November 2018 Galactic News
Platforms Directory; new events, pubs, blog posts, servers, tools and releases
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:
-
The Galaxy Platforms Directory: 125 ways to use Galaxy
- New Galaxy Platforms: SMAGEXP and the SNIC Science Cloud
- European Galaxy Days, 19-20 November, Freiburg, Germany
- 2019 Galaxy Admin Training, January at Penn State
- All upcoming events
- 104 publications, including three highlighted ones
- Two new Galactic Blog entries
- Open positions (at least 12 of them)
- Doc, Hub, and Training Updates
- ToolShed contributions
- Releases Galaxy 18.09 is released!
- And other news too
If you have anything to add to next month's newsletter, then please send it to outreach@galaxyproject.org.
The Galaxy Platforms Directory
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 (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)
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, 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 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 |
 Gareth 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 |
contact@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 |
|
| 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 |
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 |
Instructors |
| July 1st 2019 | 2019 Galaxy Community Conference (GCC2019) | Freiburg, Germany |
Organizers |
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.
- Dynamic Framework for Reconfiguring Computing Resources in the Inter-cloud and Its Application to Genome Analysis Workflows, Tomoya Tanjo, Jingtao Sun, Kazushige Saga, Atsuko Takefusa, Kento Aida. In: Xiang Y., Sun J., Fortino G., Guerrieri A., Jung J. (eds) Internet and Distributed Computing Systems. IDCS 2018. Lecture Notes in Computer Science, vol 11226. Springer, Cham
- Improve your Galaxy text life: The Query Tabular Tool, James E. Johnson, Praveen Kumar, Caleb Easterly, Mark Esler, Subina Mehta, Arthur C. Eschenlauer, Adrian D. Hegeman, Pratik D. Jagtap. F1000Research 2018, 7:1604
- Next Generation Indexing for Genomic Intervals, Vahid Jalili, Matteo Matteucci, Jeremy Goecks, Yashar Deldjoo, Stefano Ceri. IEEE Transactions on Knowledge and Data Engineering 2018, doi:10.1109/TKDE.2018.2871031
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](https://www.zotero.org/groups/1732893/galaxy/tags/>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](https://www.zotero.org/groups/1732893/galaxy/tags/>Globus Genomics) | |||
| 1 | >Langille | 1 | >MPI-HLR | 1 | >Pasteur | 1 | >PSC | |||
| 1 | >UseGalaxy.eu |
New Galactic Blog Posts
There are two new Galactic Blog entries:
- Contributor of the month: Saskia Hiltemann, by Marten Čech
- Tutorial of the Month: "Galaxy 101", selected by Yvan Le Bras, by Bérénice Batut
Who's Hiring
The dark energy* of irreproducible research is threatening the science universe! Please help the Galaxy expand!
- 2-year IR/postdoc position (Analysis of Genomic Variants in Children and Young Adults with Acute Myeloid Leukemia), Analyse Bioinformatique ARTbio, Paris, France
- Research enigineer Bioinformatics/Statistics/Microbial. INRA, St Genes Champanelle, France
- Bioinformatics Cloud Architect, EMBL-EBI, Hinxton, United Kingdom
- Galaxy Developer, Cambridge, United Kingdom
- Specialist Solutions Architect - Biological Sciences, Amazon Web Services, United States
- Bioinformatics Scientist, ResearchDx, Irvine, California, United States
- NGS Scientific Applications Specialist, Integrated DNA technologies, Iowa City, Iowa, United States
- Scientist (f/m), NGS bioinformatics core facility, Helmholtz Zentrum München, Germany
- Galaxy Developers, Intero Life Sciences, United States.
- Freiburg Galaxy Team has open positions, Freiburg, Germany
- The Blankenberg Lab in the Genomic Medicine Institute at the Cleveland Clinic Lerner Research Institute is hiring postdocs.
- Galaxy Project is hiring software engineers and postdocs at Johns Hopkins, Baltimore, Maryland, United States
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
There was a mind-boggling amount of activity in the Galaxy Training Materials in October, and some Hub activity as well:
Training Materials
- New Deploying a compute cluster in OpenStack via Terraform hands-on tutorial and Slides, by Helena Rasche
- New Ansible hands-on tutoral and Slides, by Helena Rasche
- New Network analysis with Heinz slides and an updated tutorial from Cico Zhang and Saskia Hiltemann
- A general update to the Contributing to the Galaxy Training Material materials from Saskia Hiltemann
- Update to Genome annotation with Prokka tutorial from Bérénice Batut and Ekaterina Polkh
- Update to Quality Control tutorial from Anthony Bretaudeau
- Update to Reference-based RNA-Seq data analysis tutorial from Nicola Soranzo and Peter van Heusden
- Update to Calling variants in diploid systems from Nicola Soranzo
- Update to RAD-Seq de-novo data analysis tutorial from Yvan Le Bras
And from Bérénice Batut:
- A big Thank you!! to the 💯 contributors of the Galaxy Training Material! You are awesome. This project is only possible because of you!
And we would especially like to welcome new contributors Matthias313, foellmelanie, and Florian-H-Lab.
Hub
- Sorting Your Inputs, a how-to page by Jennifer Hillman-Jackson
- And the Hub now supports DataTables (in a limited fashion, look for more in the future) and Font Awesome 5 (look for more spiffy icons).
ToolShed Contributions
](http://toolshed.g2.bx.psu.edu/)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 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
- Selbst ist der Forscher: Big-Data-Analysen leicht gemacht, an article inn LABORPRAXIS about the Galaxy Freiburg team and the Backofen Lab.
- Broad, Johns Hopkins Tapped to Develop Cloud Infrastructure for NHGRI-Funded Research, GenomeWeb article about the newly launched NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-Space (AnVIL) program, of which Galaxy will be a key component.