The Latest GTN News

Keep an eye on this page for the latest news around the GTN. New tutorials, GTN features, upcoming training events, and much much more!

Want to add your own news here (e.g. new tutorial, event, publication, anything else training related)? Check out how to do that in this FAQ

banner image for the mTB training event showing the name of the course over a background of a touchscreen showing data
8 July 2024
NGS Tuberculosis Drug-resistance transmission evolution one-health

Tuberculosis (TB) is a big killer in many countries of the world, particularly in those with low and middle income. Next-generation sequencing has been key in improving our understanding of drug resistance acquisition and of transmission of Mycobacterium tuberculosis. Yet, the need for expertise guiding NGS implementation in laboratories and the lack of bioinformatic expertise, are main obstacles hindering the implementation of NGS into TB programs.

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Screenshot of the GTN Video Library showing a tutorial recording with a large youtube player and extensive metadata about who created the video (Natalie Kucher) and when, how long, etc.
14 June 2024
gtn

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!

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Hand drawn sketch of a phylogenetic tree from Charles Darwin's notebook
13 June 2024
Author(s) Melissa Burke avatar Melissa Burke
Phylogenetics Tutorial GTN Australian BioCommons

A new Galaxy Training Network tutorial has been created to take researchers back to basics to uncover the principles of phylogenetics and how tree-building methods work. A longstanding collaboration between Professor Michael Charleston from the University of Tasmania and Australian BioCommons has delivered this self-guided tutorial featuring videos and hands-on exercises. To maximise its impact, the resource was tailored specifically to be shared globally via the Galaxy Training Network, and will form the basis of an upcoming live training workshop.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
13 June 2024
Author(s) Camila Goclowski avatar Camila Goclowski
Editor(s) orcid logoWendi Bacon avatar Wendi Bacon
single-cell training education trajectory user contributor

With growing access and interest in sequencing data, Galaxy is a knight in shining armor for wet lab scientists hoping to analyze their own data. With long term intentions of increasing access to bioinformatic analyses, the Galaxy Training Network (GTN) creates a safe space where non-computer-scientists may analyze their own data and even learn to code: an invaluable skill in today’s scientific world. Galaxy introduced me to brand new skills as an undergraduate and ultimately changed the trajectory of my career. Here is my story as a biology undergraduate with no coding experience turned GTN contributor &, eventually, coding bioinformatician: thanks to Galaxy.

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screenshot of galaxy data upload interface showing a folder named GTN Training Data
3 June 2024
Author(s) orcid logoPolina Polunina avatar Polina Polunina
esg-wp4 esg

As part of the EuroScienceGateway and in cooperation with Onedata and EGI we are providing all GTN training data on a publicly accessible cloud storage. Those training datasets are curated, small but meaningful for educational purposes and contain 1530 files with a total size of 170Gb. An invaluable set of resources for everyone dealing with data science and training. Please thank the more than 350 contributors to GTN.

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A screenshot of the MINERVA Platform's COVID-19 Disease Map showing the PAMP signalling pathway submap in view in center as well as some genes in a table to the right.
28 March 2024
by-covid pathways minerva gtn infrastructure new feature

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.

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FAIR TRaining Learning Pathway By ELIXIR fellows funded by the ELIXIR UK DASH project
26 March 2024
fair dmp data stewardship data management new learning pathway

ELIXIR-UK’s Data Stewardship Fellowship is excited to announce a new learning pathway focused on FAIR Data Management! This program equips researchers and research support staff with the skills to effectively manage their research data.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
18 March 2024
Author(s) orcid logoHelena Rasche avatar Helena Rasche
Infrastructure orcid logoHelena Rasche avatar Helena Rasche
gtn infrastructure new feature

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
30 January 2024
gtn infrastructure new feature beta

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!

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swirled cluster dots surround a circle of people all holding hands, looking towards the bright center (future)
22 December 2023
gtn communications single-cell

🚀Embarking on a cosmic journey, the Galaxy Single-cell Community has clustered together to unveil a constellation of tools, making strides in RNA-stellar discoveries and creating out-of-this-world workflows. With a commitment to battling work duplication across the multiverse, this community is boldly charting a course for global domination, proving that when it comes to bioinformatics, the Galaxy is the limit!✨

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GTN logo with a multi-coloured star and the words Galaxy Training Network
18 December 2023
Author(s) Julia Jakiela avatar Julia Jakiela
computational chemistry user story gtn

As a medicinal chemistry student, I undertook a semester project on natural products isolation and derivatisation. One of the compounds my group was working on was piperine, extracted from black pepper. Inspired by literature findings, we found out that the derivatives of piperine can inhibit monoamine oxidase-B and thus can be possibly used in Parkinson’s disease. As a novelty element in our project, we came up with new structures of derivatives that could act as inhibitors.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
21 November 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
feedback testimonial gtn

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
21 November 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
gtn communications

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.

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screenshot of the Single Cell Omics subdomain page, with purple mastheader, Single Cell Tools categories along the side, and an updated logo combining the Single Cell Omics connected cells image with the Human Cell Atlas blue embyro logo
12 October 2023
gtn singlecell

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
21 June 2023
new topic new tutorial

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
20 April 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature gtn

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.

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the bottom left corner of an overview box from a training material is shown, a label short link clearly has a short link as described in the tutorial
19 April 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature gtn

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
19 April 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature gtn

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
19 April 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature gtn

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
21 March 2023
new feature community building capacity building

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
8 February 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature gtn

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
2 February 2023
Author(s) orcid logoHelena Rasche avatar 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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
24 January 2023
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature gtn

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
23 January 2023
new topic new feature

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.

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Heatmap with columns of cell types vs rows of inferred and actual cell type proportions for A and B samples. Cell colours are similar between actual and inferred.
29 November 2022
new tutorial single-cell transcriptomics

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.

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Pretty dots of different colours combined into two cell cluster plots on the sides. In the middle, a split violin plot showing the expression of unknown genes in blue on one side and the expression of the genes in an opposing sample in orange alongside. Snuck in between these three important plots is a PhD comic of data showing no trend, with the chat box “Hmm… I think there’s a clear trend happening here.”
18 November 2022
new topic single-cell new feature

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!

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screenshot from the data manipulation tutorial
11 September 2022
new tutorial

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.

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Access the workflow report from the invocations menu
2 June 2022
new tutorial Galaxy Tips & Tricks

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!

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GTN logo with a multi-coloured star and the words Galaxy Training Network
20 May 2022
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature

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.

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Gif showing a user switching between two branches of a tutorial
12 April 2022
Author(s) orcid logoHelena Rasche avatar Helena Rasche
gtn infrastructure new feature tutorial authors

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?

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Assembly of vertebrate genomes
14 March 2022
new tutorial assembly pacbio vgp

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.

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Image showing content from a tutorial, rendered as an rmarkdown html via knitting. A table of contents appears on the left, and code and outputs on the right.
28 January 2022
Author(s) orcid logoHelena Rasche avatar Helena Rasche
gtn infrastructure new feature

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
14 December 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new-feature

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
1 December 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
faq

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.

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Image showing an OpenAPI / Swagger UI to the training material API featuring several APIs like topics, tutorials, contributors, and a couple internal APIs. At the bottom are a couple of data models.
10 November 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
gtn infrastructure new feature

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
12 October 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
authors developers performance

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.

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Image comparing Markdown, GTN materials, and new Jupyter Notebook output
24 September 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
gtn infrastructure new feature

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
27 July 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
new feature

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.

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Analysis flow in the 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' tutorial. It teaches how to obtain, run and combine workflows appropriately for 4 different types of input data. Image adapted from covid19.galaxyproject.org
30 June 2021
new tutorial variant-analysis covid-19

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.

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Screenshot of Volcano Plot customised in R. Significant genes had their colour changed to red, and points and labels were made smaller.
26 June 2021
Author(s) orcid logoMaria Doyle avatar Maria Doyle
new tutorial visualization

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!

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Screenshot of the GitPod workspace. A file browser pane on the left, terminal on the bottom, text editor in the middle, and preview of the rendered GTN website on the right.
25 June 2021
new tutorial contributors

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!

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Screenshot of Apollo embedded within the Galaxy Europe interface, Apollo shows a couple of gene tracks.
4 June 2021
new tutorial genome-annotation

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
1 June 2021
new feature

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.

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Hello in many languages
20 May 2021
new tutorial español

¡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.

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Biosynthesis of miRNA in plants
10 April 2021
new tutorial transcriptomics plants mirna

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.

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Example of video player mimicking youtube's interface with a video at the top, a transcript at the bottom left, and suggested videos at the bottom right.
6 April 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
gtn infrastructure video new feature

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.

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Assembly visualisation from the Bandage tool
24 March 2021
new tutorial assembly mrsa amr nanopore illumina

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.

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GTN logo with a multi-coloured star and the words Galaxy Training Network
24 March 2021
gtn infrastructure contributors instructors new feature

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.

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Video of green coloured cells dividing on a dark background.
18 March 2021
new tutorial imaging

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.

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CoFest logo with two generic people shapes conversing next to the GTN logo and text 'gtn cofest'
18 March 2021
cofest

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!

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Galaxy News logo on dark blue background with Galaxy logo and words 'Galaxy News'
17 March 2021
Author(s) orcid logoHelena Rasche avatar Helena Rasche
galaxy

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.

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