October 2018 Galactic News

New events, pubs, blog posts, servers, tools and releases (and a Galaxy song too)

October 1st 2018

Galaxy News

The October 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.


Events

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

2018 SACNAS Pre-conference Workshops


Preconference data workshops at 2017 SACNAS Meeting

Software Carpentry

Data Carpentry

CyVerse

Galaxy

If you will be anywhere near San Antonio, Texas on October 10 then please consider participating in one of these SACNAS preconference workshops. You don't need to be registered for the 2018 SACNAS meeting to attend. Everyone is eligible and the workshops are free.

Software and Data Carpentry

Data Platforms for Life Science Researchers

Registration is free but space is limited. You are strongly encouraged to register soon. Both workshops are held October 10, the day before SACNAS starts.

Register Now

Plese note: The Galaxy Community Fund is augmenting SACNAS Travel Scholarships awards for the first ~ 28 scholarship recipients that register for these workshops. The additional funds will cover an extra night's lodging for scholarship recipients, enabling you to arrive the day before the workshops. Funds are limited, and once the funds are allocated, they are gone. (You must have received a SACNAS Travel Scholarship to be eligible.)

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. Early registration rates end October 31st.

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:

DateTopic/EventVenue/LocationContact
October 1st 2018 Reference-based RNA-seq data analysis 理研 革新知能統合研究センター(日本橋), Tokyo, Japan Atsushi Asai
October 1st 2018 Pitagora Meetup 理研 革新知能統合研究センター(日本橋), Tokyo, Japan and Online Atsushi Asai
October 2nd 2018 Genome assembly using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
October 4th 2018 ELIXIR CZ Proteomics Workshop 2018 IOCB AS CR, Prague, Czech Republic Training offered by GTN MemberBjörn Grüning
October 5th 2018 GTN - Instructor Community - First meeting (version 2) Online Berenice Batut
October 8th 2018 Workflow4Experimenters 2018 Course Pasteur Institute, Paris, France Training offered by GTN MemberGildas Le Corguillé
October 10th 2018 SACNAS 2018 Pre-Conference Workshops 2018 SACNAS, San Antonio, Texas, United States Training offered by GTN MemberCamille Avestruz, Tracy Teal, Blake Joyce, Dave Clements, Joslynn Lee
October 15th 2018 Galaxy @ eResearch Australasia Melbourne, Victoria, Australia Training offered by GTN MemberPresenters
October 15th 2018 Analyse RNAseq sous Galaxy Station marine de Roscoff, France Training offered by GTN Memberchristine.mantecon @upmc.fr
October 16th 2018 Bioinformatique - Analyse avancée de séquences Bordeaux, France Intervenants
October 17th 2018 Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it VU, Amsterdam, The Netherlands Training offered by GTN MemberCelia van Gelder
October 18th 2018 Introduction to Galaxy & the Genomics Virtual Laboratory University of Melbourne, Melbourne, Victoria, Australia Training offered by GTN MemberMelbourne Bioinformatics
October 23rd 2018 Introduction to Galaxy Australia: Differential Gene Expression from Bacterial RNA-seq Data Universities: Melbourne, Queensland, Southern Queensland, Sydney, New South Wales, Adelaide, James Cook, Monash, Tasmania; Australia Training offered by GTN Member
November 12th 2018 BioHackathon 2018 Paris Campus des Berges de Seine, Paris, France Bérénice Batut, Hervé Ménager
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 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 James 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

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

Highlighted Publications

10 Galactic and Stellar publications.

Publication Topics

# Tag # Tag # Tag # Tag
138 +Methods 47 +UsePublic 28 +Workbench 24 +UseMain
15 +RefPublic 13 +UseLocal 7 +Reproducibility 7 +Shared
7 +IsGalaxy 5 +Tools 5 +Cloud 3 +Other
3 +Unknown 2 +UseCloud 1 +HowTo 1 +Project
2 +Visualization

New Galactic Blog Posts

Galactic Blog

There are three 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?

Public Galaxy Server News

Public Galaxy Servers is becoming something ... more

In October the venerable Public Galaxy Server list and the relative upstart Galaxy Services list will be replaced with a unified directory that includes public servers, cloud services, and VMs and containers that support Galaxy.

Here's what's new:

Molecular Property Diagnostic Suite for Diabetes Mellitus (MPDS-DM)

MPDS-DM

The Molecular Property Diagnostic Suite for Diabetes Mellitus (MPDS-DM) is a Galaxy web portal that serves as an open access data repository containing available chemical and gene-level information on diabetes. MPDS-DM tools allow users to identify, explore, and characterize drug:gene relationships.

See the MPDS-DM directory entry for more.

CRAVAT-P

CRAVAT-P

CRAVAT-P is a proteomic extension of the Cancer-Related Analysis of VAriants Toolkit (CRAVAT) developed for the Galaxy-P bioinformatics platform. CRAVAT-P exists as a downstream analysis suite for peptide variants. Current support is tailored towards workflows that generate peptide sequences mapped to genomic locations.

See the CRAVAT-P directory entry for more.

Public Servers/Resources in Publications

We tag papers that use, mention, implement or extend public Galaxy servers, services and other resources. Here are the counts for the past month's publications:

# Tag # Tag # Tag # Tag
20 >Huttenhower 9 >RepeatExplorer 4 >Langille 3 >PhenoMeNal
2 >CPT 2 >Galaxy-P 2 >MGEScan 2 >Mississippi
2 >RiboGalaxy 1 >ANASTASIA 1 >ARGalaxy 1 >ARIES
1 >Cistrome 1 >CLIMB 1 >CRAVAT-P 1 >DBCLS
1 >Genomic Hyperbrowser 1 >GenOuest 1 >Globus Genomics 1 >GVL-MEL
1 >Hunter 1 >LAPPS Grid 1 >MPDSDM 1 >Orione
1 >Palfinder 1 >PreSTIGE 1 >Sciensano 1 >VirAmp
1 >Workflow4Metabolomics 1 >Jetstream

Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in September 2018.

Releases

New additions to the Galaxy Community.

GVL 4.4

The Genomics Virtual Lab (GVL) 4.4.0 has been released. The GVL is a comprehensive data analysis workbench that comes as a complete package with a variety of pre-installed and configured software (Galaxy, RStudio, Jupyter) coupled with cloud compute infrastructure. This latest release includes an upgrade of Galaxy to version 18.05, allows overridable Galaxy Configuration, and has many tools updraged to their latest revision.

See the GVL 4.4.0 release note for more.

Planemo 0.55.0

Planemo

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. See GitHub for details on this release.

galaxy-lib 18.5.14 - 18.9.1

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.

This month's updates are about mulled, Conda, and CWL tools.

And the rest ...

Other Galaxy packages that didn't have a release in the past month can be found on GitHub.


Other News

The Galaxy Training Network is starting a Community for Galaxy Instructors. This group will share best practices for giving Galaxy workshops and provide support for new instructors to get involved with Galaxy Training! Catch the first meeting October 5th, details here.