September 2020 Galactic News

BCC2020 & GCC2021, events, platforms, blog posts, tutorials, pubs, releases, obs ...

September 1st 2020

In the September 2020 issue

Galaxy News

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


BCC2020 is Done; GCC2021 is Coming

Galaxy Training at BCC2020
  • 804 people registered for one or more events
    • 592 for the three day meeting
    • 443 for training
    • 393 for CollaborationFest
  • Training
    • 60 training sessions
    • covering 36 topics (18 with a Galaxy emphasis)
    • adding up to 150 hours of live instruction
  • Presentations
    • 3 live keynotes (and then 3 recorded keynotes)
    • 70+ talks, presented in both hemispheres
    • 80+ posters and demos
  • 20 Birds-of-a-Feather & 2 Socials
Video Gallery

Videos of most presentations and training are now available on the conference web site. Training materials for many tutorials are also linked to.

Slides & Posters?

If you presented a talk or poster/demo then please upload your slides and PDFs to the F1000Research Galaxy Gateway. Once they are there, we will link to them from the conference site. (You can also send links/PDFs to outreach@galaxyproject.org.)

BCC2021 will be in Ghent
BCC2021: Pack your bags for Ghent

The 2021 Galaxy Community Conference (GCC2021) will be held in Ghent, Belgium, 5-12 July. We are hoping to be back in person next year. GCC2021 will end shortly before the The Ghent Festivities, 10 days of varied and free offer (music) performances, (street) theatre, exhibitions, animation for children, fairs, parades and much more.

Watch this space for details, and we hope to see you there.

More Event News

Despite COVID-19, there is still a lot going on. Some of it is virtual, but live events are starting to happen again, especially in Europe. We have updated our list of events to reflect what we know. Some highlights:

Galaxy Developer Roundtable

The next two roundtables are September 3 (this Thursday) and September 17. This week's topics are interactive PR commands by Alex Mahmood, and workflow updates - format, tooling, and GUI by John Chilton.

MIGALE

Five workshops this fall, all in Jouy-en-Josas and in French, and starting September 10. Oui.

5 Workshops

There are two upcoming Galaxy Australia workshops offered by QCIF on Galaxy (Intro and RNA-Seq Analysis). The first one is 8 September.

Upcoming Events
Upcoming Events

There are 15 events in the next 4 months

  • 5 are online
  • The remaining 10 are in France (6), Australia (2), and the United States (2)

And material from some recent events is now available:

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 the recent platform news we know about:

PiRATE

PiRATE, a Pipeline to Retrieve and Annotate Transposable Elements, is a Galaxy VM for detecting, classifying and annotating TEs of non-model organisms. It has a tutorial and user support. PiRATE is supported by IFREMER.

UseGalaxy.fr

The UseGalaxy.fr server is a general purpose omics analysis server hosted by the French Institute of Bioinformatics (IFB). In addition, this server also hosts the specialized Workflow4Metabolomics and ProteoRE servers.

User support is provided through a discourse-based forum.

ML Workbench

A comprehensive set of data preprocessing, machine learning, deep learning and visualisation tools, consolidated workflows for end-to-end machine learning analysis and training materials to showcase the usage of these tools. This workbench includes scikit-learn, Keras (a deep learning library based on TensorFlow) and various other tools to transform, learn and predict and plot your data. The server is supported by the Goecks Lab at OHSU and the Freiburg Galaxy Project.

deepTS

deepTS is a Galaxy platform for identifying, visualizing and analyzing Transcriptional Switch (TS) events from pairwise, temporal and population transcriptome data. A tutorial and user support are provided. deepTS is available as both a server and a Docker container. It is supported by Northwest A&F University.

BioCompute Object Galaxy

BioCompute Objects and BioCompute Object Galaxy server supports the IEEE 2791-2020 standard for bioinformatics pipelines/workflows in the High-Throughput Sequencing (HTS) space. This effort is supported by the FDA and the HIVE Lab at George Washington University.

Galactic Blog Activity

Here's what people are saying right now:

By Nuwan Goonasekera, Alexandru Mahmoud, Mohamad Safadieh, Enis Afgan

A data browser, project-level isolation, and the latest release of Galaxy.

GVL Beta 5

By StreetScience

Studying the RNA modifications of SARS-CoV-2 to improve understanding of SARS viruses.

StreetScience

By Anne Fouilloux

July has been a very busy month for Galaxy Climate ending with several sessions dedicated to Climate Science at BCC2020.

Climate Science Workbench

By Björn Grüning and Beatriz Serrano-Solano

How you can get your software tool into a Galaxy server and thus, exposed to thousands of researchers. For this purpose, we will follow David Lopez’s steps to add the very generic UNIX diff tool to Galaxy.

By Peter van Heusden

The COVID-19 pandemic has forced a rapid - and unplanned - shift towards online events instead of the usual roster of face-to-face seminars and conferences.

BCC2020 training and more

By Dave Clements

Ten thousand publications have used, referenced, extended and implemented Galaxy in the past 15 years. Half of those pubs appeared in just the last 3 years. Learn about this and other trends in the Galaxy community, as revealed by what we are publishing.

Top 20 Galaxy Journals

By Delphine Lariviere, Sergei Kosakovsky Pond, Anton Nekrutenko + HyPhy and Galaxy Teams

An on-line, curated resource that serves two functions:

Comparing Coronaviruses

Doc, Hub, and Training Updates

This tutorial was updated by Pavankumar Videm to use the most recent versions of tools. Learn how to use CLEAR-CLIP data in your analysis.

ChiRA

By Peter van Heusden, Simon Gladman, and Thoba Lose

A tutorial on variant calling in M. tuberculosis. This was first conceived at a workshop at NUBRI in Khartoum, Sudan, then presented at the African Society for Bioinformatics and Computational Biology meeting in Kumasi, Ghana in November 2019.

This tutorial was updated and expanded by Simon Bray. An introductory guide to using GROMACS (Abraham et al. 2015) in Galaxy to prepare and perform molecular dynamics on a small protein.

GROMACS

Job configuration in Ansible

Sections on job configuration in Ansible were added to the Galaxy Installation with Ansible tutorial by Simon Gladman and to the Running Jobs on Remote Resources with Pulsar by Helena Rasche.

Ansible, or else

This tutorial saw a major revamp by Helena Rasche. Learn how to use Ansible for your deployment recipes.

Ansible, or else

By Helena Rasche

The new GTN in Galaxy Webhook enables trainees to view training directly within Galaxy. This has been well received:

This is awesome! Magic @hexylena!
@bgruening

Bloody oath! This is an awesome idea. Grouse.

By Helena Rasche

The GTN in Galaxy Webhook enables trainees to view training directly within Galaxy. As part of this, trainees can click on tools, and have those tools directly activated in Galaxy.

Tool IDs

By Xavier Garnier, Anthony Bretaudeau, Anne Siegel, and Olivier Dameron

This new tutorial (and matching slides)uses data from the RNA-seq counts to genes tutorial in the AskOmics web application to do data integration and querying using the semantic web technologies

Using semantic web and RNA-Seq

By Marius van den Beek

Learn how to use Galaxy's Workflow Editor to construct different reusable workflows.

make a connection

These slides were updated by by Nicola Soranzo to reflect the 14.0 release of BioBlend. BioBlend is a Python library for interacting with Galaxy programmatically.

Tool details with BioBlend

This tutorial got a major update from Helena Rasche. Feeling overwhelmed by all the work you have done in Galaxy? Don't be. Use History search to find what you are looking for.

Searching histories

This slide deck and related resources got a thorough update from John Chilton. John also created several videos on this topic as well.

Galaxy Code Architecture

Ask and you shall receive. Thanks to work by Saskia Hiltemann and Helena Rasche there is now a GTN statistics page, listing all sorts of cool information about the state of the GTN library.

What's going on

Publications

671 new publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library in June, July and August. There were a boatload1 of Galactic and Stellar publications added, and a truckload1 of them are open access:

1 Who needs a Units of Measurement Ontology!

Suderman, K., Ide, N., Marc, V., Cochran, B., & Pustejovsky, J. (2020, June 30). ACL 2020 Workshop NLP-COVID.

Gu, Q., Kumar, A., Bray, S., Creason, A., Khanteymoori, A., Jalili, V., Grüning, B., & Goecks, J. (2020). BioRxiv, 2020.06.25.172445. doi: 10.1101/2020.06.25.172445

Rasche, H., & Gruening, B. A. (2020). BioRxiv, 2020.08.23.263509. doi: 10.1101/2020.08.23.263509

Lopez-Delisle, L., Rabbani, L., Wolff, J., Bhardwaj, V., Backofen, R., Grüning, B., Ramírez, F., & Manke, T. (2020). Bioinformatics. doi: 10.1093/bioinformatics/btaa692

Tangaro, M. A., Donvito, G., Antonacci, M., Chiara, M., Mandreoli, P., Pesole, G., & Zambelli, F. (2020). GigaScience, 9(4). https://doi.org/10.1093/gigascience/giaa033

McGowan, T., Johnson, J. E., Kumar, P., Sajulga, R., Mehta, S., Jagtap, P. D., & Griffin, T. J. (2020). GigaScience, 9(4). https://doi.org/10.1093/gigascience/giaa025

Baker, D., Beek, M. van den, Blankenberg, D., Bouvier, D., Chilton, J., Coraor, N., Coppens, F., Eguinoa, I., Gladman, S., Grüning, B., Keener, N., Larivière, D., Lonie, A., Pond, S. K., Maier, W., Nekrutenko, A., Taylor, J., & Weaver, S. (2020). PLOS Pathogens, 16(8), e1008643. https://doi.org/10.1371/journal.ppat.1008643

Lac, M. du, Duigou, T., Herisson, J., Carbonell, P., Swainston, N., Zulkower, V., Shah, F., Faure, L., Mahdy, M., Soudier, P., & Faulon, J.-L. (2020). BioRxiv, 2020.06.14.145730. https://doi.org/10.1101/2020.06.14.145730

Sargent, L., Liu, Y., Leung, W., Mortimer, N. T., Lopatto, D., Goecks, J., & Elgin, S. C. R. (2020). PLOS Computational Biology, 16(6), e1007863. https://doi.org/10.1371/journal.pcbi.1007863

Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434

Spoor, S., Wytko, C., Soto, B., Chen, M., Almsaeed, A., Condon, B., Herndon, N., Hough, H., Jung, S., Staton, M., Wegrzyn, J., Main, D., Feltus, F. A., & Ficklin, S. P. (2020). Database, 2020. https://doi.org/10.1093/database/baaa032

Sweeney, B. A., Tagmazian, A. A., Ribas, C. E., Finn, R. D., Bateman, A., & Petrov, A. I. (2020). Current Protocols in Bioinformatics, 71(1), e104. https://doi.org/10.1002/cpbi.104

Wang, J., Alvin Chew, B. L., Lai, Y., Dong, H., Xu, L., Balamkundu, S., Cai, W. M., Cui, L., Liu, C. F., Fu, X.-Y., Lin, Z., Shi, P.-Y., Lu, T. K., Luo, D., Jaffrey, S. R., & Dedon, P. C. (2019). Nucleic Acids Research, 47(20), e130–e130. https://doi.org/10.1093/nar/gkz751

McCann, J., Macas, J., Novák, P., Stuessy, T. F., Villaseñor, J. L., & Weiss-Schneeweiss, H. (2020). Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.00362

Powell, G. L., Vannan, A., Bastle, R. M., Wilson, M. A., Dell’Orco, M., Perrone-Bizzozero, N. I., & Neisewander, J. L. (2020). Scientific Reports, 10(1), 11291. https://doi.org/10.1038/s41598-020-67966-8

Thursby, S.-J., Lobo, D. K., Pentieva, K., Zhang, S.-D., Irwin, R. E., & Walsh, C. P. (2020). GigaScience, 9(6). https://doi.org/10.1093/gigascience/giaa066

Who's Hiring

Quatre postes (CDI) de bioinformaticiens / biostatisticiens (H/F) à l’Institut Pasteur (Paris).

Institut Pasteur

The Plant Computational Genomics laboratory at the University of Connecticut (Storrs, CT) has an opening for a Postdoctoral Scholar, developing mechanisms for cross-platform data/application sharing that builds on existing efforts with Galaxy, the Tripal platform, and cloud-based HPC.

UConn

The Schatz Lab at Johns Hopkins University is looking for

  • self-driven individuals that can work independently to fill multiple software development positions on the Galaxy Project.
  • ambitious individuals to fill a programmer analyst position working on the Galaxy and AnVIL projects.

Johns Hopkins

VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.

... We are building on the internationally used platform FAIRDOMhub for data management, and Galaxy (https://www.usegalaxy.be and https://usegalaxy.eu) for data analysis.

VIB

Black Canyon Consulting at NCBI, Bethesda, Maryland, United States.

Black Canyon Consulting at NCBI

Releases

Command-line utilities to help with managing users, data libraries and tools in a Galaxy instance, using the Galaxy API via the Bioblend library. This release features new commands (search toolsheds, delete users, uninstall tools), fixes & updates, and newly extended documentation.

Nebulizer

BioBlend is a Python library for interacting with CloudMan and Galaxy‘s API. BioBlend makes it possible to script and automate the process of cloud infrastructure provisioning and scaling via CloudMan, and running of analyses via Galaxy.

See the release notes for what's new in release 0.14.0.

Other news

Galaxy's graphical workflow editor includes an automatic/default workflow layout algorithm that is 10 years old. A replacement based on elkjsis on the way, thanks to work by Helena Rasche.

Workflow layout with elkjs