach at the development of Galaxy instance “stacks” that could be easily spread into the community.

The ideal candidate holds a PhD degree in computational biology and is experienced in Galaxy developments; however, this profile is not mandatory and candidates with little background in biology but strong experience in core computing sciences, computing infrastructures, mathematics and/or statistics will be welcome too. He/she will collaborate closely with a multi-disciplinary team of biologists and bioinformaticians. Excellent communication, management and reporting skills are essential for this role.

Favored Experience/Skills:

  • Experience in NGS sequencing dataset analysis
  • Advanced knowledge of a least one OOP language
  • Knowledge of Postgresql
  • Experience in tool integration in the Galaxy framework
  • Advanced use of R
  • Good notions of cloud computing
  • Autonomy and excellent relational and teamwork skills

Contract Duration: Available in January 2014 for two and half years (starting date flexible) Salary: Depending on qualifications and experience, based on CNRS salary scale.

Application: Send CV, cover letter and two references to Christophe Antoniewski <christophe DOT antoniewski AT upmc DOT fr>. Shortlisted candidates will be invited for an interview.

Lab publications

Christophe Antoniewski

Posted to the Galaxy News on 2013-09-09

Center for Medical Genomics

Are you interested in genomics and do you have skills in Bioinformatics, Computational Biology and Statistics? The Makova lab in the Department of Biology at The Pennsylvania State University is looking to hire a postdoctoral researcher for an NSF-funded project examining regional variation in mutation rates (see our recent publication in PNAS: Kuruppumullage Don, Ananda, Chiaromonte, Makova 2013). With new sequencing technologies, multiple human genomes and their detailed annotations (e.g., ENCODE) are suddenly accessible to us. This gives us a terrific opportunity to explore previously inaccessible evolutionary processes (e.g., mutation) and other biological associations (location of genes in certain mutation states, as identified by HMMs). Such knowledge is vital in a clinical setting where disease mutations need to be evaluated. Our resources and links with medical researchers at Hershey Medical School and computational biologists from the Galaxy team put us in a great position to address these questions.

Candidates should have experience in bioinformatics, working knowledge of statistics and should have a broad understanding of molecular biology and genetics. Familiarity with next-generation sequencing data analysis is desirable. A PhD is required. You will be joining an established dynamic group. We are part of the Center for Medical Genomics and of the Center for Comparative Genomics and Bioinformatics. Penn State is a vibrant scientific community with particular strengths in genomics, bioinformatics and molecular evolution. Our location, in State College, Pennsylvania, is known for excellent schools and numerous opportunities for outdoor activities.

The starting date is flexible, with an earlier date preferred. This position is funded for one year from date of hire, with good possibility of refunding. Interested applicants should send a pdf with a CV, a statement of research interests, and contact information for three referees to Kateryna Makova <kmakova AT bx DOT psu DOT edu>, indicating postdoc in the subject line. Employment will require successful completion of background check(s) in accordance with University policies. Penn State is committed to affirmative action, equal opportunity, and the diversity of its workforce.

Posted to the Galaxy News on 2013-09-09

September 2013 Galaxy Update

The September 2013 Galaxy Update is hot off the press:

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-08-30

GCC 2013
GCC 2013
Complete News Brief

Highlights:
  • Upgrades to Data Manager including improved installation actions

  • Visualization Framework tunings, plus updates to Phyloviz, Scatterplot, and Trackster

  • Workflows include new reproducibility controls and editing features

  • Multiple Tool Shed enhancements, features, and tunings

  • Plus additional updates to the UI, Admin and Core, and API, an important Security Fix reminder, and 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_2013.08.12

Thanks for using Galaxy,

The Galaxy Team

Posted to the Galaxy News on 2013-08-12

Take the Galaxy training survey

Help guide Galaxy's 2014 training efforts by taking the Galaxy Training Survey! Please take a few minutes to let us know what you would like to see offered, and where you would like training to be held.

Thanks,

Dave Clements
Galaxy Training and Outreach

Posted to the Galaxy News on 2013-08-05

August 2013 Galaxy Update

The August 2013 Galaxy Update is now available

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-07-31

Galaxy Proteomics Mailing List

The Galaxy community now has a mailing list dedicated to proteomics.  If you're using Galaxy to do proteomics, or if you are thinking of doing so then this list if for you.  In case you missed it, there is also a proteomics wiki page

To subscribe to the galaxy-proteomics list please add your email address to the list here:

See the complete list of mailing lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists.

Many thanks to Dave C. and the Galaxy team for setting this up.

Thanks

Ira Cooke

Posted to the Galaxy News on 2013-07-31

CloudMan

We just released an update to Galaxy CloudMan. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.

IMPORTANT - please read

Any new cluster will automatically start using this version of CloudMan. Existing clusters will be given an option to do an automatic update once the main interface page is refreshed. Note that this upgrade is a major version upgrade and thus the migration is rather complicated. The migration process has been automated but will take a little while to complete. If you have made customizations to your cluster in terms of adding file systems, upgrading the database, or similar, we do not recommend you perform the upgrade. Note that this upgrade comes with (and requires) a new AMI (ami-118bfc78), which will automatically be used when starting an instance via CloudLaunch.

This update brings a large number of updates and new features, the most prominent ones being:

  • Unification of galaxyTools and galaxyData file systems into a single galaxy filesystem. This change makes it possible to utilize the Galaxy Tool Shed when installing tools into Galaxy.

  • Added initial support for Hadoop-type workloads
  • Added initial support for cluster federation via HTCondor
  • Added a new file system service for an instance's transient storage, allowing it to be used across the cluster over NFS
  • Added a service for the Galaxy Reports webapp
  • Added optional Loggly based off-site logging support

  • Added tags to all resources utilized by CloudMan

For more details on the new features, see the the CHANGELOG and for even more details see, all 291 commit messages from 7 contributors.

Enjoy and please let us know what you think,

Enis Afgan

Posted to the Galaxy News on 2013-07-08

SlipStream Appliance - Galaxy Edition

The Galaxy Team Selects BioTeamTM as the Official Provider of Appliances to Accelerate Biomedical Research

BioTeam announced that they have formed a strategic alliance with the Galaxy Project to build and offer the SlipStream Appliance: Galaxy Edition – a high-performance, server class device pre-loaded with a fully operational Galaxy analysis platform.  This affordable appliance is designed to handle computationally intensive data analysis and, because it is a plug-and-play solution, lowers the barrier for entry into data analysis for IT-constrained researchers and laboratories.  The appliance is intended to make Galaxy more accessible by relieving some of the burdens users may experience with other methods of accessing the platform.  For example, due to the overwhelming demand, “Galaxy Main can no longer meet the community’s needs,” said James Taylor, one of the Galaxy Project founders. “Analysis needs to be decentralized, and one great way to do this is by having local Galaxy instances…Unfortunately, this presents barriers for many groups … BioTeam’s pre-built appliance eliminates all of these barriers, allowing research groups to run their own local Galaxy with minimal effort.”

The full press release can be found at www.bioteam.net.

To learn more about the SlipStream Appliance: Galaxy Edition, please visit www.bioteam.net/slipstream/galaxy-edition.

Anushka Brownley
Product Manager, BioTeam

Posted to the Galaxy News on 2013-07-01

July 2013 Galaxy Update

The July 2013 Galaxy Update is now available

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-06-30

Galaxy CiteULike Group

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

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:

#

Tag

 

#

Tag

 

#

Tag

502

methods

 

33

unknown

15

reproducibility

325

workbench

 

29

shared

9

uselocal*

49

isgalaxy

 

24

project

7

other

46

tools

 

23

howto

6

usepublic*

38

usemain*

 

18

cloud*

1

usecloud*


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

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 Training Day
GCC2013 Birds of a Feather Sessions
GCC2013

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

scatterplot
Complete News Brief

Highlights:

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

June 2013 Galaxy Update

The June 2013 Galaxy Update is now available

Highlights:

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

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:

Software Carpentry Boot Camp, 3-4 July, University of Oslo
  • 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

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 Training Day
GCC2013 Birds of a Feather Sessions
GCC2013

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

Main's Terms of Use
Main's Terms of Use

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

Your access to the Service is provided under the condition that you abide by any published quotas on data storage, job submissions, or any other limitations placed on the public Service. Attempts to subvert these limits by creating multiple accounts or through any other method may result in termination of all associated accounts.


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

May 2013 GalaxyAdmins Meetup
Pathogen Portal Galaxy

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.

Date

May 15, 2013

Time

10 am Central US Time (-5 GMT)

Presentations

Galaxy at Pathogen Portal

Andrew Warren, Virginia Bioinformatics Institute, Virginia Tech
Galaxy Project Update

Links

Meetup Link
Add to calendar


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

May 2013 Galaxy Update

The May 2013 Galaxy Update is now available

Highlights:

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

Bioinformatics

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

a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs. BioBlend makes it easy for bioinformaticians to automate end-to-end large-data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provision the required infrastructure, and automate complex analyses over large data sets within the familiar Galaxy environment.

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

University of Birmingham

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).


BGI

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.

GigaScience Journal

"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

61st ASMS Conference on Mass Spectrometry and Allied Topics

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

A security vulnerability was recently discovered that would allow a malicious person to delete the contents of a history that does not belong to them.  The vulnerability was in a method designed to allow users to switch between histories as a convenience from certain messages and is not used for most normal history switching operations.  A fix has been provided in the stable branch of the Galaxy distribution and tagged as security_2013.04.08.  Administrators are strongly encouraged to upgrade to at least the listed tag or to implement one of the provided workarounds. This changeset is not included in the most recent (April 1, 2013) stable release.

To upgrade:

   1 % hg pull
   2 % hg update security_2013.04.08

Additional details, including workarounds for those who are unable or unwilling to perform a full upgrade, can be found in the mailing list announcement.

Thanks for using Galaxy,

The Galaxy Team

Posted to the Galaxy News on 2013-04-08

GigaScience Journal

The 2013 Galaxy Community Conference (GCC2013) and BioMed Central are announcing a special thematic series in GigaScience, a new journal co-published in collaboration between BGI Shenzhen and BioMed Central focused on studies utilizing large-scale datasets and workflows. Galaxy is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. All accepted oral presentations from the meeting will be eligible for consideration in the series, and working with the scientific committee, peer review will be coordinated, thorough and timely. BGI has been generously covering the open-access article-processing charges for the journal’s launch, and this offer will be extended to all submissions from the 2013 conference. 

GCC2013

Covering the themes of the conference, discussion and research is considered highlighting best practice for local Galaxy installation, management and use, as well as interesting tools, data sources, or novel uses of Galaxy. Addressing many of the goals of Galaxy to enable more accessible, reproducible, and transparent genomic science, submissions can utilize a novel format, where all of the workflows, tools and supporting data can be hosted and integrated into accepted papers using independently citable digital object identifiers from the journal's Giga-Galaxy server and GigaDB database.

Please contact the conference organizers <gcc2013-sci@galaxyproject.org> or GigaScience editors <editorial@gigasciencejournal.com> for further information, or submit a manuscript or conference abstract, mentioning you would like to be considered in the series. The deadline for consideration for oral presentations to the meeting is 12th April, but later submissions for exceptional poster presentations (deadline 3rd May) and related work utilizing Galaxy may also be considered for the open series.

Scott Edmunds
Executive Editor
GigaScience

Posted to the Galaxy News on 2013-04-04, updated 2016-08-16

Due to a security vulnerability, administrators are strongly encouraged to upgrade to the April 8, 2013 Security Release, which is was not included in the original April 1, 2013 distribution.


Complete News Brief

tool shed
Highlights:

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 security_2013.04.08

Thanks for using Galaxy,

The Galaxy Team

Posted to the Galaxy News on 2013-04-02

Galaxy Linked In Group

A Galaxy Group now exists on LinkedIn.  The group is open to anyone and is a forum to post announcements, discussions, and jobs of interest to the Galaxy community.

Note that this is not an official support forum for the Galaxy Project.  Please continue to use the mailing lists for that purpose.

If you are on LinkedIn, please consider joining the group today.

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-03-18

March 2013 GalaxyAdmins Meetup

The next meeting of the GalaxyAdmins Group will be held on March 20, 2013, at 10 AM Central US time.

NBIC Galaxy (Andromeda) was migrated to a HPC cloud hosted by Surfsara in September 2012. In this presentation, we will present the setup of this HPC cloud and the architecture of our NBIC Galaxy. We will also share our experience on the installation of the NBIC Galaxy using the CloudMan scripts. The presentation will finish with a list of issues and our possible future plans.

Date

March 20, 2013

Time

10 am Central US Time (-5 GMT)

Presentation

NBIC Galaxy at SURFsara's HPC cloud  

Presenters

Hailiang "Leon" Mei <hailiang DOT mei AT nbic DOT nl>
There will also be a Galaxy Project Update from Dan Blankenberg of the Galaxy Team

Links

Join Meetup, Meetup Invite


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.

Srinivas Maddhi

Posted to the Galaxy News on 2013-03-12

The Galaxy Public Main Galaxy Server at http://main.g2.bx.psu.edu (usegalaxy.org) and Test Galaxy Server at http://test.g2.bx.psu.edu will be down on Thursday, March 14, while the team relocates core hardware to a new server room.

Rerun a job

Please note that ALL jobs running at the time of the shutdown will be terminated. Once the move is complete, any terminated jobs can be easily restarted using the "re-run" function. 

The yellow banner on Main and Test will provide updates (when the servers are up) as well our galaxyproject Twitter posts.

Galaxy's Tool Shed, GalaxyProject.org Wiki, and Mailing list services will be unaffected during this time. 

Thanks for using Galaxy!!

Galaxy Team

Posted to the Galaxy News on 2013-03-07

March 2013 Galaxy Update

The March 2013 Galaxy Update is now available

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-03-01

2013 Galaxy Community Conference (GCC2013)

We are pleased to announce that early registration and paper and poster abstract submission are now open for the 2013 Galaxy Community Conference (GCC2013).  GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo.

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Day for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics.

If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending.  GCC2013 is aimed at:

2013 Galaxy Community Conference (GCC2013) Training Day
  • Bioinformatics tool developers and data providers
  • Workflow developers and power bioinformatics users
  • Sequencing and Bioinformatics core staff
  • Data archival and analysis reproducibility specialists

Early registration is now open. Register early and save up to 75% off regular registration costs.  Early registration is very 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 session becomes full, it will be closed to new registrations.  Early registration closes 24 May. 

Abstract submission for both oral presentations and posters is also open.  Abstract submission for oral presentations closes 12 April, and poster abstract submission closes 3 May.  Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.

Thanks, and hope to see you in Oslo!

The GCC2013 Organizing Committee

PS: And please help us get the word out!

Posted to the Galaxy News on 2013-02-23

GMOD Project

There are a couple of things going on with the GMOD Project that the Galaxy Community might be interested in. If you aren't familiar with GMOD, it is a federation of open-source projects and tools  that enable visualizing, annotating, managing, and analyzing biological research data.  GMOD includes Galaxy and several other widely used tools such as BioMart, InterMine, MAKER, Chado and GBrowse and JBrowse.

The first is that GMOD is running a community-wide survey through March 1. The survey "aims to find out how you are using GMOD, what you find useful (or otherwise), what support you need, and some information on the GMOD components you use."  The survey results will be published and past surveys have been extremely useful to the project.  If that's not enough motivation, once you are done with the survey, you can enter to win a free genome profile from 23andMe.

GMOD 2013

The second is that registration is now open for the 2013 GMOD Meeting being held in Cambridge, UK, April 5 and 6.  There will be a Galaxy presence (at least a project update, and I'm lobbying for a CloudMan workshop as well (and you could lobby too! <help AT gmod DOT org>)).

Finally, Biocuration 2013 is immediately after the GMOD Meeting, and also in Cambridge.  Biocuration will feature a GO Galaxy Workshop about using Galaxy to reason with ontologies.

Dave Clements

Posted to the Galaxy News on 2013-02-19

Complete News Brief

width="200px"
Highlights:
  • Improvements to our release process. Release tag must be used in the hg update command to upgrade. More at usegalaxy.org.

  • Tool Shed Complex repository dependencies are introduced, streamlining core dependency use across individual tools.

  • Also updated in the Tool Shed: multiple repository installation, dependency installation (when defined - see graphic on right for an example), and many usability enhancements and fixes.
  • New Bedgraph-to-bigwig tool plus Filter tool updated.

  • Workflows now include option to export an image and the core Framework now allows more unified reference genome usage and access.

  • Ten Community Pull-Requests incorporated, plus another contribution to the tool Shed, addressing general usability, API, tools, error handling, workflows, and more. Thanks!!

  • Review highlights from the latest monthly Galaxy Update newsletter and Galaxy Project Stats!

  • Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools.

http://getgalaxy.org

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

http://galaxy-dist.readthedocs.org

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

upgrade: $ hg pull 
         $ hg update release_2013.02.08

To receive email updates about Galaxy Distributions and News Briefs, be sure to subscribe to the Galaxy-Announce mailing list, a low-volume list dedicated to News Items and priority messages from the Galaxy community and project core team.

Thanks for using Galaxy,

The Galaxy Team

Posted to the Galaxy News on 2013-02-09

February 2013 Galaxy Update

The February 2013 Galaxy Update is now available

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-02-01

2013 Galaxy Community Conference (GCC2013) Training Day
2013 Galaxy Community Conference (GCC2013)

A list of possible topics for the GCC2013 Training Day is now available.  Please take a few minutes to review these possibilities and then vote for your favorite three topics.*

Your votes will determine not only the topics that are offered, but also which topics should be offered more than once, assigned to which rooms, and which ones should not be scheduled at the same time.  Your vote matters.  

Once voting closes on 11 February, we will contact possible instructors and publish a Training Day schedule before registration opens on 22 February.


About the GCC2013 Training Day:

The 2013 Galaxy Community Conference (GCC2013) will start on 30 June with a Training Day featuring 4 parallel tracks, each with three workshops, each of which are two hours long, for a total of twelve sessions. There will be at least one complete track (3 consecutive workshops) about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances.

As always, please let us know if you have any questions.

Thanks,

The GCC2013 Organizing Committee

*

You don't have to vote for exactly three topics. You can vote for fewer topics and have each vote count for more, or you can vote for more topics and have each vote count for less.

Posted to the Galaxy News on 2013-01-28

Galaxy is Hiring

The Galaxy Project is expanding and we are looking for highly-motivated, seeking-a-challenge, computationally-savvy, biologically-aware software engineers and post-docs to work on Galaxy. See the GalaxyIsHiring page for details.

Galaxy a great project with a great community. If you or someone you know would be interested in working with this thriving community on a rapidly evolving high performance platform that is used by thousands of researchers around the world every day, then please consider joining the Galaxy team.

As always, please let me, or any of us, know if you have any questions.

Dave Clements

Posted to the Galaxy News on 2013-01-25

Complete News Brief

width=200
Highlights:

http://getgalaxy.org

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

http://galaxy-dist.readthedocs.org

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r a4113cc1cb5e

Thanks for using Galaxy,

The Galaxy Team

Posted to the Galaxy News on 2013-01-11

January 2013 GalaxyAdmins Meetup

The next meeting of the GalaxyAdmins Group will be held on January 16, 2013, at 10 AM Central US time.

John Chilton of the Minnesota Supercomputing Institute will cover "Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan"

Date

January 16, 2013

Time

10 am Central US Time (-6 GMT)

Presentation

Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan

Presenter

John Chilton of the Minnesota Supercomputing Institute

Links

Presentation @ Prezi.com
Related Technical Documentation @ ReadTheDocs.org
Meetup


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.

Srinivas Maddhi

Posted to the Galaxy News on 2013-01-07

January 2013 Galaxy Update

The January 2013 Galaxy Update is now available.

Highlights:

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

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2013-01-02