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.

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:

Bérénice Batut

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

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.

Bérénice Batut

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

Helena Rasche

Accessibility Improvements

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.

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!

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!

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.

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.

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!

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.

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.

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.

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.

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.

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.

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.

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.

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!

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

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.

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.

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.

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