September 2018 Galactic News

New events, pubs, blog post, jobs, ...

September 13th 2018

Galaxy News

The September 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

As always, there is a lot going on in the Galaxy:

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, 19-20 November, Freiburg, Germany

European Galaxy Days

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.

Upcoming events

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

DateTopic/EventVenue/LocationContact
September 17th 2018 6th Galaxy high-throughput sequencing (HTS) data analysis workshop University of Freiburg, Freiburg Germany Training offered by GTN MemberFreiburg Galaxy Team
September 18th 2018 Variant detection using Galaxy QFAB, St Lucia, Queensland, Australia Training offered by GTN Membertraining@qfab.org
September 25th 2018 Gateways 2018 University of Texas, Austin, Texas, United States Katherine Lawrence
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 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
December 6th 2018 Molecular Dynamics and Analysis using BRIDGE Cape Town, South Africa Organizers
July 1st 2019 2019 Galaxy Community Conference (GCC2019) Freiburg, Germany Training offered by GTN MemberOrganizers

Publications

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

Highlighted Publications

Four Galactic and Stellar publications.

Publication Topics

# Tag # Tag # Tag # Tag
41 +Methods 17 +Workbench 13 +RefPublic 13 +UsePublic
5 +UseLocal 5 +UseMain 4 +Cloud 4 +Tools
2 +IsGalaxy 2 +Reproducibility 1 +HowTo 1 +Unknown

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

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.

Contributor of the Month: Carrie Ganote

Galactic Blog

There is one new Galactic Blog entry:


Public Galaxy Server News

There are over 100 publicly accessible Galaxy servers and several Galaxy services. One of each were added in the past month.

epiGeEC

epiGeEC

epiGeEC compares user-provided epigenomic datasets with thousands of public datasets in a few minutes. It can also directly compare user’s datasets. This server is provided by the Genetics and genomics Analysis Platform (GenAP) project, thereby leveraging Compute Canada's advanced research computing infrastructure. A tutorial is available and anonymous access and account creation are both supported."

See the epiGeEC directory entry for more.

MetaCentrum - Czechia

MetaCentrum

MetaCentrum supports Galaxy instances on the Czech National Grid Infrastructure (NGI), that are available to employees and students of research and academic organizations of Czechia and for scientific purposes only. Use requires registering for an account.

See the Metacentrum directory entry for more.

Public Servers in Publications

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

# Tag # Tag # Tag # Tag
5 >RepeatExplorer 4 >Huttenhower 3 >Ballaxy 3 >DBCLS
3 >GrAPPA 2 >ARGs-OAP 1 >Cistrome 1 >epiGeEC
1 >EpiToolKit 1 >GenAP 1 >GVL-Cloud 1 >IAPTK
1 >Kmer-SVM 1 >MetaCentrum 1 >Oqtans 1 >Osiris
1 >Pitagora 1 >RiboGalaxy 1 >Workflow4Metabolomics

Hub and Doc Updates


Tools

ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in August 2018.

Releases

New additions to the Galaxy Community.

CloudBridge

CloudBridge v1 has been released!

  • One interface to major Infrastructure-as-a-Service (IaaS) cloud providers
  • CloudBridge v1 supports Amazon Web Service (AWS), Microsoft Azure, and OpenStack clouds
  • Thanks to help from the AnswerALS project and Microsoft, Azure now has complete implementation of all CloudBridge capabilities

For other features and changes contained in this release, please take a look at the CHANGELOG.

BioMAJ2Galaxy

BioMAJ2Galaxy does the following actions on a Galaxy server:

  • Add new items to data libraries
  • Remove items from data libraries
  • Add new items to tool data tables using data managers
  • Remove items from tool data tables

These scripts are primarily designed to be used as BioMAJ post processes, but they can probably used directly from the command line if you need to.

Galaxy Docker Image 18.05

The Galaxy Docker project has a matching release, for Galaxy 18.05. The release features the 18.05 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

CellOrganizer for Galaxy

  • CellOrganizer for Galaxy is a set of tools that enables users to train generative models of the cell from microscopy images, analyze trained generative models, and synthesize instances using CellOrganizer, a tool for learning and managing generative models of cell organization directly from images.