June 2017 Galaxy News

Galaxy News

Welcome to the June 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.

GCC2017 is almost here!

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.

Regular Registration Rates Extended to June 16

If you missed the May 31 regular registration deadline then don't worry because it has been extended to June 16. Regular registration starts at 75€ / day for post-docs and students. You can also book low cost conference housing when you register.


Eytan Domany

Personalized Analysis of Cancer Data: From Genes to Pathways (and Back)

Dr. Eytan Domany will cover his work in human genomics and computational biology principally in the cancer domain. Eytan Domany is a Professor of Computational Systems Biology in the Department of Physics and Complex Systems at the Weizmann Institute of Science in Rehovot, Israel. The main focus of his group is to mine data from large-scale experiments in biology. The work includes development of mathematical methods, their implementation in algorithms (which are incorporated in user-friendly computational tools), which are then applied to study biological data. Eytan was awarded the Sergio Lombroso Award in Cancer Research in 2016 for his research efforts.

Anton Nekrutenko & James Taylor

The Galaxy Project: from the Planck epoch to Montpellier

Dr. Anton Nekrutenko and Dr. James Taylor will present a keynote reviewing the history of the Galaxy project, and how it went from a humble Perl script to having its own international meeting in the South of France in the summer of 2017.

If you are reading this, you probably already know who they are. If not, see their bios here.

And the rest of the schedule ...

... will be published this week on the conference schedule web site.

Submit a Lightning Talk!

Stike out and strut your work with a GCC2017 lightning talk!

Lightning talks are an excellent chance to share your work, preliminary or otherwise, with the community. Lightning talks are 7 minutes long and are the quickest way to make a lasting impression on, and get feedback from all participants. Submit your lightning talk proposal by June 23.

Talk, Poster and Demo Submission is Closed, but ...

Abstract submission for regualr talks, posters and demos closed in May. However you can still submit late oral prentations abstracts, posters and demos. Late oral presentation abstracts are considered as cancellations occur, and posters and demos will be reviewed until the space is full.

2017 Galaxy Community Conference Sponsors

GCC2017 Sponsors

GCC2017 has 11 sponsors! Sponsors are potential partners in your research and sponsorships greatly lower the cost of conference registration. Have a look at the GCC2017 sponsor list and plan on learning what they have to offer (and thanking them) while you are in Monpellier.

Hack the Universe: Capture the Flag at GCC2017!

Capture the flag at GCC2017!
(Quite possibly the first animated GIF used in a Galaxy Newsletter.)

GCC2017 Call for BoFs!

2017 Galaxy Community Conference 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.


Galaxy Tutorial @ ISMB/ECCB 2017

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

Know someone who needs to learn more about deploying Galaxy in their organization? There will be a half day Making Galaxy Work for You tutorial 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!

All events

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

Date Topic/Event Venue/Location Contact
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
June 29th 2017 Using Galaxy for RNA-seq analysis MDC, Berlin, Germany Dilmurat Yusuf, Bora Uyar
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 6th 2017 Stratégies D'Analyse Données Omiques - Ateliers Introductifs Galaxy et Cytopscape Université François-Rabelais, Tours, France Franziska Liesecke
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 MemberNicola Soranzo, Graham Etherington
September 25th 2017 Computational Genomics and RNA Biology Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany Training offered by GTN Membercompgen@mdc-berlin.de
October 23rd 2017 Gateways 2017 University of Michigan, Ann Arbor, Michigan, United States Enis Afgan
October 23rd 2017 Analyse avancée de séquences Carreire de l'Université Bordeaux Segalen, Bordeaux, France Aurélien Barré, Raluca Uricaru, Benjamin Dartigues

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

Training Material Re-use Hackathon Reports

GTN materials overview

The ELIXIR/GOBLET/GTN hackathon for Galaxy training material re-use was held last month in Cambridge, UK. A lot was accomplished:

New Publications

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

Some highlights from the papers added last month:

Publication Topics

# Tag # Tag # Tag # Tag
49 methods 21 usepublic 16 usemain 15 workbench
10 refpublic 5 tools 5 isgalaxy 4 cloud
3 reproducibility 2 uselocal 1 shared 1 project
1 unknown 1 other

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 May

ImmPort Galaxy Update

ImmPort Galaxy new visualizations

A new release of ImmPort Galaxy is out:

  • R is all up to date logicle trans,
  • Added a transformation algorithm to the Automated gating
  • Transformation and Converson of FCS files to text tool,
  • And a couple of tools to generate 1D Density plots.

More cool visualizations to look at your flow cytometry data!


New Public Galaxy Servers


Genomics Virtual Lab Melbourne

Galaxy Melbourne is a general purpose Galaxy based on the Genomics Virtual Lab platform. Support options include GVL Help, tutorials at GVL Learn and Galaxy Tut. Registration is required but anyone can register. The default quota of 100GB which can be increased on request. GVL MEL is supported by the Genomics Virtual Lab, Melbourne Bioinformatics, and Nectar.


ChimeRScope Galaxy

ChimeRScope Galaxy is a tool publishing server for fusion gene discovery from transcriptome-sequencing (RNA-seq) datasets. ChimeRScope is a java application that uses a novel alignment-free approach for discovering fusion genes from transcriptome-sequencing (RNA-seq) datasets. Prediction results from simulated datasets and real datasets show that our method achieves the best prediction accuracy, comparing to all other popular methods.

See You Li, Tayla B. Heavican, Neetha N. Vellichirammal, Javeed Iqbal, Chittibabu Guda; ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. Nucleic Acids Research 2017 gkx315. doi: 10.1093/nar/gkx315

There is a ChimeRScope Manual including a FAQ. The server supports anonymous access and creation of user logins. ChimeRScope Galaxy is supported by the Guda Lab at the University of Nebraska Medical Center.


Qiime and mothur

Qiime: Quantitative Insights Into Microbial Ecology     mothur

Galaxy has reached many different communities far beyond classical NGS. To support this the IUC is organising regularly contribution fests dedicated to special topics, with the aim to increase tool coverage and develop re-usable workflows. One of the first contribution fests focused on metagenomics, a field that is gaining more traction in the Galaxy community. Here we highlight two pull requests that were recently merged and added Qiime (Quantitative Insights Into Microbial Ecology) and mothur to Galaxy. These tools are the most popular pipelines used by the microbial ecology community to perform microbiome analyses from raw DNA sequencing data.

Based on previous work by James Johnson, ~150 tools were developed and adapted to the most recent IUC standards for Galaxy tools, including integration with BioConda and BioContainers. This effort was led by Saskia Hiltemann and Bérénice Batut and several reviewers and contributors, who created more than 300 commits and touched more than 600 files (including test-data). Thanks Saskia and Bérénice for this effort!

The tools can be installed via the Galaxy Tool Shed:

Both tool suites and many more metagenomics tools are integrated into the metagenomic Galaxy flavor.

Björn Grüning

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions from May.


May 2017 Galaxy Release (v 17.05)


Tag your datasets to keep track of where computed datasets came from
# Tags are propogated
in histories

Drag and drop with Galaxy Histories and Tools
Drag and drop in Galaxy 17.05

The Galaxy Committers published the 17.05 release of Galaxy in May.

Tag your data with propagating hashtags

  • Large Galaxy histories used to be messy. Hashtags make it easy to track dataset (and collection) relationships.
  • These two movies (both under a minute) explain how to use this with datasets and with collections.
  • Learn more about Galaxy histories in our updated tutorial.

Drag & Drop datasets into tool inputs

  • Interface now allows dragging datasets from history panel into the content selectors of the tool form.
  • Implemented in Pull Request 3871.

Upload directly to a collection

  • You can now bypass the history manipulation and upload your data straight into a collection for convenience.
  • Learn more about collections and how to use them in a new tutorial.

We extend special thanks to the 64 New Contributors to Galaxy in the past year.

Additionaly there are New Configuration Options and New Datatypes sections.

Galaxy Docker Image 17.05

The Galaxy Docker project has seen a new release, following Galaxy 17.05. Major features are an additional Docker compose setup with SLURM and HT-Condor deployments, BioContainers integration and much more automatic testing.


Parsec 1.0.0 - 1.0.2

Parsec is a newly released set of command-line utilities to assist in working with Galaxy servers. It uses automatically generated wrappers for BioBlend functions. Manage histories, launch workflows, and more, all from the command line. The README includes several examples.

Planemo 0.41.0

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.

BioBlend 0.9.0

BioBlend is a Python library for interacting with CloudMan and Galaxy‘s API. BioBlend makes it possible to script and automate the process of cloud infrastructure provisioning and scaling via CloudMan, and running of analyses via Galaxy.

See the release notes for what's new in release 0.9.0.

galaxy-lib 17.5.9-11

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.

Galaxy CloudMan 17.05 on AWS

A new release of Galaxy CloudMan is available on the Amazon Web Services cloud infrastructure. This release includes Galaxy 17.05, an updated tool list, and Slurm configuration changes to improve job performance. To get started, vist https://beta.launch.usegalaxy.org/ or take a look at the Getting Started guide.

Earlier Releases

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


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.

And the rest ...

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

Other News