May 2017 Galaxy News

Galaxy News

Welcome to the May 2017 Galactic News, a summary of what is going on in the Galaxy community. If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.

2017 Galaxy Community Conference

2017 Galaxy Community Conference (GCC2017)

GCC2017 will be in Montpellier, France, 26-30 June and will feature two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, all about data-intensive biology and the tools and infrastructure that support it. GCC2017 also includes data and coding hacks, and two days of training covering 16 different topics.

GCC2017 will be held at Le Corum Conference Centre in the heart of Montpellier, just 10km from the Mediterranean. This event will gather several hundred researchers addressing diverse questions and facing common challenges in data intensive life science research. GCC participants work across the tree of life, come from around the world, and work at universities, research organizations, industry, medical schools and research hospitals.

Early registration closes May 15

Early registration ends May 15. Early registration starts at less than 55€ / day for post-docs and students. You can also book low cost conference housing when you register.

Poster and Demo submission closes May 27

Abstract submission for posters and demos closes May 27. Note that you can also still submit late oral prentations abstracts. Late abstracts are considered as cancellations occur. Lightning talk submissions close June 23.

New GCC2017 Sponsors

We are pleased to welcome BioTeam and GenomeWeb as returning GCC sponsors.

GenomeWeb

GenomeWeb

GenomeWeb is sponsoring GCC for the fourth year in a row. GenomeWeb is an independent online news organization that provides in-depth coverage of the scientific and economic ecosystem spurred by high-throughput genome sequencing. GenomeWeb news is the leading information source for scientists, executives, and clinicians who use and develop advanced life science tools. As a conference attendee, GenomeWeb is pleased to offer you a three month trial to access their premium news content by contacting customerservice@genomeweb.com and indicating you are a Galaxy Conference 2017 attendee. If you are an academic professional or non-profit researcher, you automatically have access to GenomeWeb premium content and can register here to join using your work email address.


BioTeam

BioTeam Appliance Galaxy Edition

BioTeam is pleased to announce special pricing for the BioTeam Appliance Galaxy Edition now through Jun 30, 2017 (the last day of GCC2017). The BioTeam Appliance Galaxy Edition allows the researcher to get up and running fast with Galaxy. The Galaxy Appliance comes preinstalled with a production instance of Galaxy, bioinformatics tools, and reference datasets. "Science on Day One" To request more information click here.

Model Price
Galaxy Appliance Base Model 384/32 $29,995 USD
Galaxy Appliance Base Model 384/96 $45,495 USD
Galaxy Appliance Enhanced Model 512/32 $32,995 USD
Galaxy Appliance Enhanced Model 512/96 $48,995 USD

Technology Financing is available for qualified institutions/companies. Will ship globally.

GCC2017 Call for BoFs!

There is no better place than a Galaxy Community Conference to meet and learn from others doing data-intensive biology. GCC2017 continues this tradition by again including Birds of a Feather (BoF) meetups. Birds of a Feather meetups are informal gatherings where participants group together based on common interests.

BoF meetups are encouraged throughout GCC2017. The current list of BoFs is available on the conference web site. BoFs are posted as soon as they are proposed. The exact time and schedule for each will be set in mid to late June.

Want to plan a BoF?

To launch a Birds of a Feather meetup submit your BoF idea here. Once submitted, the conference organizers will create the BoF in the conference schedule, and give you edit access.

BoF Support

The conference enables and encourages BoFs by

  • Encouraging conference participants to organize BoFs
  • Promote BoFs to all conference participants, over and over, both before and during the conference.
  • Coordinate and reserve rooms for BoFs, and allocate time in the schedule for them too.

Galaxy Tutorial @ ISMB/ECCB 2017

Galaxy Tutorial at ISMB/ECCB 2017: Making Galaxy Work for You

Ther will be a half day tutorial on Making Galaxy Work for You at ISMB/ECCB 2017 in Prague, Czechia. The tutorial will provide a practical, hands-on guide to adapting the Galaxy platform to the specific needs of individuals attending the ISMB.

Participants will learn to

  • Create Galaxy compatible tool and workflow definitions that are publicly accessible and that make it easy for any instance administrator to add your work to their server.
  • Deploy Galaxy and scale it up to target production-ready resources such as a Postgres database, NGINX webserver, and distributed resource managers such SLURM or PBS.

Interested? Sign up when you register for ISMB/ECCB (and register before the tutorial fills up).

We also expect a lot of other Galaxy-related content at ISMB/ECCB 2017 and BOSC 2017. We'll add the presentations to the Galaxy @ ISMB/ECCB 2017 & BOSC 2017 event page as the schedules are posted. (And, please let us know if you have anything on the program.)

See you in Prague!

Gateways 2017 Call for Participation (1st deadline: June 5)

Gateways 120

Gateways 2017 (October 23-25, at the University of Michigan, Ann Arbor) is now accepting submissions of papers, demos, tutorials, and panels (2-4 pages) on the topic of science or engineering gateways, which are integrated, user-friendly interfaces to scientific computing, data, and other domain-specific resources to support research and education.

Submissions may focus on design, use, impact, development processes, sustainability, best practices, or any other aspect that you think fellow gateway creators or users will find interesting to learn. We also welcome educational topics directed toward the next generation of gateway creators.

The primary submission DEADLINE IS JUNE 5, 2017, and a poster session deadline (open to all) will be September 8. Read more details in the Call for Participation.


All upcoming events

There are a plenitude of Galaxy related events coming up in the next few months:

DateTopic/EventVenue/LocationContact
May 4th 2017 Introduction to Genomics in Medicine Using Galaxy Platform Tanta University Faculty of Mediciene, Tanta, Egypt Training offered by GTN MemberAbdelazeem_Abdelhameed2015505 @ yahoo.com
May 15th 2017 Data Analysis Workshop [hub page] NGS 2017 Glasgow, Glasgow, United Kingdom Julian Augley, Graham Hamilton, David Meltzer and Mani Mudaliar
May 16th 2017 Formation Galaxy4Imaging Nantes, France Comité d'organisation
May 22nd 2017 ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use University of Cambridge, United Kingdom Frederik Coppens
May 29th 2017 Bioinformatics for Cancer Genomics [hub page] Toronto, Ontario, Canada organizers
May 29th 2017 Workflow4Experimenters International Course [hub page] Pasteur Institute, Paris, France Training offered by GTN MemberChristophe Caron
June 4th 2017 Galaxy @ ASMS 2017 [hub page] ASMS 2017, Indianapolis, Indiana, United States Tim Griffin, Pratik Jagtap
June 6th 2017 Formation détection et annotation des éléments transposables dans les génomes eucaryote INRA, Versailles, France Nathalie Choisne, Olivier Inizan
June 20th 2017 G-OnRamp Beta Testers Workshop Washington University in St. Louis, Missouri, United States Training offered by GTN MemberJeremy Goecks, Sarah Elgin
June 26th 2017 2017 Galaxy Community Conference (GCC2017) [hub page] Montpellier, Fance Training offered by GTN MemberGalaxy community
July 2nd 2017 Computation and reproducibility in molecular evolution SMBE 2017, Austin, Texas, United States Training offered by GTN MemberAnton Nekrutenko, Sergei Kosakovsky Pond
July 20th 2017 OpenBio Codefest 2017 Brmlab, Prague, Czechia Brad Chapman, Matúš Kalaš, Heather Wiencko
July 21st 2017 Galaxy @ ISMB/ECCB 2017 & BOSC 2017 Prague, Czechia Training offered by GTN MemberPresenters
July 25th 2017 G-OnRamp Beta Testers Workshop Washington University in St. Louis, Missouri, United States Training offered by GTN MemberJeremy Goecks, Sarah Elgin
September 1st 2017 The Galaxy Bioinformatics Platform: learning to use Galaxy for RNA-seq analysis [hub page] Genome 10K and Genome Science, Earlham Institute, Norwich, United Kingdom Training offered by GTN Member
October 23rd 2017 Gateways 2017 University of Michigan, Ann Arbor, Michigan, United States Enis Afgan

See the Galaxy Events Google Calendar for details on other events of interest to the community.


New Publications

110 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in April.

Some highlights from the papers added last month:

Publication Topics

# Tag # Tag # Tag # Tag
72 methods 31 usepublic 17 workbench 13 usemain
12 refpublic 10 uselocal 8 reproducibility 3 cloud
3 tools 3 unknown 3 isgalaxy 2 shared
2 other 1 howto

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.



Public Galaxy Server News

There are over 90 publicly accessible Galaxy servers and six semi-public Galaxy services. Here's what happened with them in April

New Galaxy Services

United Kingdom: CLIMB

MRC CLIMB (Cloud infrastructure for Microbial Bioinformatics
  • Links:
  • Eligibility:
    • To register for a CLIMB group account, you must:
      • Be a UK academic or public sector worker working on microbial genomics
      • Run your own research group (i.e. be a principal investigator)
      • Have a .ac.uk (or .gov.uk or .nhs.uk email account)
      • Agree to our service terms and conditions
  • Comments:
    • The CLIMB project (Cloud Infrastructure for Microbial Bioinformatics) develops and deploys a world leading cyber-infrastructure for microbial bioinformatics; providing free cloud-based compute, storage, and analysis tools for academic microbiologists in the UK.
    • The project is supported by three world class Medical Research Fellows, a comprehensive training program and two newly refurbished Bioinformatics facilities in both Warwick and Swansea.
    • The Galaxy component of CLIMB is based on GVL. CloudBridge, and CloudMan infrastructure.
  • User Support:
  • Quotas:
  • Sponsor(s):
    • The CLIMB project is a collaboration between Warwick, Birmingham, Cardiff and Swansea Universities.
    • CLIMB is funded by the UK’s Medical Research Council.

New Public Galaxy Servers

Antigen Receptor Galaxy (ARGalaxy)

Antigen Receptor Galaxy
  • Link:
  • Domain/Purpose:
    • Automate the analysis and visual reporting of T- and B-cell receptor repertoire sequencing data.
  • Comments:
    • Consists of four parts: the demultiplex tool, the IMGT concatenate tool, the immune repertoire pipeline and the SHM&CSR pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, dependent on the available data and the question of interest
      • The demultiplex tool allows data trimming and demultiplexing of samples
      • The concatenate tool allows the merging of multiple IMGT/HighV-QUEST output files into a single file.
      • The immune repertoire pipeline allows analysis of both B- and T-cell receptor rearrangements and was developed to visualize V(D)J gene usage, CDR3 characteristics (length and amino acid usage), junction characteristics and calculate the diversity of the immune repertoire.
      • The SHM&CSR pipeline allows analysis of somatic hypermutations (SHM) and/or class switch recombination (CSR) in B-cell receptor rearrangements. It analyzes the frequency and patterns of SHM, antigen selection (including BASELINe), clonality (Change-O) and CSR.
  • User Support:
  • Quotas:
    • Account creation required. Anyone can create an account.
  • Sponsor(s):

Releases

galaxy-lib 17.5.8

galaxy-lib is a subset of the Galaxy core code base designed to be used as a library. This subset has minimal dependencies and should be Python 3 compatible. It's available from GitHub and PyPi.

Earlier Releases

Other packages that have been released in the prior 4 months.

17.01 Galaxy Release

GalaxyProject

The Galaxy Committers published the 17.01 release of Galaxy in February.

Highlights

Some highlights:

  • Conda auto initialization is enabled by default
  • New interface for user preferences
  • Support for compressed FASTQ formats
Release Notes

For full details on all of the enhancements and fixes in this release, please see the full release notes.

Galaxy Docker Image 17.01

And, thanks to Björn Grüning, there is also now a Docker image for Galaxy 17.01 as well.

CloudLaunch

Technically, the all-new Galaxy CloudLaunch service has been in public beta since February but keep in mind that it will replace the current CloudLaunch service eventually so give it a try and let us know how it performs for you.

CloudBridge 0.2.0

CloudBridge aims to provide a simple layer of abstraction over different cloud providers, reducing or eliminating the need to write conditional code for each cloud. It is currently under development and is in an Alpha state. Release 0.2.0 includes several fixes and enhancements.

Planemo 0.39 - 0.40


Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. These releases included numerous fixes and enhancements.

See GitHub for details.

Starforge 0.3

Starforge

Starforge is a collection of scripts that supports the building of components for Galaxy. Specifically, with Starforge you can:

These things will be built in Docker. Additionally, wheels can be built in QEMU/KVM virtualized systems.

Documentation can be found at starforge.readthedocs.org.

Pulsar 0.7.4

Pulsar

A Pulsar update was released in February. 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.

This release contains Conda and flake8 updates.

sequence_utils

Galaxy's sequence utilities are a set of Python modules for reading, analyzing, and converting sequence formats.

And the rest ...

Other Galaxy packages that haven't had a release in the past four months can be found on GitHub.



Galaxy ToolShed

ToolShed Contributions

Tool Shed contributions from April.

Other News

Guardians of the Galaxy Workflow