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.

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:

Galaxy Events Google Calendar Galaxy Calendar RSS Feed This calendar now lists only events that feature Galaxy content. Pretty much, if it's on the Events page, it's also in this calendar.

Galaxy Other Events Google Calendar Galaxy Calendar RSS Feed This lists additional events and deadlines that are relevant to the Galaxy Community, but that are not known to feature significant Galaxy content.

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

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
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
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
September 21-23 JHU-DaSH: Data Science Hackathon North America Baltimore, Maryland, United States Email
September 21-25 Traitement des données métabolomiques sous Galaxy Europe Station Biologique de Roscoff, France
Training offered by GTN Member
W4M Course Organisers
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
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

May 2015 Galaxy Release (v 15.05) Release Notes v 15.05

BioBlend 0.6.0 and 0.6.1 BioBlend version 0.6.1 was released in July. 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:


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 The most recent edition of CloudMan was released in August.

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