Author(s) | Helena Rasche |
The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.
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The following list includes only slides and tutorials where the individual has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.
This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.
Author(s) | Helena Rasche |
The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryEvery 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!
Full StoryAuthor(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.
Full StoryTwo 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.
Full StoryAuthor(s) | Helena Rasche |
One of our contributors (@gtn:mtekman) 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.
Full Story¡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 @gtn:pclo y @gtn:ales-ibt (EMBL-EBI) así como a las miembros existentes de GTN @gtn:beatrizserrano (University of Freiburg), @gtn:shiltemann & @gtn:hexylena (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a @gtn:nomadscientist (The Open University/EBI) como líder de proyecto.
Full StoryAuthor(s) | Helena Rasche Erik Schill Simon Bray |
Thanks to the great tutorial developed by first time contributor @gtn:rikeshi and edited by @gtn:simonbray, we noticed that they defined a number of abbreviations and re-used those throughout their tutorial.
Full StoryAuthor(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.
Full StoryAfter 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.
Full StoryAuthor(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!
Full StoryAuthor(s) | Helena Rasche |
One of our community members suggested on twitter that we support alternative formats for accessing our JavaScript based slides, as this can be difficult for users using screen readers. We’ve now added support for “plain text slides”, where we render the slide decks as a single long document.
Full StoryAuthor(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.
Full StoryAs 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:
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(s) | Saskia Hiltemann Helena Rasche |
Infrastructure | 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.
Full StoryAuthor(s) | Saskia Hiltemann Helena Rasche |
Infrastructure | 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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(s) | Helena Rasche |
This is an external post, please follow the link to read it.
Full StoryAuthor(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.
Full StoryAuthor(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?
Full StoryAuthor(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.
Full StoryAuthor(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!”
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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!
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(s) | Helena Rasche |
Tester(s) | Paul Zierep Wolfgang Maier |
WorkflowHub
Full StoryAuthor(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.
Full StoryAuthor(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.
Full StoryAuthor(s) | Helena Rasche |
While most GTN tutorials include their associated workflow directly in the GTN, some may wish to write a tutorial about running workflows from WorkflowHub, e.g. leveraging the IWC workflow collection.
Full StoryAuthor(s) | Mehmet Tekman |
Editor(s) | Helena Rasche |
Infrastructure | Mehmet Tekman Helena Rasche |
🤖💬 Bleep bloop! Good news everyone! We have deployed some bots to enable our Matrix regulars to better engage with the contributions and questions of our users on the non-Matrix side of the Galaxy-verse.
Full StoryAuthor(s) | Mehmet Tekman |
Editor(s) | Helena Rasche |
Infrastructure | Mehmet Tekman Helena Rasche |
🤖💬 Bleep bloop! Good news everyone! We have deployed some bots to enable our Matrix regulars to better engage with the contributions and questions of our users on the non-Matrix side of the Galaxy-verse.
Full StoryAuthor(s) | Helena Rasche |
Tester(s) | Wendi Bacon |
Infrastructure | Helena Rasche |
Based on user feedback of the difficulties of the GTN news submission process we have significantly simplified and removed the need for manually editing a YAML file by providing a quick and easy Google Form
Full StoryAuthor(s) | Helena Rasche |
Tester(s) | Wendi Bacon |
Infrastructure | Helena Rasche |
Based on user feedback of the difficulties of the GTN news submission process we have significantly simplified and removed the need for manually editing a YAML file by providing a quick and easy Google Form
Full StoryAuthor(s) | Helena Rasche Jennifer Hillman-Jackson Wendi Bacon Martin Čech |
Tester(s) | Jennifer Hillman-Jackson |
Infrastructure | Helena Rasche |
Howdy teachers and support staff! We are exploring displaying GTN content directly in the Galaxy Help site, furthering the integration between the GTN and the Galaxy community infrastructure. When you paste a GTN Frequently Asked Questions URL into the Galaxy Discourse, it will now be rendered directly in Discourse!
Full StoryAuthor(s) | Helena Rasche Jennifer Hillman-Jackson Wendi Bacon Martin Čech |
Tester(s) | Jennifer Hillman-Jackson |
Infrastructure | Helena Rasche |
Howdy teachers and support staff! We are exploring displaying GTN content directly in the Galaxy Help site, furthering the integration between the GTN and the Galaxy community infrastructure. When you paste a GTN Frequently Asked Questions URL into the Galaxy Discourse, it will now be rendered directly in Discourse!
Full StoryAuthor(s) | Mehmet Tekman |
Editor(s) | Helena Rasche |
Infrastructure | Mehmet Tekman |
Hey Galaxy admins! Have you ever wanted to administer your own instance from the luxury of your pocket?
Full StoryAuthor(s) | Helena Rasche Anthony Bretaudeau |
Infrastructure | Helena Rasche |
Building upon the work previously done for the SARS-Cov-2 Topic we have further expanded the ‘tag based topics’ to support a new GMOD topic.
Full StoryAuthor(s) | Helena Rasche Anthony Bretaudeau |
Infrastructure | Helena Rasche |
Building upon the work previously done for the SARS-Cov-2 Topic we have further expanded the ‘tag based topics’ to support a new GMOD topic.
Full StoryAuthor(s) | Helena Rasche Bérénice Batut |
Infrastructure | Helena Rasche |
We know the GTN has a lot of learning materials (400 and counting!) which can make it quite difficult to figure out where to start in some topics.
Full StoryAuthor(s) | Helena Rasche Bérénice Batut |
Infrastructure | Helena Rasche |
We know the GTN has a lot of learning materials (400 and counting!) which can make it quite difficult to figure out where to start in some topics.
Full StoryAuthor(s) | Helena Rasche |
Infrastructure | Helena Rasche |
At the Galaxy Training Network we are really committed to ensuring our training materials are Findable, Accessible, Interoperable, and Reusable. This means that we want to make sure that the URLs to our training materials are persistent and don’t change. The GTN wants you to be able to rely on our URLs once you’ve added them to a poster or training material, without having to worry about them breaking in the future.
Full StoryAuthor(s) | Helena Rasche |
Infrastructure | Helena Rasche |
At the Galaxy Training Network we are really committed to ensuring our training materials are Findable, Accessible, Interoperable, and Reusable. This means that we want to make sure that the URLs to our training materials are persistent and don’t change. The GTN wants you to be able to rely on our URLs once you’ve added them to a poster or training material, without having to worry about them breaking in the future.
Full StoryAuthor(s) | Helena Rasche Marek Ostaszewski |
Infrastructure | Matti Hoch Helena Rasche |
As part of the work of BeYond COVID, we have developed a new integration between the MINERVA Platform’s COVID-19 Disease Map and Galaxy! Datasets created within Galaxy can now be seamlessly visualized in the MINERVA Platform, allowing you to explore your data in the context of the COVID-19 Disease Map.
Full StoryAuthor(s) | Helena Rasche Marek Ostaszewski |
Infrastructure | Matti Hoch Helena Rasche |
As part of the work of BeYond COVID, we have developed a new integration between the MINERVA Platform’s COVID-19 Disease Map and Galaxy! Datasets created within Galaxy can now be seamlessly visualized in the MINERVA Platform, allowing you to explore your data in the context of the COVID-19 Disease Map.
Full StoryAuthor(s) | Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche Bérénice Batut |
We are happy to report that over the years of our fruitful collaboration with ELIXIR TeSS, all GTN materials should receive a perfect score on the FAIR-Checker.
Full StoryAuthor(s) | Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche Bérénice Batut |
We are happy to report that over the years of our fruitful collaboration with ELIXIR TeSS, all GTN materials should receive a perfect score on the FAIR-Checker.
Full StoryAuthor(s) | Saskia Hiltemann |
Infrastructure | Saskia Hiltemann Helena Rasche |
Are you organizing a training event using GTN materials? You can now add your event directly to the GTN!
Full StoryAuthor(s) | Bérénice Batut Helena Rasche Saskia Hiltemann |
The Galaxy Training Network (GTN) has reached an exciting milestone: our 400th tutorial! This achievement is a testament to the dedication and hard work of our community of educators, researchers, and developers over the last 9 years.
Full StoryAuthor(s) | Teresa Müller |
Editor(s) | Helena Rasche |
We are happy to announce the Galaxy Training Academy 2024, a global online training event, where learners can get to know Galaxy and learn how to analyze data for various research topics.
Full StoryAuthor(s) | Saskia Hiltemann Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche |
Many GTN tutorials already have recordings. These recordings were made by members of the community for a variety of (online) training events. Up until now, this video library were part of the Gallantries Project. We have now integrated this video library directly into the GTN, and made it even easier to add video recordings to GTN tutorials or slide decks! Just use a Google Form to submit your video recordings!
Full StoryAuthor(s) | Saskia Hiltemann Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche |
Many GTN tutorials already have recordings. These recordings were made by members of the community for a variety of (online) training events. Up until now, this video library were part of the Gallantries Project. We have now integrated this video library directly into the GTN, and made it even easier to add video recordings to GTN tutorials or slide decks! Just use a Google Form to submit your video recordings!
Full StoryAuthor(s) | Saskia Hiltemann Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche Bérénice Batut |
We recently presented the GTN at the 2024 Galaxy Community Conference. This presentation was a summary of the updates and new features that were added to the GTN in the past year.
Full StoryAuthor(s) | Saskia Hiltemann Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche Bérénice Batut |
We recently presented the GTN at the 2024 Galaxy Community Conference. This presentation was a summary of the updates and new features that were added to the GTN in the past year.
Full StoryAuthor(s) | Helena Rasche Saskia Hiltemann |
Infrastructure | Saskia Hiltemann Helena Rasche |
Since the last time we announced GTN news posting via Google Form, we’ve found that this has been an excellent fit for the community and decided to greatly expand the use of Google Forms for GTN contributions.
Full StoryAuthor(s) | Helena Rasche Saskia Hiltemann |
Infrastructure | Saskia Hiltemann Helena Rasche |
Since the last time we announced GTN news posting via Google Form, we’ve found that this has been an excellent fit for the community and decided to greatly expand the use of Google Forms for GTN contributions.
Full StoryAuthor(s) | Vlad Visan |
Data provider(s) | Matthias Bernt Lucille Delisle Hans-Rudolf Hotz |
Editor(s) | Helena Rasche |
Have you wondered how difficult Galaxy is to run? How much time people must spend to run Galaxy? In February 2024, we collected 9 responses from the Galaxy Small Scale Admin group. The questions cover various time burdens and technological choices. The report provides answers to prospective future admins’ most common questions.
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