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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 <outreach AT galaxyproject DOT org>.

New Papers

XX 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

-

Cloud

-

Project

-

Tools

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UsePublic

-

HowTo

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RefPublic

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UseCloud

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Visualization

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IsGalaxy

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Reproducibility

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UseLocal

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Workbench

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Methods

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Shared

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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.

Upcoming Events

There are upcoming events on XX continents in XX countries. 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

IUC, 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 <kchamp@bioplatforms.com>

December 4

Variant Detection Using Galaxy

December 18

Galaxy Session

Europe
III Bioinformatics and Computational Biology Symposium, Barcelona, Spain

Email <scb@iec.cat>

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 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


https://pypi.python.org/pypi/planemo/

Planemo 0.19.0 - 0.20.0

Planemo saw a regular Oort cloud of activity in November with 2 releases.

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Planemo 0.20.0 is the most recent release. See the release history.

Other Releases

GalaxyProject

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.

    CloudMan

    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 November.


Other News