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April 2021 Galactic News

GCC2021 Abstracts and Registration are open, plus lots more.

Galaxy News

This newsletter coincides with the anniversary of James Taylor's death on April 2, 2020. James was a Galaxy Project founder and PI, and losing him at the same time as the global COVID-19 shutdown made for a tough month, and then a tough year for the Galaxy Community. To mark this, there are two items about James below. First, a call to share your favorite story about James via a 30 second video (by April 30). Second, there is a link to a note to James written by project leadership (mainly Anton).

The other big news is that registration, abstract submission, and fellowship applications for the 2021 Galaxy Community Conference are now open. Abstracts and fellowship applications are due by May 7.

And as always there are sections on

It's been a memorable twelve months. It would have been easy to curl up and hide, but we kept going, addressed gaps, and helped address the global pandemic as well.

Thanks for supporting each other,

Dave Clements and Beatriz Serrano-Solano, Editors


Featured news

James Taylor

Share your favorite James Taylor story

It's been a year since James Taylor passed away. To remember him, and mark his upcoming birthday (May 18) we would like to create a community video. We are asking you to tell us your favorite story about James in ~ 30 seconds. We will combine your clips into a video that will be prominently featured on all Galaxy-related sites.

Here is what we will need you to do before April 30:

  1. Think of your favorite story/interaction/event involving James
  2. Pick a nice location and record the video!
  3. The video should be:
  • in a high-resolution
  • without background noise
  • in a horizontal orientation (not vertical!)
  • ≲ 30 seconds in length
  1. Deposit video file to your Google Drive or Dropbox folder (or any other location that would allow us to retrieve it)
  2. Send a link to the video, your name and location as you would like them to appear in the final video to: outreach@galaxyproject.org

Thank you all in advance and please feel free to invite other friends of James to participate.

James Taylor

The project leadership marked the one year anniversary of James's passing with a letter to him summarizing the year he missed. It starts with

"What a year. It was difficult."

and then goes on to describe the community's progress and perseverance over the year. It's a powerful reflection on James, this community, and the past year. Please take a look.

Community News

GCC2021 is coming

The 2021 Galaxy Community Conference will be held 28 June through July 10. It will be virtual, affordable, and globally accessible.

GCC2021 will start on 28 June with a week of online training. Training will largely use the GTN Smörgåsbord model: lectures will be prerecorded, with live help available on chat for the duration of the week. This model allows participants to learn at their own pace, avoids scheduling conflicts that are inherent with our usual multi-track training, and enables those with low bandwidth internet connections to fully participate.

We will reuse the BCC2020 model for talks, posters, and demos: posters and demos will be live (sometimes in both hemispheres), and talks will be prerecorded.

And GCC2021 is looking for sponsors too!

GCC2021 is coming

June 25

GCC2021 registration is open until June 25.

Registering before May 24 saves 50% off of the full rates. Registration discounts will be available to researchers from low and lower-middle income countries. For everyone else, registration are downright cheap too: the rates start in €15.00 for the training week and in €25.00 for the 3-day conference. The CoFest is free.

GCC2021 is coming

May 7

The Galaxy Community Fund is offering fellowships to students, post-docs, and other non-profit / academic / government researchers based in lower, lower-middle and upper-middle income countries who will benefit from attending GCC2021, and for whom the cost of registration is a barrier.

It will cover the full registration for any GCC2021 events. Apply here.

GCC2021 is coming

Submissions due May 7

GCC2021 is seeking oral presentations, lightning talks, posters, and demos, from researchers using Galaxy, and all over the world. If you would like to present your work, please submit your abstract by May 7!

Open Genome Informatics

The Open Genome Informatics Consortium of which Galaxy is a part, has been accepted to participate in the 2021 Google Summer of Code.

Interested? Please review the Galaxy project proposals and apply to GSoC by April 12. Questions? Please contact the mentor(s) for each proposal.

Event News

Despite COVID-19, there is still a lot going on, and most of it is online. See the full list of events. Some highlights:

Galaxy @ ISMB/ECCB & BOSC ?

Submissions due May 6

ISMB/ECCB 2021 is one of the largest bioinformatics conferences and every year Galaxy has had a significant presence. ISMB/ECCB is built from community building blocks, and this year that includes the Bioinformatics Open Source Conference (BOSC) (our 2018 and 2020 conference partner), as well as communities focused on high-throughput sequencing, mass spec, bioinformatics education, visualization, microbiomes, bioinformatics core facilities, and many others.

BOSC is a particularly good match for the Galaxy community. Topics include software development practices that promote open science standards and sharing of biological data and code, as well as approaches for building diverse communities.

Most of these are accepting talk and poster submissions through the ISMB/ECCB website, but BioInfo-Core is taking talk submissions here. All submissions are due May 6.

BioInfo-Core
Galaxy Resources for You Webinars

Our next webinar series will focus on Galaxy resources for several different communities. Webinars are held every other Wednesday at 10:00 Eastern US / 16:00 Central European time. The first two webinars are:

Galaxy Resources for Researchers, April 14 21 (postponed one week)

Galaxy Resources for Educators and Trainers, April 28

Space is, um, unlimited! But sign up today anyway and we will send you a reminder.

In addition, there are two more webinars this month:

ELIXIR & Galaxy Project, April 16

Building a bioinformatics platform: Lessons learned from immuneML, April 28

Papercuts CoFest
[April Papercuts CoFest](/src/events/2021-04-papercuts/index.md)

15 April, Online, Global

Please join us for the 7th Papercuts CoFest day on April 15 to help the Galaxy Ecosystem become a better place, and to help new contributors come on board.

We will be on Gitter for chat all day long, and on 3 calls spread across the day. Please take advantage of both to communicate with your collaborators around the world.

UseGalaxy.NO

13 April

ELIXIR Norway is pleased to announce the first online course on using the Norwegian e-infrastructure for Life Science (NeLS) and the nationally supported usegalaxy.no. There are 3 identical events. Please register for only one of them.

Galaxy Developer Roundtable

The next roundtable meetups will be:

~~April 15: TBD~~

April 29: Scalability and Challenges, led by Aysam Guerler

That is, they will be if anyone volunteers to lead discussions on topics of interest. (Kudos to Sam!)

21 April, Online, Australia

Step through genome assembly using chloroplast sequencing data and the Galaxy Australia web platform.

Register here!

19-23 April, Online, Global

The purpose of this workshop is to gain knowledge on Next Generation Sequencing (NGS) with a special focus on bulk and single-cell RNA-Seq data analysis in Arabidopsis thaliana. Although it is designed to deal with plant transcriptome data analysis, most of the analysis can be adapted to other organisms too.

Register here!

4-6 May, Bordeaux, France

Savoir rechercher des informations dans les banques de données. Maîtriser les outils d'analyse de séquences tels que les alignements et savoir interpréter les résultats. Maîtriser les formats et les analyses des nouvelles données issues du séquençage (NGS).

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:

IPK Blast Consortia

The IPK Galaxy Blast Suite is part of the IPK Crop Analysis Tools Suite (CATS). Offers access to genomic references published by IPK and collaborative projects. Provides BLAST for Barley, Wheat, and Rye data. Comes with an introduction, tutorials, and email support.

... on the Human Cell Atlas Galaxy instance of course. This write-up from EMBL-EBI discusses both the user interface and the back end implementation of this server.

Human Cell Atlas
Australian BioCommons

We asked the submitter for some background on what research they were doing. We found a fascinating story.

[UseGalaxy.*](/src/usegalaxy/index.md) News

UseGalaxy.*

Galactic Blog Activity

By Nolan Woods

Tips for collections, mapping, AWK, flow control, writing tool wrappers, and more.

Flow Control: Conditional
TIaaS Feedback

We heard from a lot Training Infrastructure as a Service (TIaaS) users this month:

TIaaS is coming to both UseGalaxy.org and UseGalaxy.org.au. Watch this space for updates.

TIaaS

Doc, Hub, and Training Updates

By Wendi Bacon

Fully process single-cell data, remove low quality cells, reduce the many dimensions of data that make it difficult to work with, and ultimately define clusters and find biological meaning and insights!

Figure 12: Appearance is everything
[How to import a workflow from the Workflow Hub and run it on remote COVID-19 data](https://galaxyproject.eu/posts/2021/03/25/wfh-video/)

Thanks to a great Collaboration between the Galaxy Community, Dockstore and the Workflow Hub, it is possible to import a workflow directly into Galaxy and run it. This is using the GH4GH API TRS.

[Recordings of the Galaxy-ELIXIR webinar series: Advanced features](https://galaxyproject.eu/posts/2021/03/25/elixir-webinar-series-advanced-features/)

Four weeks of webinars are now over. In these four sessions, the Galaxy community gave an excellent overview of recent features in Galaxy that may have remained unknown to many users, due to the rapid developments in this very large and very active community.

If you missed them, the recordings are now available on the ELIXIR Europe YouTube channel.

Galaxy-ELIXIR webinar series
scRNA

By Mehmet Tekman and Beatriz Serrano-Solano

Single cell RNA-seq analysis provides a great level of detail in understanding the underlying dynamic processes within tissues. This tutorial uses scRNA-Seq to highlight some of the key differentiation pathways that plant root cells undergo.

CellProfiler

By Beatriz Serrano-Solano, Yi Sun and Jean-Karim Hériché

This tutorial tracks dividing nuclei in a short time-lapse recording of one mitosis of a syncytial blastoderm stage Drosophila embryo expressing a GFP-histone gene that labels chromatin.

By Cristóbal Gallardo, Pavankumar Videm and Beatriz Serrano-Solano

Brassinosteroids are phytohormones that have the ability to stimulate plant growth and confer resistance against abiotic and biotic stresses. This tutorial details the necessary steps to identify potential targets of brassinosteroid-induced miRNAs.

Arabidopsis thaliana

GTN FAQ Page

The Galaxy Training Network now has a Frequently Asked Questions (FAQ) page that is automatically populated from reusable snippets that are already in the GTN.

Publications

Pub curation activities are on a semi-hiatus right now but a few publications referencing, using, extending, and implementing Galaxy were added to the Galaxy Publication Library anyway. Here are the new open access Galactic and Stellar pubs:

Guerler, A., Baker, D., Beek, M. van den, Bouvier, D., Coraor, N., Schatz, M. C., & Nekrutenko, A. (2021). BioRxiv, 2021.03.17.435706. https://doi.org/10.1101/2021.03.17.435706

Maier, W., Bray, S., Beek, M. van den, Bouvier, D., Coraor, N., Miladi, M., Singh, B., Argila, J. R. D., Baker, D., Roach, N., Gladman, S., Coppens, F., Martin, D., Lonie, A., Gruning, B., Pond, S. K., & Nekrutenko, A. (2021). BioRxiv, 2021.03.25.437046. https://doi.org/10.1101/2021.03.25.437046

Patel, J. A., Dean, D. A., King, C. H., Xiao, N., Koc, S., Minina, E., Golikov, A., Brooks, P., Kahsay, R., Navelkar, R., Ray, M., Roberson, D., Armstrong, C., Mazumder, R., & Keeney, J. (2021). Database, 2021(baab008). https://doi.org/10.1093/database/baab008

Yao, E., Buels, R., Stein, L., Sen, T. Z., & Holmes, I. (2020). PLOS Computational Biology, 16(8), e1007261. https://doi.org/10.1371/journal.pcbi.1007261

Topal, S., Van, C., Xue, Y., Carey, M. F., & Peterson, C. L. (2020). Cell Reports, 32(10), 108106. https://doi.org/10.1016/j.celrep.2020.108106

Bray, S. A., Senapathi, T., Barnett, C. B., & Grüning, B. A. (2020). Journal of Cheminformatics, 12(1), 54. https://doi.org/10.1186/s13321-020-00451-6

Lima, J. S. (2020). [Thesis, University of Otago]. https://ourarchive.otago.ac.nz/handle/10523/10560 (and see this article for more about the author and her research)

Releases

Planemo
Planemo 0.74.4

Planemo is a set of command-line utilities to assist in developing Galaxy and Common Workflow Language artifacts - including tools, workflows, and training materials. This release includes:

  • New flag --download_outputs for the run command.
  • Simultaneous file upload configurable for the run and test commands.
  • Add option to add tags to a history with the run command.
  • Revise Allure reporting experience for workflows.

See GitHub for details.