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GalaxyUpdates/2015_09

The September 2015 Galactic News!

Galaxy News

Welcome to the September 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 September News, please send it to Galaxy Outreach <outreach AT galaxyproject DOT org>.

New Papers

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

The new papers were tagged with:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

7

Cloud

2

Project

5

Tools

18

UsePublic

1

HowTo

4

RefPublic

1

UseCloud

1

Visualization

3

IsGalaxy

3

Reproducibility

7

UseLocal

22

Workbench

57

Methods

2

Shared

12

UseMain

First 2500 papers by tag and year

Galaxy's First 2500 Publications

And in case you missed it, we reached 2500 publications in the Galaxy CiteULike Library. This writeup analyzes the papers by CiteULike tag and journal, across the past 11 years, and identifies some trends. Of those 2500 papers, less than 2% have a Galaxy Team member as a coauthor.


IUC Tools & Collections Hackathon

We are planning a remote hackathon on September 17th and 18th for Galaxy tool developers to hack on dataset collections.

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.

The remote nature of this gives people who don't have the opportunity to come to GCC hackathons (which have always been productive and a lot of fun) a chance to participate in a Galaxy hackathon. Having a well defined topic will allow us to accomplish a lot and let people who don't have particular tasks in mind find something to work on very quickly.

We are collecting ideas to work on, but we expect to attract the most participation by simply getting tool developers interested in getting help adding collection support to their existing tools and workflows to show up and participate.

If you are interested in participating in the hackathon but not interested in actual tool development - we will assemble a list of smaller, manageable Python and JavaScript tasks to work on and certainly documentation is a chronically lacking for collections so we could use help there and no actual coding would be required.

This is the first remote hackathon we have organized and we encourage ideas or advice about how to organize it please let us know. A core group of will be available on IRC all day and we will have 4 google hangouts across those days to organize, answer questions, and report progress.

Thanks,
Galaxy IUC

Galaxy Project Google Calendars

If you want to know what events are happening in the Galaxy Community, the goto place has always been the Galaxy Events page. This lists any upcoming events we know about that feature Galaxy content. This events list provides dates, locations, and contact information for each event.

Galaxy Calendar

There has also been the complementary Galaxy Events Google Calendar which listed events of interest to the community, whether or not they featured significant Galaxy content. To make this calendar more useful, we have split it in to two:

This split allows us to present Galaxy events in a much sparser calendar, that is more useful for setting reminders and publishing Galaxy events. And we will continue to link to past Galaxy events (and presentations, videos, examples, ...) from the Events Archive.

August GalaxyAdmins Slides and Video

GalaxyAdmins meetup August 20

IRIDA

The next GalaxyAdmins meetup on August 20 was attended by 27 GalaxyAdmins. Aaron Petkau covered Genomic data management at Canada's National Microbiology Laboratory with IRIDA and Galaxy and Enis Afgan presented Adding transparency and automation into the Galaxy tool installation process.

In case you missed it, slides and video are now available online.

GalaxyAdmins is a special interest group for Galaxy community members who are responsible for Galaxy installations. Our next meeting will be on October 15 where David Kovalic of Analome will present. Hope to see you there.

Upcoming Events

http://bit.ly/gxycal

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

Scaling Up Bioinformatics Workflows with Dynamic Job Expansion: A Case Study Using Galaxy and Makeflow @ IEEE eScience 2015   Workshop: Extended RNA-Seq analysis RNA-seq data analysis NGS Course Using Galaxy for Analysis of High Throughput Sequence Data  

Date

Topic/Event

Venue/Location

Contact

September 2

Scaling Up Bioinformatics Workflows with Dynamic Job Expansion: A Case Study Using Galaxy and Makeflow

Europe
IEEE eScience 2015, Munich, Germany

Nicholas Hazekamp

September 2-3

Workshop: Extended RNA-Seq analysis

Australia
QFAB, University of Queensland, St Lucia, Australia

Training offered by GTN Member
Mark Crowe

September 7-9

RNA-seq data analysis NGS Course

Europe
Leiden University Medical Center, The Netherlands

Training offered by GTN Member
BioSB Education <education@biosb.nl>

September 14-18

Using Galaxy for Analysis of High Throughput Sequence Data

North America
UC Davis Bioinformatics Core, Davis, California, United States

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

September 15

Towards accessible, reproducible, and transparent research in the life sciences: an innovative open source VRE approach in Western France

North America
HUBbub 2015, Indianapolis, Indiana, United States

Yvan Le Bras

September 17-18

Remote Hackathon for Tools and Dataset Collections

Around the world
Online

IUC <galaxy-iuc@lists.galaxyproject.org>

September 21-23

JHU-DaSH: Data Science Hackathon

North America
Baltimore, Maryland, United States

Email <jhuDaSH@jhu.edu>

September 21-25

Traitement des données métabolomiques sous Galaxy

Europe
Station Biologique de Roscoff, France

Training offered by GTN Member
W4M Course Organisers <w4mcourse2015.organisation@sb-roscoff.fr>

September 28

Mutational Analysis with Random DNA Identifiers (MARDI), a High-Fidelity NGS Approach That Simultaneously Identifies Gene Marker Mutations from Heterogeneous Mutant Cell Populations

North America
Environmental Mutagenesis and Genomics Society (EMGS), New Orleans, Loisiana, United States

Javier Revollo

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

Hans-Rudolf Hotz, Dave Clements

October 19

Workshop: Variant detection using Galaxy

Australia
QFAB, University of Queensland, St Lucia, Australia

Training offered by GTN Member
Mark Crowe

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

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

2 new publicly accessible Galaxy servers were added in August.

Workflow4Metabolomics

Workflow4metabolomics Galaxy server

Workflow4Metabolomics Sponsors
Sponsors

EpiToolKit

EpiToolKit Galaxy Server
  • Link:

  • Domain/Purpose:

    • Computational immunology for the development of novel epitope-based vaccines.
  • Comments:

    • EpiToolKit "provides a collection of methods from computational immunology for the development of novel epitope-based vaccines including HLA ligand or potential T-Cell epitope prediction, an epitope selection framework for vaccine design, and a method to design optimal string-of-beads vaccines. Additionally, EpiToolKit provides several other tools ranging from HLA typing based on NGS data, to prediction of polymorphic peptides."

    • See EpiToolKit—a web-based workbench for vaccine design by Benjamin Schubert, Hans-Philipp Brachvogel, Christopher Jürges and Oliver Kohlbacher, Bioinformatics (2015) 31 (13): 2211-2213. doi: 10.1093/bioinformatics/btv116

  • User Support:

  • Quotas:

    • Anyone can create an account. Alternatively, a guest account is provided with login test_user@informatik.uni-tuebingen.de and password workflowTest. Please note that the guest account shares uploaded data with all other guest users.

    • Data of unregistered users and delete data will be permanently deleted after 7 days.
  • Sponsor(s):



Releases

Security Advisories

Two security vulnerabilities were recently discovered in Galaxy, and a third in the Galaxy Tool Shed. Because of this, 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


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


One new new Galaxy Training Network member was added in August:



Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in August.

Other News