November 2018 Galactic News

Platforms Directory; new events, pubs, blog posts, servers, tools and releases

November 1st 2018

Galaxy News

The November 2018 Galactic News is here! This is a summary of what is going on in the Galaxy community. Here's what's happening:

If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.


The Galaxy Platforms Directory

125+ platforms to use Galaxy on

We are pleased to announce the new Galaxy Platform Directory. This directory lists 125 platforms where you can use or deploy your own Galaxy Server with minimal effort, including

  • Public Galaxy servers
  • Academic and commercial cloud services that support Galaxy
  • Containers and VMs that run Galaxy

And

  • Almost all of them are free to use (Commercial clouds are the exception)
  • Almost all of them are open to everyone (Academic clouds are the exception)
  • All of the resources can be used, either immediately, or shortly after getting an account

These resources cover a wide spectrum of domains all across life sciences. There are resources for genomics (lots of them), metagenomics, transcriptomics, proteomics, drug discovery and even some outside biology like natural language processing (a couple of them), and social science.

This directory replaces the previously separate public server, cloud service, and virtual appliance directories. Everything is now in one spot.

New Galaxy Platforms

And there are several new platforms for running Galaxy this month too:

SMAGEXP

SMAGEXP

SMAGEXP (Statistical Meta-Analysis for Gene EXPression) provides a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities. A Galaxy instance is provided in a Docker container. SMAGEXP comes with an Installation and user guide, including two step-by-step examples. It is supported by Univ. Lille Droit et Santé, Lille, France and Inria Lille-Nord Europe, MODAL, Lille, France.

SNIC Science Cloud (SSC)

SNIC Science Cloud (SSC)

Swedish National Infrastructure for Computing (SNIC) Science Cloud (SSC) is a community cloud and use of the resources is free of charge to Swedish PIs and their collaborators. As for other SNIC allocations you need an affiliation with a Swedish higher education institution to be eligible to apply for a project. It's a national-scale cloud infrastructure for Swedish Academia.

SNIC offers support and training. SNIC Science Cloud is currently a pilot project and not a production resource. You can request a project here. quotas:


Events

Tired of sitting in the same old office/lab/cafe table? Here are some upcoming events to help get you out and about.

European Galaxy Days

European Galaxy Days, 19-20 November, Freiburg, Germany

European Galaxy Days will be held 19 and 20 November 2018 in Freiburg, Germany. The first day will give an overview of the current state of the Galaxy framework with several talks and demonstrations. The second day will focus on developing and extending the Galaxy ecosystem.

The event is free and registration is open. See the event home page for more.

2019 Galaxy Admin Training

Galaxy Admin Training

Galaxy Admin Training will be offered January 28 through February 1 at Penn State University, where the Galaxy Project got started over ten years ago. The workshop is split into a 2 day introductory session and a 3 day advanced topics session. Participants can register for one or both sessions.

Registration is open, but space is limited!

See the Galaxy 2019 Admin Training page for more details.

Upcoming events

These and other Galaxy related events are coming up in the next few months:

Date Topic/Event Venue/Location Contact
November 4th 2018 Galaxy Australia – The Free Genetics and Genomics Analysis Platform AGTA, Adelaide, Australia Training offered by GTN MemberGareth Price
November 5th 2018 An introduction to the Galaxy platform for computational biology FORTH, Heraklion, Crete Alexandros Kanterakis, Vangelis Kritsotakis
November 6th 2018 NGS Introduction using Galaxy Ghent University, Ghent, Belgium Paula Andrea Martinez, VIB
November 7th 2018 Galaxy @ Cold Spring Harbor 2018 Biological Data Science meeting Cold Spring Harbor, New York, USA Presenters
November 12th 2018 BioHackathon 2018 Paris Campus des Berges de Seine, Paris, France Bérénice Batut, Hervé Ménager
November 12th 2018 Brno Bioinformatics Workshop CEITEC, Brno, Czechia Jan Oppelt, Jelle Scholtalbers
November 13th 2018 Galaxy for NGS Data Analysis UCLA, Los Angeles, California, United States, and Online Weihong Yan
November 14th 2018 Analyse des données RNA-Seq sous l'environnement Galaxy Lyon, France Training offered by GTN Membercontact@biosciencesco.fr
November 14th 2018 Introduction to Galaxy Australia – Metagenomics Universities: Melbourne, Queensland, Southern Queensland, Sydney, New South Wales, Adelaide, James Cook, Monash, Tasmania; Australia Training offered by GTN Member
November 15th 2018 GTN CoFest on Training Material Online Bérénice Batut, Saskia Hiltemann
November 19th 2018 RNA-seq analysis in Galaxy National Institutes of Health (NIH), Bethesda, Maryland, United States mo@galaxyproject.org
November 19th 2018 European Galaxy Days Freiburg, Germany Hans-Rudolf Hotz, Björn Grüning, Jean-François Dufayard
November 28th 2018 Computational Genomics CSHL, Cold Spring Harbor, New York, United States Training offered by GTN MemberJames Taylor
December 6th 2018 Molecular Dynamics and Analysis using BRIDGE Cape Town, South Africa Organizers
January 28th 2019 2019 Galaxy Admin Training Penn State University, State College, Pennsylvania, United States Training offered by GTN MemberInstructors
July 1st 2019 2019 Galaxy Community Conference (GCC2019) Freiburg, Germany Training offered by GTN MemberOrganizers

Publications

104 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in October.

Highlighted Publications

Galactic and Stellar publications from October.

Publication Topics

# Tag # Tag # Tag # Tag
67 +Methods 34 +UsePublic 15 +Workbench 11 +RefPublic
8 +UseMain 6 +Reproducibility 5 +UseLocal 2 +HowTo
2 +IsGalaxy 2 +Other 2 +Shared 1 +Cloud
1 +Project 1 +Tools 1 +Unknown 1 +Visualization

Galaxy Platforms in Publications

We tag papers that use, mention, implement or extend public Galaxy platforms (servers, services, clouds, containers...). Here are the counts for the past month's publications:

# Tag # Tag # Tag # Tag
23 >Huttenhower 4 >Workflow4Metabolomics 2 >Genomic Hyperbrowser 2 >GVL-QLD
2 >PhenoMeNal 2 >RepeatExplorer 2 >UseGalaxy.org 1 >A-Game
1 >ABiMS 1 >ARGs-OAP 1 >Biomina 1 >ErasmusMC
1 >GalaxEast 1 >GigaGalaxy 1 >GIO 1 >Globus Genomics
1 >Langille 1 >MPI-HLR 1 >Pasteur 1 >PSC
1 >UseGalaxy.eu

New Galactic Blog Posts

Galactic Blog

There are two new Galactic Blog entries:


Who's Hiring

Please Help! Yes you!

The dark energy* of irreproducible research is threatening the science universe! Please help the Galaxy expand!

Have 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.

* Seems more sinister than dark matter don't you think?

Doc, Hub, and Training Updates

There was a mind-boggling amount of activity in the Galaxy Training Materials in October, and some Hub activity as well:

Training Materials

Galaxy Training Materials

And from Bérénice Batut:

And we would especially like to welcome new contributors Matthias313, foellmelanie, and Florian-H-Lab.

Hub


ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in October 2018.

Releases

New additions to the Galaxy Community.

Galaxy Release 18.09

We are pleased to announce the release of Galaxy 18.09. This release has extensive workflow enhancements, new group tags, and Python 3 Beta Support. Please see the full release notes for more information, including how to upgrade today!

Planemo 0.56.0

Planemo

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.


Other News