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News/Archive/2015

2015 News Item Archive

This page shows older news items that were posted to the Galaxy News page/feed in 2015.

See also 

 

2016 Galaxy Community Conference

We are pleased to announce that the 2016 Galaxy Community Conference website is now online and includes registration information and the full training schedule.

GCC2016 will be held June 25-29 at Indiana University in Bloomington, Indiana, United States. This will be the 7th annual gathering of the Galaxy community, and we are expecting over 200 participants again this year.

Registration information includes the different registration packages, rates, and deadlines. Our inexpensive early registration rates start at less than $40 per day for students and post-docs.

Registration will open within a month.

The training schedule includes session descriptions, prerequisites, and instructors. Many thanks to everyone who nominated and voted on topics, and especially to the many instructors who are contributing their time and effort to make GCC2016 a success.

Indiana University Pervasive Technology Institute (PTI)

Thanks also go to the Indiana University Pervasive Technology Institute (PTI), who are supporting GCC2016 as a Platinum Sponsor. PTI is home to the National Center for Genome Analysis Support (for which NSF funding was recently renewed), and the Galaxy Trinity instance, and is a long time supporter of the Galaxy Community. PTI pairs fundamental academic computational research with the widely known strengths of Indiana University through innovations and service delivery in networking and high performance computing. See the PTI website for more information.

We continue to seek other sponsors as well and offer a wide range of sponsorship plans. If your organization is interested in having a presence at GCC2016, please contact the GCC2016 Exec <gcc2016-exec@lists.galaxyproject.org> for more information.

The GCC2016 Exec <gcc2016-exec@lists.galaxyproject.org>

Posted to the Galaxy News on 2015-12-18

Software Engineering Position at Oregon Health and Science University. People interested in Galaxy and large scale workflow deployment are encouraged to apply. The Computational Biology Program at Oregon Health and Science University (OHSU), Portland, Oregon is committed to leading the development of next-generation patient care through discoveries made by big data analytics, enabled by values of open access data, open source code, highly collaborative team science, and professional software engineering methodologies.

Go to the OHSU jobs site and search for IRC50157

About OHSU

OHSU

OHSU is ranked as one of the nation’s top biomedical institutions in patient care, research, and education, with an annual operating budget of over $2.3 billion, over $340 million in annual grant funding, over 4,000 students and trainees, and nearly 1 million patient visits per year. Multiple departments rank among the top 5 in annual grant funding, including neuroscience, microbiology, ophthalmology, otolaryngology, and emergency medicine. OHSU is one of the nation’s fastest growing biomedical institutions, bolstered by long-term resource commitments, such as the $1 billion Phil and Penny Knight “challenge” to support research in OHSU’s Knight Cancer Institute, led by Dr. Brian Druker, who pioneered the concept of gene targeted therapy by demonstrating the efficacy of the revolutionary cancer drug Gleevec in chronic myelogenous leukemia. OHSU provides substantial resources to enable data intensive science, including a world-class exascale supercomputing cluster, close interactions and resource commitments by leading technology companies such as Intel, tight integration with clinical and basic research programs across campus, graduate training programs in quantitative biosciences, biostatistics, biomedical informatics, bioinformatics and computational biology, and substantial long-term resource commitments, including the $1 billion Phil and Penny Knight "challenge" to support cancer research, with a significant focus on computation.

Posted to the Galaxy News on 2015-11-10

GCC2016 Training

   Vote now!   

Voting is now open on what training topics are offered at GCC2016 Training.

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.

Topic voting closes November 6. The Training schedule, including instructors, will be published before early registration opens.

About GCC2016 Training:

The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29 at Indiana University in Bloomington, Indiana, United States. GCC2016 features two full days of training on June 26-27. Each day will have multiple tracks, with each track featuring several sessions throughout the day.

Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along.

If you work in data-intensive biomedical research, there is no better place than GCC2016 to present your work and to learn from others.

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

Thanks,

The GCC2016 Exec

Posted to the Galaxy News on 2015-10-26

GalaxyProject

October 2015 Galaxy Release Notes Release Notes v 15.10

Release Highlights

  • Reports Application- The reports web application has been greatly enhanced - including improved styling, new landing page, more reports, pagination, and sparklines. Huge thanks to Daniel Bouchard (@Airistotal) for these enhancements.

  • Upload - The Galaxy upload widget now features support for composite datatypes and improved styling.

  • Data Libraries - Improved API and UI for data libraries - including support for library folder management and search.

About

Thanks for using Galaxy!
The Galaxy Team

Posted to the Galaxy News on 2016-01-13

https://github.com/galaxyproject/tools-iuc/issues/239

The Intergalactic Utilities Commission organised it's first online Codefest with the aim to make more tools collection aware.

The IUC was available for two days in a Hangout to answers questions and to work together with the Galaxy community to enhance our tools and the overall Galaxy ecosystem. Scientists from three different continents participated in this and made it a very nice experience and a success story, which the IUC would like to repeat more often.

A list of all awesome contributions from all participants is given below.

Tools:

Peter Van Heusden (@pvanheus) wrote a nice summary about his experience during the IUC Codefest and data collections in his blog titled "Adventures in Galaxy output collections".

We hope you all will enjoy the outcome of this Codefest and hope to see you at our next Codefest, stay tuned.

Your IUC

Posted to the Galaxy News on 2015-09-29

GCC2016 Training

The 2016 Galaxy Community Conference (GCC2016) features two full days of training on June 26-27. Each day will have multiple tracks, with each track featuring several sessions throughout the day. GCC2016 will be held at Indiana University in Bloomington, Indiana, United States.

GCC2016 Training topics are nominated by you, the Galaxy Community. Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations. 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 as they come in. Topic nomination closes Friday, October, 16.. Topics will be compiled into a uniform list by the GCC2016 Organizing Committee, and topics will be voted on by the Galaxy Community from October 26 through November 6.

Topics will then be selected and scheduled based on topic interest, and the organisers' 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.

GCC2016 Exec Committee

Posted to the Galaxy News on 2015-09-28

GCC2011  

2012 Galaxy Community Conference   

GCC2014, June 30-July2   

2013 Galaxy Community Conference (GCC2013)   

2015 Galaxy Community Conference (GCC2015)

2016 Galaxy Community Conference (GCC2016)

GCC2017 needs a host!
(and a logo)
(and we found both!)


Hello all,

The Galaxy Community Conference has been held annually since 2010. GCC2016 will be held June 25-29 at Indiana University in Bloomington, Indiana, United States.

We are now seeking proposals from organizations interested in hosting GCC2017.

Galaxy's informal policy of rotating between North America and elsewhere every other year is now a formal policy: Hosts for GCC2017 need to be located outside of North America.

GCC draws 200+ participants from data-intensive life science research. Participants come from around the world, from all career stages, and do research spanning the tree of life. Universities, hospitals and medical schools, research organizations, and industry are all represented, including some of the largest and most influential research organizations in the world.

What do you need to host GCC2017, you ask? In approximately decreasing order of importance:

  • Enthusiasm to plan and organize several events over 5 days for more than 200 people.

  • Space for 4-6 parallel training sessions over two full days, with each space able to accommodate 25 to 75 participants.
  • Central meeting space with capacity for 250-300 people.
  • Affordability (or access to sponsorship funds; there's a reason we've always held GCC in academic settings)
  • Nearby space for breakouts, poster sessions and sponsors.
  • Nearby space for lunch, coffee breaks.
  • Good wifi for all events (that's 200+ people and their devices).
  • Space for hackathons for 2 days before the event.
  • Easy to get to by air.
  • Nearby, affordable housing, or easy walking distance or easy public transport from lodging options to conference facilities
  • Close proximity to a pub and other social hubs.

Hosts get copious (and enthusiastic) organizational support from Galaxy's Outreach Team (who have been helping to organize GCC since 2011), and even more copious gratitude (even adulation!) from the Galaxy Community.

See the full call for host proposals for more details on what should be covered in proposals. Proposals are due by the end of 30 October 30 November 2015. If you are interested in possibly hosting GCC2017 then please contact Galaxy Outreach <outreach@galaxyproject.org> with any questions. Our goal is to announce GCC2017 at GCC2016 this coming June.

Hoping to work with you in 2017!

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2015-09-14, updated 2015-09-17, updated 2016-07-15

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 or imposed quotas. Once running, you have complete control over Galaxy, including the ability to install new tools.

This is the most complete update of the Galaxy on the Cloud platform to date with all the cloud components being built from the ground up. The following is a summary of the major changes:

See the CHANGELOG for a more complete set of changes or just give it a try: see the all new Getting Started documentation.

Posted to the Galaxy News on 2015-09-03

GalaxyProject

The July 2015 Galaxy Release is out! Release Notes v 15.07

Release Highlights

  • Interactive Environments - The interactive environments (IE) framework features several updates this release and Galaxy is now distributed with a new IE for RStudio implemented by Eric Rasche.

  • Workflow Editor Enhancements - The workflow editor has been significantly revamped - it now uses newer tool form components and allow construction of workflows with tools explicitly producing output collections.

  • Policies for Committers and Pull Requests - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - Björn Grüning, Nicola Soranzo, and Eric Rasche.

  • And much more

Thanks for using Galaxy!
The Galaxy Team

If you want to know what events are happening in the Galaxy Community, the goto place has always been the Galaxy Events page. This lists any upcoming events we know about that feature Galaxy content. This events list provides dates, locations, and contact information for each event.

Galaxy Calendar

There has also been the complementary Galaxy Events Google Calendar which listed events of interest to the community, whether or not they featured significant Galaxy content. To make this calendar more useful, we have split it in to two:

This split allows us to present Galaxy events in a much sparser calendar, that is more useful for setting reminders and publishing Galaxy events.

And we will continue to link to past Galaxy events (and presentations, videos, examples, ...) from the Events Archive.

Dave Clements

Posted to the Galaxy News on 2015-08-20

Two security vulnerabilities were recently discovered in Galaxy, and a third in the Galaxy Tool Shed. Because of this, the Galaxy Committers have released a number of fixes which have been rolled in to affected versions of Galaxy dating back to the 14.10 release.

Galaxy XSS Reflection Vulnerability

This vulnerability, affecting all known versions of Galaxy, would allow a malicious actor to exploit the workflow import form to cause a user's browser to execute javascript not originating from within Galaxy. This could allow the malicious actor to gain unauthorized access to Galaxy accounts or client data.

Exploitation of reflected XSS vulnerabilities typically requires some coordination, but the consequences of exploitation can result in data or account exposure, so the risk of leaving the issue unfixed is moderate. Administrators of affected servers are encouraged to update immediately.

See the announcement for full details and update instructions

Galaxy LDAP Authentication Vulnerability

This vulnerability would allow unauthorized access to Galaxy accounts only on Galaxy servers using the new (as of 15.05) LDAP authentication framework plugin. This is due to the fact that LDAP may be configured to allow anonymous binds, and the LDAP plugin does not check that binding with the provided username/password was not anonymous.

Administrators of affected servers are STRONGLY encouraged to update immediately, as the vulnerability allows unauthorized access to Galaxy accounts.

See the announcement for full details and update instructions

Tool Shed Unauthorized Upload Vulnerability

This vulnerability would allow a malicious actor to upload new versions to repositories on which they have not been granted access.

Because the Tool Shed is used to install software in Galaxy, if exploited, the impact could result in arbitrary code execution on Galaxy servers if a malicious tool is uploaded to a previously trusted repository, and that compromised version is subsequently installed by a Galaxy administrator. As such, Tool Shed administrators are strongly encouraged to update immediately.

See the announcement for full details and update instructions

Posted to the Galaxy News on 2015-08-13

Galaxy at CiteULike Social Bookmarking Service

The Galaxy CiteULike library recently reached a milestone: It now has over 2500 publications in it. The Galaxy CiteULike Group was launched in December 2011 and reached 1000 papers 18 months later.

To be included in the library a publication needs to reference or mention Galaxy, extend Galaxy, use or reference a Galaxy instance, or otherwise discuss Galaxy or cite one of the Galaxy Project papers.

Here's a review of those first 2500 papers.

The Tags

Each paper is reviewed and one or more tags are added to it. The initial set featured 9 tags. This wasn't quite enough, and 8 more were added in 2013, bringing the total to 17. (Papers from 2012 were back-curated with the new tags, but not before that.) The numbers for each tag in each year for the first 2500 papers are below.

Tag

2005

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

#

methods

2

15

26

50

92

196

260

325

258

1224

workbench

1

3

7

11

18

36

68

127

151

205

121

748

usemain

1

1

3

89

95

64

253

tools

3

1

8

28

36

67

37

180

usepublic

1

15

57

77

150

isgalaxy

2

2

5

16

15

26

45

24

135

cloud

1

2

13

22

38

24

100

uselocal

2

28

41

27

98

shared

1

1

7

13

21

24

17

84

other

1

1

8

8

38

21

77

refpublic

10

28

26

64

reproducibility

6

7

8

24

12

57

unknown

2

5

7

3

10

13

8

5

53

project

1

2

1

5

6

10

6

7

9

47

howto

1

2

1

3

4

12

6

11

5

45

visualization

1

1

2

3

6

3

16

usecloud

2

1

1

4


A couple of trends stand out in the tag data:

  • methods and workbench have always been the most popular. methods papers use Galaxy in their analysis. workbench either just mention Galaxy or discuss the platform itself.

  • The numbers of usepublic and refpublic publications are climbing rapidly. Respectively, these are methods studies that did their analyses on a public Galaxy server other than usegalaxy.org, and papers that reference those servers in some way (besides their methodology). Part of this increase reflects better tracking of these papers, but (I believe) most of the increase reflects both the increased number of public servers (as reflected by the isgalaxy numbers), and their increased visibility.

  • reproducibility became a hot topic (finally) in 2014.


The Journals

Information on where the papers appeared is also available. Galaxy-related papers have appeared in over 500 different publications. Publications with 15 or more Galaxy papers are:

Journal

2005

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

Total

Plos One

0

0

0

1

1

4

16

32

42

45

27

168

Nucleic Acids Research

0

1

0

1

11

13

8

21

22

29

19

125

Bmc Genomics

0

0

0

0

2

4

12

22

27

42

15

124

Bioinformatics

0

0

0

5

4

7

23

19

19

30

10

117

Bmc Bioinformatics

0

0

1

0

2

10

15

16

8

25

6

83

Genome Research

1

2

4

3

5

2

9

12

2

8

3

51

Genome Biology

0

0

0

1

3

9

11

11

4

6

2

47

Plos Genet

0

0

0

2

0

1

6

10

15

6

4

44

Briefings in Bioinformatics

0

0

0

1

1

1

3

2

8

4

9

29

Genome Announcements

0

0

0

0

0

0

0

0

4

3

19

26

Concurrency and Computation: Practice and Experience

0

0

0

0

0

0

1

3

0

11

10

25

Proceedings of the National Academy of Sciences

0

0

0

1

1

0

2

3

4

8

4

23

Cell

0

0

0

0

0

1

1

5

8

3

5

23

Plos Comput Biol

0

0

2

1

0

2

3

3

5

5

2

23

Molecular Biology and Evolution

0

0

0

0

3

0

1

1

9

2

4

20

Nature Communications

0

0

0

0

0

0

0

2

4

7

7

20

Molecular Ecology

0

0

0

0

0

1

1

1

11

4

0

18

Database

0

0

0

0

0

1

6

2

4

3

1

17

Genome Biology and Evolution

0

0

0

0

0

1

3

2

3

5

2

16

Nature

1

0

0

0

1

3

1

0

4

2

3

15

Cell Reports

0

0

0

0

0

0

0

3

5

4

3

15


There are also many unexpected publications in the list:

  • Applied Stochastic Models in Business and Industry

  • Computers & Geosciences

  • Current Opinion in Solid State & Materials Science

  • Journal of Archaeological Science

  • ...

The Summary

Finally, the total number of papers per year continues to increase, and we expect 2015 to surpass 800 papers

2005

2006

2007

2008

2009

2010

2011

2012

2013

2014

2015

Total

Total

2

4

12

31

53

107

202

394

495

703

497

2500


We will continue to report new papers in the monthly Galaxy newsletters. New tags may also show up as the project and community evolve.

In the meantime, I expect the next 2500 papers will be published in considerably less than time than the first 2500. I'm looking forward to all that research

Dave Clements

Posted to the Galaxy News on 2015-08-12

Hello all,

We are planning a remote hackathon for Galaxy tool developers to hack on dataset collections. Dataset collections enable MapReduce style workflows in Galaxy and have come a long way over the last year+. Several groups are using dataset collections and newer tools to express workflows of various degrees of complexity that were not possible in Galaxy before.

The remote nature of this should give people who don't have the opportunity to come to GCC hackathons (which have always been productive and a lot of fun) a chance to participate in a Galaxy hackathon. Hopefully having a well defined topic will allow us to accomplish a lot and let people who don't have particular tasks in mind find something to work on very quickly.

We have been collecting ideas to work on here - https://github.com/galaxyproject/tools-iuc/issues/239, but we expect to attract the most participation by simply getting tool developers interested in getting help adding collection support to their existing tools and workflows to show up and participate.

If you are interested in participating in the hackathon but not interested in actual tool development - we will assemble a list of smaller, manageable Python and JavaScript tasks to work on and certainly documentation is a chronically lacking for collections so we could use help there and no actual coding would be required.

This is the first remote hackathon we have organized and we encourage ideas or advice about how to organize it please let us know. We are currently thinking a two day event in which a core group of us would be available on IRC all day and we would have 4 google hangouts across those days to organize, answer questions, and report progress. We are also currently thinking September 17th and 18th.

Thanks,
Galaxy IUC

Posted to the Galaxy News on 2015-08-10

GalaxyProject

The May 2015 Galaxy Release is out! Release Notes v 15.05

Release Highlights

  • Authentication Plugins - Galaxy now has native support for LDAP and Active Directory via a new community developed authentication plugin system.

  • Tool Sections - Tool parameters may now be groupped into collapsable sections.

  • Collection Creators - New widgets have been added that allow much more flexibility when creating simple dataset pair and list collections.

  • And much more

The release notes have a new home at Read the Docs. We hope that you like the new format as much as we do!

Thanks for using Galaxy!
The Galaxy Team

Posted to the Galaxy News on 2015-05-14

Galaxy Data Wrangling Hackathon @ GCC2015

Love Galaxy?

We are inviting Galaxy power end-users as well as scientists and bioinformatics support researchers to join us for the inaugural Galaxy Data Wrangling Hackathon preceding the 2015 Galaxy Community Conference this July.

Questions, Feedback, or Hack idea? Post here or contact the Data Hack Organizers <gcc2015-data-org@lists.galaxyproject.org>.

Jennifer Hillman Jackson and the Data Wrangling Hackathon Organising Committee

Posted to the Galaxy News on 2015-05-08

GCC2015 Registration is open

We are tremendously pleased (and more than a little relieved) to announce that registration for GCC2015 is now open. The 2015 Galaxy Community Conference includes 2 days of hackathons, 2 days of training, and a two day meeting featuring accepted presentations, keynotes, poster sessions, lightning talks, birds-of-a-feather meetups, and plenty of networking. GCC2015 is hosted by The Sainsbury Laboratory, in Norwich, UK, and events run 4-8 July.

Registration costs depend on which events you register for, your career stage/affiliation, and when you register (register by 22 May - really, it will save you plenty). Early bird registration starts at less than £40 / day for students and postdocs, and at £55 / day for other attendees from non-profits.

You can also sign up for conference housing during (and only during) registration.

We apologize profusely for the delay in opening registration, and we thank you for your patience and faith. We promise the conference will again be spectacular.

Dave Clements and Martin Page, on behalf of the GCC2015 Organising Committee.

PS: And don't forget the poster abstract submission deadline is 1 May.

Posted to the Galaxy News on 2015-04-27

GCC2015 registration and lodging scholarships for US-based students and post-docs who and members of historically underrepresented groups

We are pleased to offer registration and lodging scholarships for GCC2015 for students and post-docs who are based in the United States, and who are members of historically underrepresented groups in life science research.

These scholarships cover registration costs for any GCC2015 events the recipients sign up for, and also covers lodging during those events in the official conference lodging on the nearby UEA campus. The scholarships do not cover travel or other expenses.

To apply for a scholarship qualifying applicants need to

  1. Submit a poster abstract. The deadline is May 1

  2. Have a faculty member / PI send a letter of recommendation to the Galaxy Community Fund Board <community-fund@lists.galaxyproject.org> no later than May 15.

  3. Submit an application form, no later than May 1.

  4. Have sufficient funds to cover your travel and other expenses.

Applicants will be notified of their scholarship status no later than May 19.

Scholarships are funded by the Galaxy Community Fund. The Galaxy Community Fund was established with the surplus funds from GCC2014, and is currently administered by the GCC2014 organizers.

Please do let us know if you have any questions, and we hope to see you at GCC2015!

Galaxy Community Fund Board <community-fund@lists.galaxyproject.org>

Posted to the Galaxy News on 2015-04-21

IFB
MetaboHub

The Worflow4Metabolomics 2015 course (W4M course 2015) will take place at the ABiMS bioinformatics institute (Roscoff, France) on Sept. 21st-25th 2015. This one-week training session is intended for MS and NMR experimenters wishing to learn the functionalities from the W4M resource. It will include an initiation to the Galaxy environment, followed by dedicated practical sessions covering the available modules for data preprocessing, statistical analysis, and annotation. Finally, a tutoring part will enable each participant to analyse its own dataset. Presentations will be given in French but course materials will be in English.Pre-registration deadline: May 8th 2015.

Christophe Caron

Posted to the Galaxy News on 2015-04-08

Hello all,

The 2015 Galaxy Community Conference (GCC2015) is being held in early July at The Sainsbury Lab in Norwich, United Kingdom. It turns out that there are several other events going on nearby in the days before and after GCC2015. Here's a list of what we know about, in case you want to extend your trip.

Sunday

Monday

Tuesday

Wednesday

Thursday

Friday

Saturday

28 June

29 June

30 June

1 July

2 July

3 July

4 July

Exploring Human Host-Microbiome Interactions in Health and Disease
Wellcome Trust, Hinxton, UK, Abstract and Bursary Deadline: 8 May; Registration Deadline: 29 May

iPlant Tools & Services Workshop
The Genome Analysis Centre (TGAC), Norwich, UK, Regis. Deadline: 29 May

GCC2015
The Sainsbury Lab, Norwich, UK
Coding & Data Wrangling Hackathons
TGAC

Exploring Plant Variation Data
EBI, Hinxton, UK, Application Deadline 19 April

BioJS Conference 2015
Norwich, UK

BioJS Hackathon
Norwich, UK

5 July

6 July

7 July

8 July

9 July

10 July

11 July

GCC2015
The Sainsbury Lab, Norwich, UK

ISMB/ECCB 2015
Dublin, Ireland, Early Registration Deadline: 5 June
The Bioinformatics Open Source Conference (BOSC 2015)
BioVis 2015

Coding & Data Wrangling Hackathons
TGAC

GCC Training Day
JICCC

GCC2015 Meeting
JICCC

GCC Training SunDay
JICCC

OpenBio Codefest 2015
Dublin, Ireland

Human Genome Analysis: Genetic Analysis of Multifactorial Diseases

12 July

13 July

14 July

15 July

16 July

17 July

18 July

ISMB/ECCB 2015
Dublin, Ireland

Human Genome Analysis: Genetic Analysis of Multifactorial Diseases
Wellcome Trust, Hinxton, UK, Application Deadline: 10 April


Norwich, UK

Hinxton, UK

Dublin, Ireland

Posted to the Galaxy News on 2015-04-08, updated 2015-05-31

Two PhD positions in bioinformatics and in biostatistics are available in Oslo (Norway) on graph-based representations of genomes, and in particular on developing methodology and software for analyzing various kinds of biological data represented on such graphs. Graphs can represent variation between individuals and thus allows a better representation of the full hereditary material of a species (or several related species). Extending the Galaxy system with functionality to allow users to construct, share and perform analyses on graph representations could make such enhanced representations available to a broad audience.

The positions are embedded within the HyperBrowser environment, which includes seven researchers and programmers working primarily on the development of genome analysis functionality, as well as around thirty more loosely coupled collaborators. For more on the HyperBrowser, check out an overview paper of previous developments, or try out our public server. The positions are also associated with a strategic research initiative that involves a group of biologists that among more have sequenced the Atlantic cod. The salary is good and there are good future career opportunities. Further details on the positions and how to apply are available in the full announcements.

Geir Kjetil Sandve

width="200"

Posted to the Galaxy News on 2015-03-30

CloudMan

BioBlend v0.5.3 has been released. BioBlend is a python library for interacting with CloudMan and the Galaxy API. (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.)

This is mostly an incremental bug fix release with the following summary of changes:

  • Project source moved to new URL - https://github.com/galaxyproject/bioblend

  • Huge improvements to automated testing, tests now run against Galaxy release_14.02 and all later versions to ensure backward compatibility (see travis.yml for details).

  • Many documentation improvements (thanks to Eric Rasche).

  • Add Galaxy clients for the tool data tables, the roles, and library folders (thanks to Anthony Bretaudeau).
  • Add method to get the standard error and standard output for the job corresponding to a Galaxy dataset (thanks to Anthony Bretaudeau).
  • Add get_state() method to JobsClient.

  • Add copy_from_dataset() method to LibraryClient.

  • Add create_repository() method to ToolShedClient (thanks to Eric Rasche).

  • Fix DatasetClient.download_dataset() for certain proxied Galaxy deployments.

  • Make LibraryClient._get_root_folder_id() method safer and faster for Galaxy release_13.06 and later.

  • Deprecate and ignore invalid deleted parameter to WorkflowClient.get_workflows().

  • CloudMan: Add method to fetch instance types.

  • CloudMan: Update cluster options to reflect change to SLURM.

  • BioBlend.objects: Deprecate and ignore invalid deleted parameter to ObjWorkflowClient.list().

  • BioBlend.objects: Add paste_content() method to History objects.

  • BioBlend.objects: Add copy_from_dataset() method and root_folder property to Library objects.

  • BioBlend.objects: Add container and deleted attributes to Folder objects.

  • BioBlend.objects: Set the parent attribute of a Folder object to its parent folder object (thanks to John M. Eppley).

  • BioBlend.objects: Add deleted parameter to list() method of libraries and histories.

  • BioBlend.objects: Add state and state_details attributes to History objects (thanks to Gianmauro Cuccuru).

  • BioBlend.objects: Rename upload_dataset() method to upload_file() for History objects.

  • BioBlend.objects: Rename input_ids and output_ids attributes of Workflow objects to source_ids and sink_ids respectively.

  • Add run_bioblend_tests.sh script (useful for Continuous Integration testing).

Enjoy and please let us know what you think,

Enis & John & Nicola Soranzo & Simone Leo & Eric Rasche

Posted to the Galaxy News on 2015-03-19

width=175

Complete Release Notes

Highlights

  • Release Versioning

    • Starting with this distribution, an updated Galaxy release versioning system has been implemented. The versioning scheme is Ubuntu-style.

    Github

    • Galaxy development has moved to Github, but stable/release changes are mirrored to Bitbucket. Deployers can continue to use Bitbucket as they have done in the past. Release branches discussed in the full release notes.

    Tool Redesign

    • Much of Galaxy’s core tool set has been redesigned. Several contain new functionality. These tools are included in the Tool Shed and many are ready for use on Galaxy Main.

Get the Galaxy Release

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_15.03



Thanks for using Galaxy!
The Galaxy Team

Posted to the Galaxy News on 2015-03-16

Galaxy Training Network Global Organisation for Bioinformatics Learning, Education & Training (GOBLET)

We are delighted to announce that the Galaxy Training Network (GTN) has officially joined the Global Organisation for Bioinformatics & Training (GOBLET).

GTN is a network of people and groups that present Galaxy and Galaxy-based training around the world. GOBLET provides "a global, sustainable support and networking structure for bioinformatics educators/trainers and students/trainees (including a training portal for sharing materials, tools, tips and techniques; guidelines and best practice documents; facilities to help train the trainers; and offering different learning pathways for different types of learner)."

GTN's GOBLET membership will raise the visibility of Galaxy, Galaxy training, and Galaxy Trainers in the bioinformatics community, and help make the Galaxy Community aware of what GOBLET and its members have to offer.

This membership was made possible by a unique arrangement where these five GTN members each contributed 20% of the cost of a Bronze Organizational Membership:

Many thanks to these GTN members for making this happen, and to the GOBLET Executive for this opportunity.

Dave Clements, on behalf of the Galaxy Training Network

Posted to the Galaxy News on 2015-03-09

The March 2015 News

As always, it's a busy time in the Galaxy. The March 2015 Galaxy News is out, and it's chock full of information. Here are some of the highlights.

UseGalaxy.org Update:

A refresh of UseGalaxy.org is underway. Find out what's changing in a new screencast.

2015 Galaxy Community Conference (GCC2015)

Sponsor GCC2015

The event schedule for GCC2015 has been released, and it features a few new events as well as all of the familiar ones:

In addition, the workshop schedules for the new Training SunDay, and the returning Training Day have been finalised. A record 15 topics will be covered in 18 sessions over two days of training. 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.

Abstract submission for oral and poster presentations is now open. We again have an arrangement with GigaScience that 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).

Finally, registration is not open yet, but the list of registration packages and their costs have been. Early registration is very affordable and starts at less than £40 per day for students and postdocs.

Other Events

And there is no shortage of other upcoming events either, including RNA-Seq and ChIP-Seq Analysis with Galaxy, UC Davis, March 23-26, and at least 12 other events in the next 2 months.

Lots of other news

In addition, there is news on:

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2015-03-02

The University Center for Information Technology (USIT) at the University of Oslo has an opening for a developer / bioinformatician (announcement: Norwegian, English).

The position includes the development and management of services aimed at life science, with particular focus on bioinformatics and our research portals that offer supercomputing via a simpler user interface. The position will maintain and implement solutions on a local Galaxy server. The position is permanent, and group communication is in English.

Applications close 12 March.

Nikolay Vazov

Opening for a developer / bioinformatician

Posted to the Galaxy News on 2015-03-02

GCC2015 Oral and Poster Presentation abstract submission is now open

We are pleased to announce that 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.

About GCC2015

GCC2015 is hosted by The Sainsbury Lab, in Norwich, United Kingdom, in July 2015. GCC has been expanded this year and will now offer two hackathons, two Training Days, and a two day conference. The Training Days cover 15 different topics spanning the full Galactic spectrum of topics. Take a look.

GCC2015 Organising Committee

Posted to the Galaxy News on 2015-02-25

Workshop
RBI, Zagreb, Croatia
2-3 March 2015

Ruđer Bošković Institute (RBI)

This 2-day workshop will cover a spread of topics in genomics. The first day will present a set of lectures and the second day will host two hands-on workshop sessions, including Introduction to RNA-Seq analysis with Galaxy presented by Enis Afgan & Davor Davidović (RBI). The event will be offered in English.

Who is this for?

Researchers, postdocs and students interested in Next Generation Sequencing, bioinformatics, data analysis, software tools, computer programming.

What will you learn?

Participants will get a broad overview of topics covering multiple facets of bioinformatics and genomics. The workshop will cover techniques as well as specific tools, including Galaxy and Ensembl. The first day will present a set of lectures and the second day will host two hands-on workshop sessions.

Registration

Registration is now open, and is free. You may register for the different parts of the event separately.

Posted to the Galaxy News on 2015-02-13

GCC2011  

2012 Galaxy Community Conference   

GCC2014, June 30-July2   

2013 Galaxy Community Conference (GCC2013)   

2015 Galaxy Community Conference (GCC2015)

GCC2016
needs a host!

(and a logo)

Hello all,

The Galaxy Community Conference has been held annually since 2010. This year's event (GCC2015) is being hosted by The Sainsbury Lab in Norwich, UK. We are now seeking proposals from any organization interested in hosting GCC2016.

GCC draws 200+ participants from data-intensive life science research. Participants come from around the world, from all career stages, and do research spanning the tree of life. Universities, hospitals and medical schools, research organizations, and industry are all represented, including the largest and most influential organizations in the world.

What do we need to host GCC, you ask? In approximately decreasing order of importance:

  • Enthusiasm to plan and organize a 3+ day event for more than 200 people.

  • Space for 4-6 parallel Training Day sessions, each able to accommodate from 25 to 75 participants.
  • Central meeting space with capacity for 250-300 people.
  • Affordability (or access to sponsorship funds; there's a reason we've always held GCC in academic settings)
  • Nearby space for breakouts, poster sessions and sponsors.
  • Nearby space for lunch, coffee breaks.
  • Good wifi for all events (that's 200+ people and their devices).
  • Space for a hackathon for 2 days before the event.
  • Easy to get to by air, from within the States, and from overseas
  • Nearby, affordable housing, or easy walking distance or easy public transport from lodging options to conference facilities
  • Close proximity to a pub and other social hubs.

Hosts get copious (and enthusiastic) organizational support from Galaxy's Outreach Team (who have been helping to organize GCC since 2011), and even more copious gratitude (even adulation!) from the Galaxy Community. If you are interested in possibly hosting GCC2016 next summer then please contact Galaxy Outreach <outreach@galaxyproject.org>. Our goal is to announce the site at this year's conference in July.

Hoping to work with you in 2016!

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2015-02-03

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.

We are looking forward to starting this group again,

Hans-Rudolf Hotz and Dave Clements

Posted to the Galaxy News on 2015-01-28

   Vote now!   

GCC2015 Training Day

What topics should be offered at the GCC2015 Training Day?

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.

Topic voting closes 30 January. 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.

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

Thanks,

The GCC2015 Organising Committee

Posted to the Galaxy News on 2015-01-19

Bioinformatics scientist/engineer for RNA bioinformatics and next-generation sequencing Berlin

The MDC Berlin-Buch is a member of the Helmholtz Association of National Research Centers, and its focus is biomedical research in the areas of Cardiovascular and Metabolic diseases, Cancer and Function and Dysfunction of Nervous System. The Berlin Institute for Medical Systems Biology (BIMSB) expands and adds systems biology approaches to major questions of gene regulatory function.

As a bioinformatics scientist/engineer you will be a member of the Scientific Bioinformatics Platform @BIMSB and report to the head of the platform, Dr. Altuna Akalin. You will be responsible for method and database development for genomics data sets relating to RNA biology and projects of the German Network of Bioinformatics (de.NBI). You will be interacting and collaborating with BIMSB research groups as well as national collaboration partners. The projects will be using Galaxy framework for tool development and data integration.

Applicants should have PhD degree or equivalent practical experience in research oriented software development in one of the following fields: computational genomics, bioinformatics, computer science, statistics or another quantitative field. We are looking for talented team members with a proven track record in software development and interest in genomics and large-scale datasets. Experience and/or interest in database technologies (SQL and/or noSQL), web technologies (HTML, XML, REST API, etc.) and traditional high-performance computing clusters is also necessary.

Please contact Altuna Akalin <altuna.akalin@mdc DASH berlin.de> for further details.

MDC Berlin-Buch Helmholtz Association of National Research Centers

Posted to the Galaxy News on 2015-01-17

width=175
Complete News Brief

Highlights

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



Thanks for using Galaxy!
The Galaxy Team

Posted to the Galaxy News on 2015-01-13

Dear Galaxy users, developers, and friends of the project,

Galaxy Project

The Galaxy project has been generously supported in the past by the National Human Genome Research Institute and the National Science Foundation. The time has come once again for us to seek continued funding for the core Galaxy development team, and we would like to ask for your help.

If you have found Galaxy to be useful, we would like to ask you to write a short letter of support. We will use this letter as a supplement to the grant renewal application we will soon be submitting.

Whether you are using the Galaxy web service, a local Galaxy installation, Galaxy on the cloud, or building your own applications on the Galaxy Platform, we hope to hear from you. All you need to do is:

  1. Send an email to <support-galaxy@bx.psu.edu>

  2. Write 2-3 sentences expressing your support for the project, and explaining how you use Galaxy and how it has helped you with your work.
  3. Include your name and institution.

Any other information you want to provide would be helpful. Not only will this show support for our continued funding, it will help us understand more about how you are using Galaxy.

Many thanks,

James Taylor and Anton Nekrutenko, on behalf of the Galaxy Team

Posted to the Galaxy News on 2015-01-07

Hey Everyone,

Galaxy Baltimore Meetups

We are looking forward to kicking off our first Galaxy Project Meetup! We will meet on January 22 at one of the Galaxy project hubs - the Department of Biology of Johns Hopkins University for a general introduction to Galaxy in the form of a social gathering. This will be an informal meeting open to anyone interested in data analysis, tools, computer infrastructure, programming, ...

We will be kicking things off with a discussion on Galaxy and how researchers around the world are leveraging it. See the meetup page for more information.

Please RSVP as space is limited.

We are hoping this will be the first of many meetups, both in the Baltimore area, and elsewhere. If you are interested in hosting a meetup in your area, please contact Galaxy Outreach <outreach@galaxyproject.org> and we will help you get the word out.

Thanks,

Enis Afgan and Nitesh Turaga, of the Galaxy Team

Posted to the Galaxy News on 2015-01-07

A postdoc position is available in Oslo (Norway) on the development of statistics/machine learning-based genome analysis methodology integrated with the Galaxy platform. The aim is to pioneer the development of sophisticated and streamlined software systems for broad use cases within integrative genomics, where the specification is deliberately somewhat broad in order to allow the visions of candidates to influence the exact direction.

The hired postdocs can exploit the Galaxy framework to ensure accessibility, interoperability and reproducibility for the systems they develop, and can further exploit the robust data management and statistical analysis functionality of the Genomic HyperBrowser framework (which is a separate, 90 000 line code base integrated with Galaxy). The positions are embedded within the HyperBrowser environment, which includes seven researchers and programmers working primarily on the development of genome analysis functionality, as well as around thirty more loosely coupled collaborators. For more on the HyperBrowser, check out an overview paper of previous developments, or try out our public server. The salary is good and there are good future career opportunities. Further details on the positions and how to apply are available in the full announcement.

Genomic HyperBrowser

Posted to the Galaxy News on 2015-01-06

January 2015 Newsletter

Happy New Year from the Galaxy Project!

January brings lots of Galaxy related news, including

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2015-01-05