Contributions

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.

GitHub Activity

Tutorials

Slides

News

Screenshot of the GTN Video Library Home page

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.

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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.

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

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

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:

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Image comparing Markdown, GTN materials, and new Jupyter Notebook output

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

Accessibility Improvements

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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

Thanks to the great tutorial developed by first time contributor AvatarErik Schill

and edited by AvatarSimon 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 AvatarPatricia Carvajal López

y AvatarAlejandra Escobar-Zepeda

(EMBL-EBI) así como a las miembros existentes de GTN AvatarBeatriz Serrano-Solano

(University of Freiburg), AvatarSaskia Hiltemann

& AvatarHelena Rasche

(Erasmus-MC), por su arduo trabajo en este proyecto de traducción y mantenimiento y, por supuesto, a AvatarWendi Bacon

(The Open University/EBI) como líder de proyecto.

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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 ( AvatarMehmet 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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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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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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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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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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