The Latest GTN News

Author(s)

Helena Rasche

I recently imported Friends Don’t Let Friends Make Bad Graphs, a fantastic and educational github repository showcasing some common visualisation mistakes, that was available under an open license, to the GTN. Then the GTN automatically made a video for me.

Author(s)

Helena Rasche

We did not formally announce it at the time, but the Galaxy Training Network has migrated from Twitter/X to Mastodon, as that platform no longer aligns with the Galaxy Project Code of Conduct nor our community values.

Author(s)	Helena Rasche
Tester(s)	Paul Zierep Wolfgang Maier

WorkflowHub

Author(s)	Wendi Bacon Pavankumar Videm
Infrastructure	José Manuel Domínguez

The European Galaxy Days 2023 CoFest combined the forces of administrator, developer and trainer to update and re-launch the single cell Galaxy instance. Where previously there were two subdomains each with their own sets of tools, there is now a unified subdomain with re-categorized tools that makes sense for users.

Author(s)	Helena Rasche
Tester(s)	Wendi Bacon

We at the GTN strive to bring you the most fun and fancy features we can in a completely static site! Today we’re addressing the question of Wendi Bacon who needed a solution for keeping her single cell subdomain up-to-date with all the latest happenings in the Single Cell world.

Author(s)	Helena Rasche
Infrastructure	Helena Rasche

We have added a new “User Preferences” page for our GTN users! This gives you more control over both how the GTN looks, and works, for you.

Author(s)

Beatriz Serrano-Solano

This is an external post, please follow the link to read it.

Author(s)

Katarzyna Kamieniecka Krzysztof Poterlowicz

Katarzyna Kamieniecka (University of Bradford), a member of the ELIXIR-UK Fellowship Programme, has just launched a new series of lessons to improve {FAIR} data management in the life sciences. The lessons are designed to help researchers and research support staff understand the principles of FAIR data management and apply them to their own work.

Author(s)

Helena Rasche

Did you ever want to run a tool, but not know where it might be available? The GTN has you covered with the Pan-Galactic Tool Search that is now available.

Author(s)

Helena Rasche

June is Pride Month in the US and countries around the world. We have automatically activated the new Progress Pride theme on the home page (Click to Activate) if you hadn’t already selected a theme.

Author(s)

Cristóbal Gallardo

The GTN hosts a new training for analyzing alternative splicing at genome-wide scale!

Author(s)	Simone Leo Paul De Geest Stian Soiland-Reyes Luca Pireddu Marco Enrico Piras
Editor(s)	Helena Rasche

As part of the BY-COVID project, the RO-Crate team and BY-COVID members have brought several RO-Crate related tutorials into the Galaxy Training Network, under a brand new {FAIR} topic!

Author(s)

Helena Rasche

The GTN has set up a very simple “redirection” service based on my.home-assistant.io which Helena discovered after reading some Home Assistant documentation and saw a really neat link which led to her own internal home assistant.

Author(s)

Helena Rasche

The GTN has added persistent URL identifiers for our tutorials, slides, and FAQs. Using the gxy.io service, we have reserved GTN namespace for our persistent URLs. These work similarly to DOIs in that they will always point to a specific training material.

Author(s)

Helena Rasche

The internal functions of the GTN have, in the past, not been very well documented. Now we have started the process of fully documenting the functions and modules available to GTN developers.

Author(s)

Helena Rasche

The GTN has implemented “click to run” workflows! One click, will get you into Galaxy with a workflow imported and ready to run. If you are on either usegalaxy.org or usegalaxy.eu, we have implemented easy buttons which you can click that will direct you straight to your Galaxy server.

Author(s)

Saskia Hiltemann Helena Rasche

Introducing Learning Pathways in the GTN! Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge step by step.

Author(s)

Helena Rasche Lucille Delisle

Numerous other training groups keep “Trainer Directories” as a way to help students meet trainers in their area, especially for hosting workshops for their local community. There have been a handful of attempts at this in the past, both in galaxyproject/galaxy-maps and in a Google Map on the GTN homepage.

Author(s)

Helena Rasche

Did you ever wonder which was the number one most used tool in the GTN? There is a new page of Top Tools where we list all of the top tools in the GTN, and which tutorials use them. We guessed “upload1”, but it seems like not every author annotates that step explicitly in their tutorial, and of course it doesn’t appear in the workflows which we also scan to create this tool listing.

Author(s)

Helena Rasche

February marks Black History Month in the United States. This year we want to celebrate that by introducing a new theme (Click to Activate), and taking a look at one of the most famous Black figures in Science: Henrietta Lacks whose contribution to science went unremarked and unappreciated for decades while white scientists took credit for advancements built on her cell line.

Author(s)

Bérénice Batut Engy Nasr

Food contamination with pathogens are a major burden on our society. Globally, they affect an estimated 600 million people a year and impact socioeconomic development at different levels. These outbreaks are mainly due to Salmonella spp. followed by Campylobacter spp. and Noroviruses.

Author(s)

Helena Rasche

Prometheus is an increasingly popular monitoring solution whereby sites expose a /metrics endpoint, and then a central Prometheus server can scrape it for data which is then plotted or visualised or alerted upon. We at the GTN are now testing out a prometheus endpoint for our completely static site which we’ll use to expose some maybe useful statistics about the GTN that others can then scrape and display in ways that are useful for them.

Author(s)

Helena Rasche Wolfgang Maier

The GTN has long struggled with the rigid hierarchy of a single level of classification: topics. All materials had to be organised into a single topic, even when their contents sometimes spanned multiple topics! We added subtopics a while back to help further organise these tutorials, but that still did not solve the issue of needing to collect multiple learn materials in a single location for people to access.

Author(s)

Bérénice Batut Saskia Hiltemann Helena Rasche

Our new paper about the Galaxy Training Network has been published this week in Plos Computational Biology: “Galaxy Training: A powerful framework for teaching!”

Author(s)

Mehmet Tekman Wendi Bacon

The still new and shiny single-cell analysis topic now boasts a deconvolution tutorial suite! What does deconvolution do you ask? Well, in this context, it infers cell proportions from bulk RNA-seq data. You heard that correctly - instead of expensive new single-cell experiments, you can re-analyse old bulk RNA-seq data and estimate cell proportions. All you need is a reasonably good single cell dataset to use as a reference and you’re good to go! The tutorial suite shows you how to build your reference from publicly available single cell data, and apply analysis to some publicly available bulk RNA-seq data.

Author(s)

Wendi Bacon Mehmet Tekman

Single-cell analysis now has it’s own topic! These tutorials were previously part of the transcriptomics topic, but due to the amazing efforts by Wendi Bacon, Mehmet Tekmanand others, we now have so many single-cell analysis tutorials that they deserve their own dedicated topic! From introductory slides and practicals, to case study tutorials generating cell clusters and trajectories from raw sequencing files, and even a growing subtopic of smaller tips and tricks for adapting analysis to user needs, the single cell topic either has what you need or is working on it. Come learn or get involved!

Author(s)

Saskia Hiltemann

Many analyses in Galaxy require small data manipulations in between tools as a sort of “glue” between analysis steps. For example, you may need to change the file format, re-order columns in a table, replace certain values, or perform some filtering operation, before you can proceed to the next step of your analysis. Galaxy offers a wide range of tools that can perform such generic data manipulation tasks, and mastering these types of operations in Galaxy can help you streamline your analysis and get the most out of Galaxy.

Author(s)

Saskia Hiltemann

Workflow reports are a great Galaxy feature that enable you to define summary reports for any workflow to display the most important results in a single view. This tutorial will guide you through the basics of viewing, customizing, and sharing such workflow reports!

Author(s)

Helena Rasche

Within the GTN we have had schemas for the various metadata we keep for a long time. It helps us automatically check community contributions to ensure they conform to all of the GTN standards, and will work correctly in our environment.

Author(s)

Helena Rasche

It has been a long discussed feature within the GTN Tutorial Author Community: how can we provide trainees with choice in their tutorials, and how can we as trainers not duplicate large tutorials just to show a slightly different path at one point?

Author(s)

Cristóbal Gallardo Delphine Lariviere Alex Ostrovsky

We are proud to announce that, as result of the collaboration with the Vertebrate Genomes Project (VGP), a new training describing the VGP assembly pipeline is now available in the Galaxy Training Network. The Vertebrate Genomes Project aims to generate high-quality, near-error-free, gap-free, chromosome-level, haplotype-phased, annotated reference genome assemblies for every vertebrate species.

Author(s)

Helena Rasche

Further building on the work in the automatic Jupyter Notebook, we’ve now re-written the Jupyter export to be faster, and more importantly added support for R and RMarkdown! Check out an example material. Here we take the content of the tutorial, written like normal GTN markdown, and we automatically convert it to Jupyter Notebooks and now RMarkdown documents! Check out the documentation on how to setup your tutorials to support this.

Author(s)

Helena Rasche

This is an external post, please follow the link to read it.

Author(s)

Helena Rasche

The Galaxy Training Network will now support annotating Funding Agencies on training materials. This is part of our ongoing effort to better annotate how people are contributing to the GTN and recognise all of the sources of contribution.

Author(s)

Anthony Bretaudeau Alexandre Cormier Laura Leroi Erwan Corre Stéphanie Robin

We have just finished a new collection of training material for genome assembly and annotation! You now have access to slides and tutorials, focused on the complete analysis of the genome of a fungus species (Mucor mucedo).

Author(s)

Helena Rasche

The GTN does a lot of work to adhere to the best practices for FAIR training materials as set out in Garcia et al. 2020 and a lot of this work is behind-the-scenes or automatic from the infrastructure we provide, and we wanted to highlight that for educators and organisers who want to use GTN materials. This is one of the ways the GTN works to makes itself a fantastic platform training. Find out how contributing simple markdown tutorials can result in fantastically FAIR training.

Author(s)

Saskia Hiltemann Helena Rasche

After runnning a number of virtual training events this year (e.g. Smörgåsbord, GCC2021), we now have a large collection of training videos around the GTN materials, created by this community.

Author(s)

Helena Rasche

As part of the work for the Gallantries Grant, we wanted to access some of the data from the GTN in a more accessible, API based way. We are working on building a Video Library based on the wild success of our Smörgåsbord and GCC2021 events and to support that we wanted to start pulling in data from the GTN to save course authors time and effort when designing their asynchronous courses.

Author(s)

Helena Rasche

Are you one of our amazing GTN Contributors? Were you ever bothered by how slow it was to build the site locally? This is now fixed completely! We have replaced one of the slowest steps of the GTN’s build process and rewritten it ourselves to be more performant.

Author(s)

Saskia Hiltemann Helena Rasche Bérénice Batut Anthony Bretaudeau Yvan Le Bras Fotis E. Psomopoulos The Carpentries

As part of our work under the Gallantries Grant we are establishing a new topic within the GTN specifically focused on Data Science skills. This topic will include tutorials covering things such as:

Author(s)

Bérénice Batut

Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.

Author(s)

Helena Rasche

As part of the work for the Gallantries Grant, we found ourselves wanting to teach a number of non-Galaxy tutorials on topics such as Python, Bash, SQL, and Git. Writing the tutorials was always a bit awkward as you would spend a lot of time writing code blocks that would be copied and pasted by students into a terminal. We thought we could do better than that, so we decided we would try to convert these to Jupyter Notebooks where the students could read the training materials and simultaneously execute the code cells directly there with the text! This worked fantastically and now we’ve built this feature into the GTN to make it easier to run all of the coding tutorials.

Author(s)

Bérénice Batut

As you have probably already seen, a feedback form is embedded on the bottom of each tutorial.

Author(s)

Helena Rasche

Accessibility Improvements

Author(s)

Bérénice Batut Wolfgang Maier

Effectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.

Author(s)

Maria Doyle

The Volcano plot tutorial introduced volcano plots and showed how they can be easily generated with the Galaxy Volcano plot tool. This new tutorial shows how you can customise a plot using the R script output from the tool and RStudio in Galaxy. A short video for the tutorial is also available on YouTube, created for the GCC2021 Training week. Happy plotting!

Author(s)

Saskia Hiltemann Helena Rasche

Want to contribute to the GTN without installing anything on your own computer? GitPod provides an online workspace for editing the GTN tutorials, and showing a live preview of the GTN website with your changes. This tutorial shows you how to set up GitPod, how to use it to get a live preview of the GTN website, and how to save any changes you make back to your GitHub fork. This makes it easier than ever to contribute to the GTN!

Author(s)

Anthony Bretaudeau Helena Rasche Nathan Dunn Mateo Boudet

After two years, the Galaxy Genome Annotation team has finally finished their much awaited tutorial on doing Genome Annotation in Galaxy! Genome annotation is a time consuming and largely manual process as it requires the synthesis of a significant amount of varied information to make inferences, a process tha cannot be accomplished without an interactive editor. To support this, Apollo was deployed on UseGalaxy.eu. Over the past two years the GGA project has pushed forward apollo and tooling around it, and it finally culminates in this look at how to annotated your genomes in Apollo.

Author(s)

Helena Rasche Saskia Hiltemann

Did you ever start teaching a GTN tutorial, only to realise something changed recently? Oh no! A while ago the GTN created an Archive to address just this concern. On every tag, we’d build a copy of the website which we would place online and never touch again. This way we’d have permanent online copies so that if someone needed to go back to an older version of the GTN, they could.

Author(s)

Erik Schill Simon Bray

The first of the developer tutorials for GCC2021 is live, first time contributor Erik Schill has produced a fantastic tutorial covering how to develop new functions in BioBlend for new APIs in Galaxy. Many thanks to Simon Bray for editing!

Author(s)

Helena Rasche Erik Schill Simon Bray

Thanks to the great tutorial developed by first time contributor Erik Schill and edited by Simon Bray, we noticed that they defined a number of abbreviations and re-used those throughout their tutorial.

Author(s)

Wendi Bacon Beatriz Serrano-Solano Patricia Carvajal López Alejandra Escobar-Zepeda Saskia Hiltemann Helena Rasche

¡El primer tutorial en español ya está disponible! Galaxy siempre ha tenido tutoriales traducidos automáticamente mediante Google-Translate, ahora nos estamos embarcando en un nuevo proyecto para estudiar la experiencia de aprendizaje con tutoriales en bioinformática traducidos por humanos. Nuestro objetivo es crear un paquete de tutoriales para el análisis de datos single-cell (célula única) en primera instancia, con el fin de estudiar su uso y utilidad en un taller para hablantes nativos de español. Agradecemos enormemente a las nuevas participantes Patricia Carvajal López y Alejandra Escobar-Zepeda (EMBL-EBI) así como a las miembros existentes de GTN Beatriz Serrano-Solano (University of Freiburg), Saskia Hiltemann & Helena Rasche (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a Wendi Bacon (The Open University/EBI) como líder de proyecto.

Author(s)

Cristóbal Gallardo Pavankumar Videm Beatriz Serrano-Solano

Plant lovers are in luck! A new tutorial on this fascinating kingdom has been added to the GTN. It details the necessary steps to identify potential targets of brassinosteroid-induced miRNAs. Brassinosteroids are phytohormones that have the ability to stimulate plant growth and confer resistance against abiotic and biotic stresses. These characteristics have led to great interest in the field of biotechnology due to its potential for increasing agricultural productivity.

Author(s)

Helena Rasche

One of our contributors ( Mehmet Tekman) found himself wanting to link to a specific time point in a video. We said “Wow, what a fantastic idea!” and then we implemented it. To support that we developed a very simple standalone video player page where you can view the GTN videos and browse through our catalog. It features the full transcript on the left, some suggested videos on the right, and a very standard <video> player.

Author(s)

Mehmet Tekman Beatriz Serrano-Solano

Single cell RNA-seq analysis is a cornerstone of developmental research and provides a great level of detail in understanding the underlying dynamic processes within tissues. In the context of plants, this highlights some of the key differentiation pathways that root cells undergo.

Author(s)

Bazante Sanders Miaomiao Zhou Helena Rasche Saskia Hiltemann

Two new assembly tutorials have been added to the GTN! These tutorials walk you through the process of assembling MRSA strains from real-world datasets. MRSA stands for “Methicillin- resistant Staphylococcus aureus, it is resistance to several antibiotics and is a common source of hospital-acquired infections and outbreaks. In this tutorial you will assess the quality of your data, perform an assembly and assess its quality, analyze your data for the presence of antimicrobial resistance (AMR) genes, and annotate the genome using Prokka and JBrowse.

Author(s)

Saskia Hiltemann Helena Rasche Bérénice Batut

Snippets have received an major overhaul! Snippets/FAQs are small reusable bits of training, often answering a single question. In addition to the general Galaxy snippets, we now also support topic-level and tutorial-level FAQs. This will allow contributors to add common questions and answers to their tutorials, which not only can be included in the tutorial text itself, but are also used to autogenerate an FAQ page for the tutorial or topic listing all common questions (and answers).This will be useful both to participants following tutorials via self-study, and also to instructors preparing for a training event.

Author(s)

Beatriz Serrano-Solano Yi Sun Jean-Karim Hériché

Most biological processes are dynamic and observing them over time can provide valuable insights. Combining fluorescent markers with time-lapse imaging is a common approach to collect data on dynamic cellular processes such as cell division. However, automated time-lapse imaging can produce large amounts of data that can be challenging to process. One of these challenges is the tracking of individual objects as it is often impossible to manually follow a large number of objects over many time points.

Author(s)

Saskia Hiltemann Helena Rasche Bérénice Batut Jennifer Hillman-Jackson Delphine Lariviere Anna Syme Maria Doyle

Every 3 months we organise one day dedicated to the GTN community! Thursday, May 20th is the next GTN CoFest. We will be working on the training materials, have discussions with the global Galaxy traning community. Do you teach with Galaxy? Want to learn how to add your tutorial to the GTN? New to the community and just want to learn more? Everybody is welcome!

Author(s)

Saskia Hiltemann

This is an external post, please follow the link to read it.

Author(s)

Saskia Hiltemann Helena Rasche

The GTN instructors community has just run the largest-ever Galaxy training event: “the GTN Smörgåsbord: A Global Galaxy Course”, co-organized with the Gallantries and the CINECA project and the Galaxy Training Network.

Author(s)

Helena Rasche

The Galaxy Team is pleased to announce the release of Galaxy 21.01! Workflows are the absolute ✨star✨, followed closely by the new Remote Files interface and much more.

Author(s)

Helena Rasche Delphine Lariviere

This past year has been a struggle for all of us, but one task has become apparent as one of the most time consuming portions of course preparation during a pandemic: Video Production.

Author(s)

Helena Rasche

The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.