The June 2015 Galactic News!

Galaxy Updates

Welcome to the June 2015 Galactic News, a summary of what is going on in the Galaxy community. These newsletters complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

New Papers

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

The new papers were tagged with:

# Tag    # Tag    # Tag    # Tag
2 Cloud - Project 6 Tools 10 UsePublic
- HowTo 3 RefPublic - UseCloud 2 Visualization
3 IsGalaxy 2 Reproducibility 5 UseLocal 14 Workbench
38 Methods 3 Shared 10 UseMain

Events

GCC2015: 4-8 July, Norwich UK

GCC2015
   Register Now   

The 2015 Galaxy Community Conference (GCC2015) is the Galaxy community's annual gathering of users, developers, and administrators. Previous GCC's have drawn over 200 participants, and we expect that to happen again in 2015. GCC2015 is being hosted by The Sainsbury Lab in Norwich, UK, immediately before BOSC and ISMB/ECCB in Dublin.

There are a lot of events going on at GCC2015, including:

Registration is Open!

registration is open, and there is still available space for most GCC2015 events. If you work in data-intensive life science research, then there is no meeting that will be more relevant this year than GCC2015. We look forward to seeing you there.

Register now.

Late Poster Abstracts

There are still a limited number of poster slots available and we welcome poster abstract submissions. Poster authors will be notified of acceptance status within two weeks. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

You can also submit late oral presentation submissions. These will be considered as cancellations happen (and they usually do).

Other Events Near GCC2015

Looking to extend your trip? There are also at least 7 other events going on in the British Isles in the week before and week after GCC2015, including events

Events nearby GCC2015

In Norwich

See the Events Aplenty Near GCC2015 news item for dates and deadlines.


Genomic Data Science Course
Data Science Specialization

GCC2015 Sponsorships

Hackathons Sponsor: Johns Hopkins University Data Science Specialization Program

We are pleased to announce that the Johns Hopkins University Data Science Specialization Program offered on Coursera is the exclusive sponsor for both the GCC2015 Coding Hackathon and the Data Wrangling Hackathon.

This program includes a Genomic Data Science course covering

  • Basic computational, biological, and statistical skills for analyzing big genomic data
  • Foundational tools for successfully engaging in this rapidly changing field
  • How to go from unprocessed next generation sequencing data to meaningful biological results

and introduces Galaxy, Bioconductor, Python, command line, and many other tools.

The series of nine MOOCs are now open for enrollment and free to anyone.

Training Day Sponsor: Amazon Web Services
Amazon Web Services

We are pleased to again have Amazon Web Services (AWS) as the sponsor for the GCC2015 Training Days. This is the 4th year in a row AWS has sponsored GCC Training Days. Many of the sessions will be using AWS directly, or servers running on AWS.

Call for Sponsors

The 2015 Galaxy Community Conference (GCC2015) is still accepting Sponsorships. Your organisation can play a prominent part in the Galaxy community by sponsoring GCC2015. Sponsorship is an excellent way to raise your organization’s visibility.

Several sponsorship levels are available, including two levels of premier sponsorships that include presentations. Premium sponsorships are limited, however, so you are encouraged to act soon.

Please let the organisers (gcc2015-org AT lists DOT galaxyproject DOT org) know if you are interested in helping make this event a success.

June GalaxyAdmins Meetup

GalaxyAdmins meetup June 18
University of Manchester

Please join us for the next GalaxyAdmins meetup on June 18 when Peter Briggs of the University of Manchester will speak on

Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester

GalaxyAdmins will also have an in-person meetup at GCC2015.

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

Other Events

63rd ASMS Conference on Mass Spectrometry and Allied Topics Cycle Workshop: RNA-Seq analysis using Galaxy   18 June GalaxyAdmins Web Meetup      2015 Galaxy Community Conference (GCC2015)

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

Date Topic/Event Venue/Location Contact
May 31 - June 4 63rd ASMS Conference on Mass Spectrometry and Allied Topics
St. Louis, Missouri, United States
Speaker List
June 2 Initiation à l’utilisation de Galaxy
Jouy-en-Josas, France
Veronique Martin, Sophie Schbath
June 3 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy
June 4 Traitement bioinformatique des données RNA-Seq sous Galaxy
June 3 Workshop: RNA-Seq analysis using Galaxy
QFAB, University of Queensland, St Lucia, Australia
Training offered by GTN Member
Mark Crowe
June 6-9 WS02: NGS Variant Analysis with Galaxy
ESHG 2015, Glasgow, United Kingdom
Training offered by GTN Member
Dave Clements
June 8-9 Introduction to Galaxy Workshop
Workshop is full, but there is a waiting list
University of Glasgow, Glasgow, United Kingdom
Training offered by GTN Member
Dave Clements
June 18 Galactic Engineering: Experiences deploying Galaxy and developing tools within the Bioinformatics Core Facility at the University of Manchester
June 2015 GalaxyAdmins Web Meetup, Online
Peter Briggs, Hans-Rudolf Hotz
June 22 Introduction to variant calling for pathologists and laboratory managers
Part of Short Course in Medical Genetics and Genetic Pathology 2015, Sydney, Australia
Training offered by GTN Member
Ross Lazarus, Andrew Lonie
June 22 Initiation à la plateforme web GALAXY
Galaxy User Group Grand Ouest (GUGGO), Angers, France
Training offered by GTN Member
Yvan Le Bras, Cyril Monjeaud
June 22 Introduction à l'analyse de données RNAseq sous Galaxy
Galaxy User Group Grand Ouest (GUGGO), Angers, France
Training offered by GTN Member
Yvan Le Bras, Cyril Monjeaud
June 25 Initiation à l'analyse de données de type RAD par le pipeline STACKS sous Galaxy
Lille, France
Training offered by GTN Member
Yvan Le Bras, Anthony Bretaudeau, Cyril Monjeaud
July 4-8 2015 Galaxy Community Conference (GCC2015)
The Sainsbury Lab, Norwich, United Kingdom
GCC2015 Organisers
July 4-5 Data Hackathon Organisers
Coding Hackathon Organisers
July 5
Training offered by GTN Member
GCC2015 Organisers
July 6
July 6-8 GCC2015 Organisers
July 6-10 An Introduction to Galaxy with the Genomics Virtual Lab: workshop
Winter School in Mathematical and Computational Biology, University of Queensland, Brisbane, Queensland, Australia
Training offered by GTN Member
Mark Crowe
July 10-14 BOSC 2015 & ISMB/ECCB 2015
10+ Galaxy related talks, posters, panel discussions, ...
Dublin, Ireland
See presenters
August 6-7 Workshop: Extended RNA-Seq analysis
QFAB, University of Queensland, St Lucia, Australia
Training offered by GTN Member
Mark Crowe
September
4, 11
Introduction to NGS data analysis
Leuven, Belgium
Janick Mathys
September 14-18 Using Galaxy for Analysis of High Throughput Sequence Data, September
UC Davis Bioinformatics Core, Davis, California, United States
Training offered by GTN Member
UC Davis Bioinformatics
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

The VirAmp server was added to the list of public Galaxy servers in May:

VirAmp

VirAmp

VirAmp is a web-based semi-de novo fast virus genome assembly pipeline designed for extremely high coverage NGS data. From VirAmp: a galaxy-based viral genome assembly pipeline, Yinan Wan, Daniel W Renner, Istvan Albert and Moriah L Szpara, GigaScience 2015, 4:19 doi:10.1186/s13742-015-0060-y VirAmp "combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze, and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices into a single, easy to use interface. We tested our pipeline with three different datasets from human herpes simplex virus (HSV)."

VirAmp includes Documentation and is supported by the Huck Institutes of the Life Sciences and the Department of Biochemistry and Molecular Biology, and Pennsylvania State University


Releases

May 2015 Galaxy Release (v 15.05)

GalaxyProject

The May 2015 Galaxy Release is out! Release Notes v 15.05

Release Highlights

  • Authentication Plugins - Galaxy now has native support for LDAP and Active Directory via a new community developed authentication plugin system.
  • Tool Sections - Tool parameters may now be groupped into collapsable sections.
  • Collection Creators - New widgets have been added that allow much more flexibility when creating simple dataset pair and list collections.
  • And much more

The release notes have a new home at Read the Docs. We hope that you like the new format as much as we do!

Thanks for using Galaxy!
The Galaxy Team

Pulsar 0.5.0

Pulsar 0.5.0 was released in May. Enhancements include:

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.

Planemo 0.12.2

Planemo saw four major and several minor releases this past month. The most recent is v0.12.2. See the release history for full details and links.

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project.

Others

CloudMan The most recent edition of CloudMan was released in August.

BioBlend V0.5.3 BioBlend v0.3 was also released in March.
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.)

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.


Other News


Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in May.