February 2019 Galactic News

Events (GCC Training, GalaxyAdmins), Platforms, Pubs, Jobs, COTM!, Doc, Training, Tools, Releases and more

February 1st 2019

Galaxy News

The February 2019 Galactic News is here! This is 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.


Event News

GCC2019 Training Topic Voting Is Open

GCC2019

The 2019 Galaxy Community Conference (GCC2019) will be held in Freiburg, Germany, 1-6 July. Like previous Galaxy Community Conferences, GCC2019 will feature invited keynotes, accepted talks, posters, demos, birds-of-a-feather gatherings, and training. The format of GCC2019 will be a bit different than the previous years: it starts with 1 day of training and then 3 days with more specialized training sessions aligned with talks. You can read more about the new format on the conference FAQ.

The GCC2019 Organizing Committee compiled training topics nominated by the community and expanded this list with community requests and topics from the previous GCC to offer a broad range of training sessions to be voted on by the community for GCC2019. Voting closes February 4th.

Training topics that are offered at GCC2019 are determined by the community so BY YOU!

You can vote for as many topics as you want, but please note that the more topics you vote for the less your vote for each one counts. What? Here's an example. If Moni votes for 4 topics then each of her votes counts for 1/4 of a point. If Dave votes for 22 topics then each of his votes counts for 1/22 of a point.

Please take a moment and vote on which training topics you would like to see at GCC2019, your vote matters!

ELIXIR Galaxy Community Workshop

GalaxyAdmins

Join the Galaxy Community of Elixir for a three day workshop at Station Biological de Roscoff, France to participate in workshops and hackathons focused on tool implementation in Galaxy, development of training materials for the Galaxy Training Network (GTN), and how to teach using GTM materials.

During the first 1 1/2 days, the attendees will learn about the integration of high-quality tools within Galaxy with their dependencies (Bioconda, Planemo) using the IUC best practice guidelines. They will also learn how to use Galaxy as a training tool and develop training material for the Galaxy Training Network. The second half of the workshop will be dedicated to Hackathon sessions where attendees will be able to bring their own projects around tool integration and/or training material and develop them collaboratively, with the support of community experts. Additional information can be found here.

Find pre-registration here.

GalaxyAdmins needs your topic suggestions

GalaxyAdmins

After a two year hiatus, the bimonthly online GalaxyAdmins meetups will return on February 28. GalaxyAdmins is a discussion group for Galaxy community members who are responsible for Galaxy installations. Our online meetups are around an hour long and feature a presentation followed by an open discussion. It's a great place to catch up on what your fellow admins are thinking about.

But, before we start meeting this month, we need to know what you care about. What do you want to learn? Who do you want to hear from? What's causing you trouble? Or, what have you worked that your fellow GalaxyAdmins would benefit from knowing?

Got some ideas? Nominate them

Upcoming events

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

Date Topic/Event Venue/Location Contact
January 31st 2019 12th Workflow Meetup 理化学研究所, Osaka and Tokyo, Japan Manabu Ishii
February 4th 2019 Traitement de données de séquences par Galaxy AGROCAMPUS OUEST, Rennes, France Training offered by GTN MemberSandrine Lagarrigue
February 21st 2019 GTN CoFest and call on Galaxy Training Material Online Bérénice Batut, Saskia Hiltemann
February 25th 2019 Galaxy HTS data analysis workshop University of Freiburg, Freiburg, Germany Training offered by GTN Membercontact at usegalaxy.eu
February 28th 2019 GalaxyAdmins February 2019 Meetup Online Helena Rasche, Dave Clements
March 6th 2019 Galaxy for linking bisulfite sequencing with RNA sequencing University of Rostock, Rostock, Germany Training offered by GTN Memberdestair [at] leibniz-fli.de
March 18th 2019 Gatersleben Research Conference: Applied Bioinformatics for Crops Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany Björn Grüning
March 20th 2019 Introduction into Galaxy and how to design your own analysis workflow Computational Biology Starter, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany Anne Fiebig
April 23rd 2019 Elixir Galaxy Community - Workshop at Roscoff/France Station Biological De Roscoff, Roscoff, France Training offered by GTN MemberGildas Le Corguillé
July 1st 2019 2019 Galaxy Community Conference (GCC2019) Freiburg, Germany Training offered by GTN MemberOrganizers

Publications

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

Highlighted Publications

Galactic and Stellar publications from January:

Ten of the fourteen highlighted publications are open access.

Publication Topics

# Tag # Tag # Tag # Tag
111 +Methods 47 +UsePublic 23 +UseMain 16 +Workbench
11 +UseLocal 10 +RefPublic 10 +IsGalaxy 9 +Tools
6 +Reproducibility 3 +Other 2 +Cloud 2 +HowTo
2 +Shared 2 +Project

Galaxy Platforms News

The Galaxy Platform Directory lists resources for easily running your analysis on Galaxy, including publicly available servers, cloud services, and containers and VMs that run Galaxy. Here's what's been added since last month:

QuanTP

QuanTP

QuanTP is a Docker image containing a fully-operational Galaxy instance with pre-installed QuanTP, a suite of tools and functionalities critical for proteo-transcriptomics, including statistical algorithms for assessing the correlation between single transcript–protein pairs as well as across two cohorts, outlier identification and clustering, along with a diverse set of results visualizations.

QuanTP is available in this Docker image, and on the Proteogenomics Gateway and UseGalaxy.eu. It has an Installation guide, and Supporting information, including Instructions for accessing the QuanTP tool on Jetstream, Instructions for accessing and running the Mouse data, and Accessing the QuanTP on the usegalaxy.eu. QuanTP is supported by the University of Minnesota, Minneapolis.

miCloud

miCloud is a Docker Image that leverages cloud technologies to provide an easy-to-use streamlined NGS data analysis using local computational hardware. It includes three preconfigured and ready-to-execute NGS pipelines: two for single or paired-end ChIP-Seq data and one for paired-end RNA-Seq data. miCloud can also provide access to a large selection of ready-to-execute bioinformatics pipelines, available from online Docker repositories such as BioContainers, DockStore, or BioShadock. It provides a workflow-centric interface to a Galaxy engine, using BioBlend.

miCloud is supported by Weill Cornell Medicine and Department of Biological Sciences, Hunter College of the City University of New York.

RNA Workbench

RNA Workbench

RNA Workbench, in addition to being available as a Docker container, is also available as public server hosted at UseGalaxy.eu. RNA Workbench has a collection of over 50 tools dedicated to different research areas of RNA biology, including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-Seq analysis, and RNA target prediction. This server has been up for a while, but we are just adding it to the platforms directory.

The workbench is developed by the RNA Bioinformatics Center (RBC). This center is one of the eight service units of the German Network for Bioinformatics Infrastructure, running the German ELIXIR Node.

Hi-C Explorer

Hi-C Explorer is another server that has been up for a while, but is also new to the Galaxy Platform Directory. It facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. See the "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer tutorial and example history.

Hi-C Explorer is also hosted at UseGalaxy.eu.

G-OnRamp

G-OnRamp

G-OnRamp provides a user-friendly, web-based platform for collaborative, end-to-end annotation of eukaryotic genomes using UCSC Assembly Hubs and JBrowse/Apollo genome browsers with evidence tracks derived from sequence alignments, ab initio gene predictors, RNA-Seq data, and repeat finders. It is available as a virtual machine that can be deployed locally, and as an Amazon Machine Image that can be run on AWS and launched with CloudLaunch.

Use the G-OnRamp output to visualize large genomics datasets, and can utilize the output to drive collaborative genome annotation projects in both research and educational settings. It has documentation:

AmrPlusPlus

G-OnRamp is supported by Washington University in St. Louis and Oregon Health & Science University

AmrPlusPlus

AmrPlusPlus is a Docker container with a Galaxy-based metagenomics pipeline that is intuitive and easy to use. AmrPlusPlus takes advantage of current and new tools to help identify and characterize resistance genes within metagenomic sequence data. The pipeline can be used under a local instance of Galaxy and installed via Galaxy's Main Tool Shed. It is also available as a Galaxy-based Docker Image, using base images developed by Björn Grüning at the University of Freiburg. It has Documentation and Email support. AmrPlusPlus is supported by Colorado State University.

Lifeportal

LifePortal

Lifeportal is a Galaxy server available to any researcher in Norway (and possibly any other user willing to use the service). LifePortal implements about 400 applications. It runs Galaxy version 18.09 and jobs are executed on the Abel cluster (~650 nodes) using the slurm-drmaa library. User support is available via email.

Every user with their own project in Lifeportal can manage it through the menus built in the Galaxy GUI. Lifeportal is supported by University of Oslo, Norwegian Bioinformatics Platform, MLS UiO, and UninetT Sigma2

LAPPS Grid

And from this cool writeup (that has nothing to do with life science): Learning from data: Using technology to gain deeper meaning from archives, by Emily Mercer of San Jose State University, describing work by James Pustejovsky of Brandeis University:

One example is the collaboration between the American Archive of Public Broadcasting and James Pustejovsky, professor at Brandeis University. In this collaboration James and his research team have created a software package using the Galaxy Workflow Engine and Language Application Grid (LAPPS Grid) for automatic extraction of metadata from video assets using machine learning methodologies (Oomen et al., 2018; Pustejovsky et al., 2017). What was once a time exhaustive process of real-time viewing and transcribing of film and video is now as simple as uploading a video file and applying a workflow. Processing takes seconds and afterwards the user has access to the metadata, for example, the text captions on the screen. This metadata can be exported as PBCore, a metadata standard specific to public broadcasting (Oomen et al., 2018; Pustejovsky et al., 2017).

There's also some Jetstream in the mix too.

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 6 >RepeatExplorer 5 >ARGs-OAP 3 >ABiMS
3 >Cistrome 3 >Galaxy-P 3 >UseGalaxy.eu 2 >LAPPS Grid
2 >RNA Workbench 2 >UseGalaxy.org 1 >AmrPlusPlus 1 >ASH
1 >G-OnRamp 1 >GeneLab 1 >Genomic Hyperbrowser 1 >GIO
1 >GmT 1 >GVL-MEL 1 >GVL-QLD 1 >Halogen Bonding
1 >HiCExplorer 1 >Martin Luther 1 >miCloud 1 >Peptimapper
1 >PRABI 1 >QuanTP 1 >SouthGreen 1 >TDPortal
1 >TreeGenes 1 >Trinity 1 >UseGalaxy.org 1 >Workflow4Metabolomics

New Galactic Blog Posts

Genome annotation with Prokka

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 push it back!

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.


Doc, Hub, and Training Updates

Updates from the Galaxy Training Materials in January, and the Hub as well:

GTN Training Materials

Galaxy Training Materials

Hub


ToolShed Contributions

Galaxy ToolShed

Tool Shed contributions in January 2019.

Releases

New additions to the Galaxy Ecosystem.

galaxy-lib 18.9.2

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.

Planemo 0.58.1

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

PAG 2019 Presentations and Posters are Available

Copies of most of the Galaxy related presentations and posters form the Plant and Animal Genome Conference are now online. Many thanks to the all the presenters for sharing their during and after the conference.