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GalaxyUpdates/2015_05

The May 2015 Galactic News!

Galaxy Updates

Welcome to the May 2015 Galactic News, a summary of what is going on in the Galaxy community. These newsletters complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

New Papers

66 new papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in April. Highlights include:

The new papers were tagged with:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

4

Cloud

1

Project

5

Tools

10

UsePublic

-

HowTo

4

RefPublic

-

UseCloud

-

Visualization

3

IsGalaxy

-

Reproducibility

6

UseLocal

13

Workbench

41

Methods

3

Shared

13

UseMain

Events

GCC2015: 4-8 July, Norwich UK

GCC2015

   Register Now   

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

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

Early Registration is Open!

But it closes 22 May!

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

Register now.

Poster Abstract Deadline is TODAY

On-time poster abstract submission closes today. Poster authors will be notified of acceptance status within two weeks. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

Registration and Lodging Scholarships: Applications due TODAY

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

See the full announcement for further details.


Oliver Stegle will present the keynote address at GCC2015

Keynote Speaker: Oliver Stegle

The GCC2015 Scientific Committee is pleased to announce that the GCC2015 Keynote Speaker is Oliver Stegle of the Statistical genomics and systems genetic research group at the European Bioinformatics Institute (EBI). Dr Stegle will speak on his work in Modeling molecular heterogeneity between individuals and single cells.

Dr Stegle is featured in a Young Investigator Profile this month on GenomeWeb (which also happens to be a GCC2015 Sponsor).

Other Events Near GCC2015

Looking to extend your trip? There are also at least 7 other events going on in the British Isles in the week before and week after GCC2015, including events

Events nearby GCC2015

See the Events Aplenty Near GCC2015 news item for dates and deadlines.

GCC2015 Sponsorships

We are pleased to announce new GCC2015 Silver Sponsorships from ELIXIR and GigaScience.

Elixer    
ELIXIR is building a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine, agriculture, bioindustries and society. ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the massive amounts of data being generated every day by publicly funded research. It is a pan-European research infrastructure for biological information. This is the second time ELIXIR has sponsored a GCC. Please welcome them back!

GigaScience Journal

GigaScience journal is co-published as a collaboration between BGI Shenzhen and BioMed Central focused on studies utilizing large-scale datasets and workflows. This is the third GCC that GigaScience has sponsored. Please welcome them back!

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

Call for Sponsors

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

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

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

April GalaxyAdmins Meetup: Slides and Video

GalaxyAdmins meetup April 16

Slides and video from the April GalaxyAdmins online meetup are now available. Carrie Ganote from the National Center for Genome Analysis Support (NCGAS) and Pervasive Technology Institute at Indiana University presented her Galaxy work with Trinity, IU Galaxy, and the Open Science Grid. Sam Guerler of the Galaxy Project talked about Galaxy'a new tool form support.

Please join us for the next GalaxyAdmins meetup on June 18 when Peter Briggs of the University of Manchester will speak on Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester. GalaxyAdmins will also have an in-person meetup at GCC2015.

GalaxyAdmins is a special interest group for Galaxy community members who are responsible for Galaxy installations.

Other Events

Cycle "Bioinformatique par la pratique" 2015 QFAB Workshop: Variant detection using Galaxy Getting Bioinformatics Done with Galaxy   Galaxy Meetups @ Penn State  

http://bit.ly/gxycal

There are upcoming events in 7 countries on 3 continents. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date

Topic/Event

Venue/Location

Contact

May 12

Initiation à l’utilisation de Galaxy

Jouy-en-Josas, France

Veronique Martin <veronique.martin@jouy.inra.fr>, Sophie Schbath <sophie.schbath@jouy.inra.fr>

May 13

Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy

May 13

Workshop: Variant detection using Galaxy

QFAB, University of Queensland, St Lucia, Australia

Training offered by GTN Member
Mark Crowe

May 13

Getting Bioinformatics Done with Galaxy

BGI @ UC Davis workshop series, Davis, California, United States

Training offered by GTN Member
UC Davis Bioinformatics <bioinformatics.core@ucdavis.edu>

May 15

RNA-Seq Galaxy Workshop

Penn State University, State College, Pennsylvania, United States

Training offered by GTN Member
Martin Cech, Anton Nekrutenko

May 22, 29

Introduction to the analysis of NGS data

Leuven, Belgium

Janick Mathys

May 25-29

MIPRO

Opatija, Croatia

Enis Afgan

May 26-28

Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis in Plants

České Budějovice, Czech Republic

Jiri Macas <macas@umbr.cas.cz>

June 2

Initiation à l’utilisation de Galaxy

Jouy-en-Josas, France

Veronique Martin <veronique.martin@jouy.inra.fr>, Sophie Schbath <sophie.schbath@jouy.inra.fr>

June 3

Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy

June 4

Traitement bioinformatique des données RNA-Seq sous Galaxy

June 3

Workshop: RNA-Seq analysis using Galaxy

QFAB, University of Queensland, St Lucia, Australia

Training offered by GTN Member
Mark Crowe

June 6-9

WS02: NGS Variant Analysis with Galaxy

ESHG 2015, Glasgow, United Kingdom

Training offered by GTN Member
Dave Clements

June 18

Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester

June 2015 GalaxyAdmins Web Meetup, Online

Peter Briggs, Hans-Rudolf Hotz

June 22

Introduction to variant calling for pathologists and laboratory managers

Part of Short Course in Medical Genetics and Genetic Pathology 2015, Sydney, Australia

Training offered by GTN Member
Ross Lazarus, Andrew Lonie

June 29-30

Introduction to NGS Data Analysis with Galaxy

University of Edinburgh, Edinburgh, United Kingdom

Training offered by GTN Member
Bert Overduin <bert.overduin@ed.ac.uk>, Dave Clements

July 4-8

2015 Galaxy Community Conference (GCC2015)

The Sainsbury Lab, Norwich, United Kingdom

GCC2015 Organisers <gcc2015-org@lists.galaxyproject.org>

July 4-5

Data Hackathon Organisers <gcc2015-data-org@lists.galaxyproject.org>

Coding Hackathon Organisers <gcc2015-hack-org@lists.galaxyproject.org>

July 5

Training offered by GTN Member
GCC2015 Organisers <gcc2015-org@lists.galaxyproject.org>

July 6

Training offered by GTN Member
GCC2015 Organisers <gcc2015-org@lists.galaxyproject.org>

July 6-8

GCC2015 Organisers <gcc2015-org@lists.galaxyproject.org>

July 6-10

An Introduction to Galaxy with the Genomics Virtual Lab: workshop

Winter School in Mathematical and Computational Biology, University of Queensland, Brisbane, Queensland, Australia

Training offered by GTN Member
Mark Crowe

July 10-14

Using Biological Cyberinfrastructure to Scale Science and People – Applications in Data Storage, HPC, Cloud Analysis, and Bioinformatics Training

ISMB / ECCB 2015, BOSC 2015, Dublin, Ireland

Dave Clements

Designates a training event offered by GTN Member

Designates a training event offered by GTN member(s)


Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.



New Public Galaxy Server: The ReproGenomics Viewer

The ReproGenomics Viewer
  • Link:

  • Domain/Purpose:

    • "The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community. The system is based on the implementation of a JBrowse genome browser and a Galaxy bioinformatics workflow environment. It was developed to provide a one-stop genomic working environment and aims to assist scientists in the analysis and the mining of a wide range of high-throughput repro-genomics data, including sequencing data.

      RGV allows hosting, visualization, and direct comparison of users’ data to published genomics studies as well as to relevant genetic variations linked to reproduction. One way it does this is by enabling various genomic file format conversions.

      The ReproGenomics Viewer currently hosts datasets that are oriented mainly towards testis biology and spermatogenesis. In the near future, these will extend to other areas of reproduction, including gonad development, urogenital cancers, and reproductive toxicology."

  • Comments:

  • User Support:

    • Email <support@genouest.org>

  • Quotas:

  • Sponsor(s):


Galaxy Community Hubs

Galaxy Training Network

Galaxy Community Log Board

Galaxy Deployment Catalog

Share your training resources and experience now

Share your experience now

Describe your instance now


One new Community Log Board entry was added in April:

And one new Training Resource:


Releases

Pulsar 0.4.0

Pulsar 0.4.0 and 0.3.0 were released in April. These included:

  • Python 3 support. Pull Request 62

  • Add pulsar-run script for issues commands against a Pulsar server (experimental). 3cc7f74

  • Changed the name of project to Pulsar, moved to Github.

  • New RESTful web services interface.
  • SCP and Rsync file staging options added by Eric Rasche. Pull Request

  • Allow YAML based configuration.
  • Support for more traditional pip/setup.py-style installs.

And dozens of smaller bugfixes and documentation updates.

Pulsar is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the results are transferred back to the Galaxy server - eliminating the need for a shared file system.

Planemo 0.8.4

Planemo saw two major and several minor releases this past month. The most recent is v0.8.4.

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project.

Others


Other News



Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in April.