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!

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

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.

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.

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.

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

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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GTN logo with a multi-coloured star and the words Galaxy Training Network

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

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GTN logo with a multi-coloured star and the words Galaxy Training Network

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

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Hello in many languages

¡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 LópezPatricia Carvajal López y Alejandra Escobar-ZepedaAlejandra Escobar-Zepeda (EMBL-EBI) así como a las miembros existentes de GTN Beatriz Serrano-SolanoBeatriz Serrano-Solano (University of Freiburg), Saskia HiltemannSaskia Hiltemann & Helena RascheHelena Rasche (Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a Wendi BaconWendi Bacon (The Open University/EBI) como líder de proyecto.

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Biosynthesis of miRNA in plants

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.

One of our contributors (Mehmet TekmanMehmet 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.

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Arabidopsis clusters with trajectory from meristematic cells towards trichoblasts

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.

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Assembly visualisation from the Bandage tool

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

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.

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'

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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GTN logo with a multi-coloured star and the words Galaxy Training Network

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

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Wordcloud of emoji with them in different sizes based on frequency

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.

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Galaxy News logo on dark blue background with Galaxy logo and words 'Galaxy News'

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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GTN logo with a multi-coloured star and the words Galaxy Training Network

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.

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GTN Logo on a spiral galaxy background with text 'galaxy admin training'

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

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