Galactic December News!

Galaxy News

Welcome to the December 2015 Galactic News, a summary of what is going on in the Galaxy community.

If you have anything to include in the next News, please send it to Galaxy Outreach.

New Papers

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

The new papers were tagged with:

# Tag    # Tag    # Tag    # Tag
4 Cloud 1 Project 5 Tools 14 UsePublic
1 HowTo 6 RefPublic - UseCloud - Visualization
7 IsGalaxy 2 Reproducibility 3 UseLocal 23 Workbench
37 Methods 1 Shared 11 UseMain

Events

Spanish Galaxy Community Meetup: 18 December, Barcelona

Galaxy Session at III Bioinformatics and Computational Biology Symposium

There will be a session at the end of the III Bioinformatics and Computational Biology Symposium being held in Barcelona on 18 December:

where users and developers can, not only share information and code, but also plan how to coordinate for future Galaxy workshops and other activities. Chairs of this session are Toni Espinosa (UAB) and Gonzalo Vera (CRAG).

See the announcement PDF and the announcement email for further details.

Galaxy Day 2015 Presentations

Galaxy Day 2015

Galaxy Day 2015 was held in Paris on 19 November. It was preceded by a Galaxy Hackathon. Both events were well attended and the events were yet another successful gathering of the French Galaxy community. Presentations from Galaxy Day and a summary of the Hackathon are now available online (click on "Archives Galaxy").

GCC2016 Registration will open this month

GCC2016 registration will open this month. The full training schedule will also be posted at that time. We'll announce this on all Galaxy channels - you won't miss it.

Upcoming Events

There are many upcoming events in the next few months. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Galaxy Training from Bioplatforms Australia and Intersect Galaxy Session at III Bioinformatics and Computational Biology Symposium  Biodiversity Knowledge Integration Center  Galaxy @ Plant and Animal Genome (PAG 2016)
Date Topic/Event Venue/Location Contact
November 30 - December 1 IUC Contribution Fest - Metagenomics Tools and Workflows Around the World Online /src/iuc/index.md, John Chilton
December 3 RNA-Seq Analysis Using Galaxy Australia University of Newcastle, Newcastle, NSW, Australia Training offered by GTN Member Mark Crowe, Katherine Champ
December 4 Variant Detection Using Galaxy
December 18 Galaxy Session Europe III Bioinformatics and Computational Biology Symposium, Barcelona, Spain Email
2016
January 8 Introduction to Galaxy Workshop North America Arizona State University, Tempe, Arizona, United States Training offered by GTN Member Nico Franz, Melissa A. Wilson Sayres, Anton Nekrutenko
January 9-13 Plant and Animal Genome (PAG XXIV) North America San Diego, California, United States See presenters
January 19 An introduction to clinical bioinformatics Europe Festival of Genomics London, London, United Kingdom Ang Davies
February 11 BioTeam Galaxy Appliance: Simplify Hosting Your Own Galaxy (Software Demo) North America AGBT, Orlando, Florida, United States Anushka Brownley
February 15-19 Analyse bioinformatique de séquences sous Galaxy Europe Montpellier SupAgro, Montpellier, France Training offered by GTN Member Yolande Olivier, Dominique Alhinc
February 20-23 (SW4) The Galaxy Platform for Multi-Omic Data Analysis and Informatics North America ABRF 2016, Fort Lauderdale, Florida, United States Training offered by GTN Member Pratik Jagtap, Tim Griffin, Dave Clements, Candace Guerrero, Getiria Onsongo
June 25-29 2016 Galaxy Community Conference (GCC2016) North America Indiana University, Bloomington, Indiana, United States Training offered by GTN Member Organizers
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 Servers

Two new publicly accessible Galaxy servers were added in November, bringing the total precipitously close to 80.

Galaxy Integrated Omics (GIO)

Galaxy Integrated Omics (GIO)

RNA-Seq Portal

RNA-Seq Portal - Analyzing RNA-seq Data for Agricultural Animal Species
  • Links:

  • Domain/Purpose:

    • Analyzing RNA-seq Data for Agricultural Animal Species.
  • Comments:
    • From the portal landing page: The goal of this project is to develop a web portal with integrated tools for RNA-seq based gene expression analysis for agricultural animals.
      • improve genome annotation of agricultural animal species, including (but not limiting to) cattle, pig, chicken, turkey, horse, sheep, and goat as well as catfish;
      • develop and integrate needed bioinformatics tools and pipelines, visualization interfaces, and statistical methods;
      • build a web portal that enable RNA-seq based transcriptomics analysis in aforementioned animal species.
  • User Support:
  • Quotas:

  • Sponsor(s):


Releases


Planemo 0.19.0 - 0.21.1

Planemo saw a regular Oort cloud of activity in November with 3 releases.

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Planemo 0.21.1 is the most recent release. See the release history.

Other Releases

GalaxyProject

July 2015 Galaxy Release (v 15.07) Galaxy Release v 15.07 includes enhancements to Interactive Environments and the Workflow Editor, an update of the Policies for Committers and Pull Requests and much more.

BioBlend 0.7.0

BioBlend version 0.7.0 was released at the beginning of November. 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.) From the release CHANGELOG.

Mid 2015 Galaxy CloudMan Release

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

Security Advisories

Three security vulnerabilities were announced and patched in August. 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.

Pulsar Pulsar 0.5.0 was released in May. 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.

blend4j v0.1.2 blend4j v0.1.2 was released in December 2014. blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.


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




Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in October and November.


Other News