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June 2019 Galactic News
GCC2019 registration / Poster/Demo abstracts / sponsors, GTN CoFest, Platforms, Pubs, Jobs, Blog!, Training, Tools, Releases and more!
2019-06-03

Galaxy News

The June 2019 Galactic News is here! This is a summary of what is going on in the Galaxy community.

If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.


GCC2019, 1-8 July, Freiburg, Germany

GCC2019

GCC2019 will be held the first week of July in Freiburg, Germany. The tenth GCC features more presentations and more training than any GCC before it. If you are working in data intensive life science research then there will not be a better place to share your work, learn from others, and find new collaborators.

Advance Registration ends 7 June - this Friday

Advance registration for the 2019 Galaxy Community Conference (GCC2019) is ends this this Friday, 7 June. Register this week and avoid late registration fee hikes that start on Saturday morning. (Insert your favorite Saturday morning hangover joke here.)

Poster & Demo Abstract Submission Deadline: 10 June

Abstracts for poster presentations and software demonstrations are still being accepted for consideration. Got something to show? Submit your abstract before the 10 June deadline!.

Conference Schedule is Online

The full conference schedule is now online. There are

GCC2019 Schedule is available

Upcoming events

These and other Galaxy related events are coming up:

Date Topic/Event Venue/Location Contact
June 2nd 2019 Galaxy @ ASMS 2019 ASMS 2019, Atlanta, Georgia, United States Tim Griffin, Pratik Jagtap
June 3rd 2019 Norwegian e-Infrastructure for Life Sciences (NeLS) University of Oslo, Oslo, Norway Training offered by GTN MemberStåle Nygård, Jon Lærdahl, Radmila Kompova
June 11th 2019 RNA-seq workshop for beginners: from sequences to visualization using Galaxy Training offered by GTN Memberberenice.batut@gmail.com
June 11th 2019 Bioinformatics for Beginners National Institutes of Health (NIH), Bethesda, Maryland, United States training@faes.org
June 12th 2019 Traitement bioinformatique et analyse différentielle de données d'expression RNA-seq sous Galaxy Cycle "Bioinformatique par la pratique" 2019, INRA, Jouy-en-Josas, France Training offered by GTN MemberVéronique Martin
July 1st 2019 **2019 Galaxy Community Conference (GCC2019)** Freiburg, Germany Training offered by GTN MemberOrganizers
July 3rd 2019 An introduction to Galaxy with the NeCTAR Genomics Virtual Laboratory 2019 Winter School in Mathematical & Computational Biology, Brisbane, Queensland, Australia Training offered by GTN MemberIgor Makunin
July 10th 2019 Analyse fonctionnelle et interprétation de données de protéomique avec la plate-forme ProteoRE Campus de Beaulieu, Rennes, France proteome@univ-rennes1.fr
July 29th 2019 Getting started with Galaxy and NGS Platforms QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
July 30th 2019 Genome assembly using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
July 31st 2019 Variant detection using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
August 1st 2019 "Teaching undergraduate genomics with Galaxy” and “Resources and recommendations for teaching undergraduate genomics with Galaxy" ASMCUE 2019, Tyson, Virginia, United States Training offered by GTN MemberMohammad Heydarian, Anton Nekrutenko
August 1st 2019 RNA Seq analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
August 2nd 2019 Metagenomics analysis using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org

Publications

150 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in the last month.

Highlighted Publications

There were 10 Galactic and Stellar publications added, and 9 of those are open access:

Publication Topics

# Tag # Tag # Tag # Tag
95 +Methods 43 +UsePublic 23 +Workbench 18 +RefPublic
17 +UseMain 11 +UseLocal 9 +IsGalaxy 7 +Tools
4 +Reproducibility 3 +Shared 2 +Education 2 +Project
2 +Visualization 1 +HowTo

Galaxy Platforms News

The Galaxy Platform Directory lists resources for easily running your analysis on Galaxy, including publicly available servers, cloud services, and containers and VMs that run Galaxy. A lot was added in March:

The TGM pipeline

tgmpipeline

The TGM pipeline is a platform combining tranSMART server, Galaxy Server, and MINERVA platform to enable visually-aided exploration, analysis, and interpretation of high-throughput translational medicine data. The TGM pipeline enables establishing workflows with Galaxy for data processing using tools and resources of the tranSMART server.

ARGA

arga

The Antibiotic Resistance Gene Analyzer (ARGA) is a pipeline used for identification of antibiotic resistance genes using the Sequence Database for ARGS (SDARGS). The ARGA Galaxy instance provides all of the nucleotide and protein sequences in SDARG and ARGs primer databases in the Shared Data and Data Libraries sections for users. A guide for recommended usage of ARGA can be found here.

NGPhylogeny.fr

ngphylogeny

NGPhylogeny.fr is a free and simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. The NGPhylogeny service allows users to execute and customize Galaxy workflows while employing a novel interface to Galaxy. Additional documentation can be found here.

NanoGalaxy

nanogalaxy

NanoGalaxy is a webserver for processing, analysis, and visualization of long-read nucleic acid sequencing data from Oxford Nanopore Technologies (ONT) and Pacific Biosystems (PacBio) with Galaxy. This specialized Galaxy instance provides access to a collection of best practice workflows and commonly used tools for analysis of long-read sequence data.

Galaxy Workbench for Mass Spectrometry Imaging

This is a custom docker image for doing mass spectrometry image processing in a Galaxy platform. The tools available in this image are also available on the UseGalaxy.eu platform.

Rice Galaxy

Rice Galaxy

The Rice Galaxy server is a revamped version of IRRI's previously existing Galaxy server. It features tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice−bacterial pathogen diagnostics, and a suite of published genomic prediction methods and has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes.

Galaxy Platforms in Publications

We tag papers that use, mention, implement or extend public Galaxy platforms (servers, services, clouds, containers...). Here are the platforms that were referenced at least twice in the past month's publications:

# Tag # Tag # Tag # Tag
21 >Huttenhower 9 >CPT 7 >Workflow4Metabolomics 5 >RepeatExplorer
3 >ARGs-OAP 3 >Galaxy-P 3 >UseGalaxy.org.au 2 >deepTools
2 [>Globus Genomics](https://www.zotero.org/groups/1732893/galaxy/items/order/dateAdded/sort/desc/tag/>Globus Genomics) 2 >IRProfiler 2 >RiboGalaxy

Galaxy Cloud Bursting

New Galactic Blog Post: Enabling Cloud Bursting for Galaxy

For the second month in a row we have a new Galactic Blog post from Enis Afgan and Vahid Jalili:


Who's Hiring

Please Help! Yes you!

The dark energy of irreproducible research is threatening the science universe! Please help the Galaxy push it back!

Have 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.


Doc, Hub, and Training Updates

Galaxy Training Materials

Updates from the Galaxy Training Materials:

Hub updates:


ToolShed Contributions

Tool Shed contributions in April and May 2019.

Releases

New additions to (and editions in) the Galaxy Ecosystem.

Planemo 0.60.0

Planemo

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included numerous fixes and enhancements.

See GitHub for details.

Pulsar 0.11.0

Pulsar

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.

ephemeris 0.10.0

Ephemeris is a small Python library and set of scripts for managing the bootstrapping of Galaxy plugins - tools, index data, and workflows. It has extensive documentation. This release features numerous newly contributed features.


Other News

Galaxy Status web site

Galaxy Services Status Web Site

Automated status tracking of our most important services is available at status.galaxyproject.org. This is updated in real time, and will be used to post status updates whenever there are issues.

Black Duck Open Hub updates it's Galaxy project stats

Black Duck's Open Hub web site reports stats on open source projects such as Galaxy. They just updated their summary of Galaxy:

  • Over the past twelve months, 198 developers contributed new code to Galaxy Bioinformatics Platform. This is one of the largest open-source teams in the world, and is in the top 2% of all project teams on Black Duck's Open Hub.

Take a look.

data.galaxyproject.org directory view.

From Enis Afgan:

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