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GalaxyUpdates/2015_10

The October 2015 Galactic News!

Galaxy News

Welcome to the October 2015 Galactic News, a summary of what is going on in the Galaxy community. It's been, and will be, a busy few months. If you have anything to include in the October News, please send it to Galaxy Outreach <outreach AT galaxyproject DOT org>.

New Papers

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

The new papers were tagged with:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

-

Cloud

-

Project

6

Tools

12

UsePublic

-

HowTo

-

RefPublic

-

UseCloud

-

Visualization

1

IsGalaxy

-

Reproducibility

9

UseLocal

9

Workbench

46

Methods

1

Shared

9

UseMain


Events

October GalaxyAdmins Meetup

GalaxyAdmins meetup October 15

Analome

The next GalaxyAdmins meetup on October 15 will feature David Kovalic speaking on Galaxy at Analome – Outreach, Opportunity and Challenges:

  • At Analome Galaxy has found another home and we like it for numerous reasons. In this talk we will present the multifaceted role Galaxy plays at Analome and how it supports ongoing bioinformatics projects while at the same time providing opportunities for social good.

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

Hope to see you there.


GCC2016 Call for Training Topic Nominations

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.


Call for GCC2017 Hosts

GCC2011   2012 Galaxy Community Conference    2013 Galaxy Community Conference (GCC2013)    GCC2014, June 30-July2    2015 Galaxy Community Conference (GCC2015)    2016 Galaxy Community Conference (GCC2016)

GCC2017 needs a host!
(and a logo)

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

GCC draws 200+ participants from the full range of 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 several of the largest and most influential research organizations in the world.

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.

Hoping to work with you in 2017!

Dave Clements and the Galaxy Team


IUC Tools & Collections Hackathon Report

News/IUCCollectionsCodefest

A Galaxy tool developers to hack on dataset collections hackathon was held on September 17th and 18th.

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.

See the full report details.


Upcoming Events

Galaxy Events Calendar
Galaxy Other Events Calendar

There are upcoming events in 4 countries on 4 continents. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Analyse avancée de séquences October Galaxy Admins Meetup Workshop: Extended RNA-Seq analysis Analyse de données RNA-seq sous l’environnement Galaxy Galaxy Day 2015

Date

Topic/Event

Venue/Location

Contact

October 1

Proteogenomics and Metaproteomics using the GalaxyP Platform

Asia
CSIR-Institute of Genomics & Integrative Biology (IGIB), New Dehli, India

Pratik Jagtap

October 9

Introduction to Integrative Analysis with GenomeSpace Workshop

North America
ASHG 2015, Baltimore, Maryland, United States

GenomeSpace <gs-help@genomespace.org>

October
12-14

Analyse avancée de séquences

Europe
Bordeaux Bioinformatics Center, University Bordeaux Segalen, France

Email <cfe.contact@cnrs.fr>

October 15

October Galaxy Admins Meetup

Around the world
Online

David Kovalic, Hans-Rudolf Hotz, Dave Clements

October 28-29

Workshop: Extended RNA-Seq analysis

Australia
QFAB, University of Queensland, St Lucia, Australia

Training offered by GTN Member
Mark Crowe

October 28 - November 3

Computational & Comparative Genomics Course

North America
Cold Spring Harbor Laboratory, New York, United States

Training offered by GTN Member
James Taylor

November 3

Galaxy for the Analysis of Very Large Biomedical Data Workshop

North America
Festival of Genomics California, San Mateo, California, United States

Training offered by GTN Member
Anton Nekrutenko, James Taylor

Single-Cell Sequencing: Analysis & Visualization of Copy Number Variations Workshop

Robert Aboukhalil, Tyler Garvin

November 15-16

Analyse de données RNA-seq sous l’environnement Galaxy

Europe
PRABI, Lyon, France

Training offered by GTN Member
Email <contact@fc3bio.fr>

November 17-18

Analyse de données RNA-seq sous l’environnement Galaxy

Europe
PRABI, Lyon, France

Training offered by GTN Member
Email <contact@fc3bio.fr>

November 19

Galaxy Day 2015

Soumissions à envoyer avant le 5 octobre

Europe
Institut Pasteur, Paris, France

Email <gtgalaxy@groupes.france-bioinformatique.fr>

December
7-11

Galaxy and the Genomics Virtual Lab

Australia
BioInfoSummer 2015, University of Sydney, NSW, Australia

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

1 new publicly accessible Galaxy servers was added in September, bringing the total dangerously close to 80.

ABiMS Tools

ABiMS Tools Galaxy Server
  • Link:

  • Domain/purpose:

  • Comments:

    • Available tools:
      • MicRhoDE workflow: places query sequences into MicRhoDE tree (type-1 rhodopsin phylogeny).

      • Renkan Blast: blast query sequences on 18S and 28S radiolaria databases (blastn).

      • WiseScaffolder: genome scaffolding of pre-assembled contigs using mate-pair data.

      • HECTAR: HEterokont subCellular TARgeting is a statistical prediction method designed to assign proteins to five different categories of subcellular targeting: Signal peptides, type II signal anchors, chloroplast transit peptides, mitochondrion transit peptides and proteins which do not possess any N-terminal target peptide.

  • User support:

    • For any question or request for tools or account, send an email at ABiMS Support <support.abims@sb-roscoff.fr>

  • Sponsor(s):



Galaxy Training Network News

There are two active discussions happening on the Galaxy-Training mailing list.

Software & Data Carpentry Train the Trainer Workshop at GCC2016?

Data Carpentry      Software Carpentry

We are considering offering a Software Carpentry / Data Carpentry Train the Trainer workshop immediately before GCC2016. This workshop would run for two days, and accommodate 24 people.

This idea came up at the GCC2015 GTN BoF. Software and Data Carpentry (S/DC) teach scientists core essentials of programming and data management. Their model is to train and certify trainers, and then provide a common curriculum and teaching infrastructure that enables those trainers to teach scientists how to program and manage data well.

If you think we should (or should not) offer this training at GCC2016, please contribute <galaxy-training@lists.galaxyproject.org> to the discussion on the mailing list.

Galaxy Training Network and GOBLET

2015 GOBLET Meeting

GTN became a member of the Global Organisation for Bioinformatics & Training (GOBLET) earlier this year. The 2015 GOBLET Meeting will be held 18-20 November, in Cape Town, South Africa. Fourie Joubert of the Centre for Bioinformatics and Computational Biology at the University of Pretoria will be representing GTN at GOBLET 2015.

If you have anything you'd like to have discussed at the meeting, then please join this conversation.


Galaxy Developer Code of Conduct

The Galaxy Project now has a Developer Code of Conduct.

From the introduction:

  • This code of conduct outlines our expectations for participants within the Galaxy community, as well as steps to reporting unacceptable behavior. We are committed to providing a welcoming and inspiring community for all and expect our code of conduct to be honored. Anyone who violates this code of conduct may be banned from the community.

The Code of Conduct includes

  • Guidelines on interaction,
  • Commitment to diversity,
  • and procedures for addressing issues if they arrise.

Thanks to everyone who helped put these together.

Releases

July 2015 Galaxy Release (v 15.07)

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

Mid 2015 Galaxy CloudMan Release

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.

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.

Other Releases

GalaxyProject
  • BioBlend 0.6.0 and 0.6.1


https://pypi.python.org/pypi/planemo/
  • Planemo 0.13.2

    • Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Planemo 0.13.2 is the most recent release. See the release history.

    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


1 new Galaxy Training Network member was added in September:



Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in September.


Other News


Galaxy Turns 10

Galaxy Turns 10

People remembered! Many thanks to Keith Bradnam for highlighting this milestone.