Helena Rasche

Affiliations

Erasmus Medical Center avatar ErasmusMC Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries BeYond-COVID avatar BeYond-COVID ELIXIR Europe avatar ELIXIR Europe ELIXIR-CONVERGE avatar ELIXIR-CONVERGE

Former Affiliations

de.NBI avatar de.NBI Avans Hogeschool avatar Avans University of Freiburg avatar UFR

Contributions

The following list includes only slides and tutorials where the individual or organisation 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.

Editorial Roles

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.

Tutorials

Slides

FAQs

Video Recordings

Events



GitHub Activity

Issues Reported

743 Merged Pull Requests

See all of the Pull Requests and Commits by Helena Rasche.

Reviewed 1414 PRs

We love our community reviewing each other's work!

News

Galaxy 21.01 released!
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.

Full Story

Next GTN CoFest May 20, 2021
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!

Full Story

New Feature: FAQs
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.

Full Story

New Tutorials: Genome assembly of a MRSA genome
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.

Full Story

New Feature: Video Player
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.

Full Story

¿Hablas español?: The first curated tutorial in Spanish!
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.

Full Story

Oh no, it changed! Quick, to the archive menu.
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.

Full Story

New Tutorial: Genome Annotation with Apollo
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.

Full Story

New Tutorial: GitPod for contributing to the GTN
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!

Full Story

Accessibility Improvements
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.

Full Story

New Feature: Automatic Jupyter Notebooks
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.

Full Story

Attention Contributors: GTN Performance Enhancements
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.

Full Story

New Feature: GTN API with OpenAPI 3 specification
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.

Full Story

New FAQs: How does the GTN stay FAIR and Collaborative
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.

Full Story

Support for annotating Funding Agencies
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.

Full Story

New Feature: Automatic RMarkdown
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.

Full Story

New Tutorial Feature: Choose Your Own Tutorial
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?

Full Story

GTN Metadata Schemas
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.

Full Story

New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic
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.

Full Story

New Feature: Prometheus Metrics endpoint
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.

Full Story

GTN Celebrates Black History Month
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.

Full Story

What are the most used tools in the GTN?
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.

Full Story

New Feature: Trainer Directory! (Add yourself today!)
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.

Full Story

New Feature: Click-to-run Workflows
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.

Full Story

New Feature: GTN Rdoc
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.

Full Story

New Feature: Persistent URLs (PURLs) / Shortlinks
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.

Full Story

New Feature: my.galaxy.training
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.

Full Story

GTN has left Twitter/X as of October
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.

Full Story

Feedback: Easy slide recordings
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.

Full Story

GTN in Discourse
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!

Full Story

GTN in Discourse
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!

Full Story

Cool URLs Don't Change, GTN URLs don't either.
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.

Full Story

Cool URLs Don't Change, GTN URLs don't either.
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.

Full Story

Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy
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.

Full Story

Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy
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.

Full Story

GTN Video Library 2.0: 107 hours of learning across 154 videos
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!

Full Story

GTN Video Library 2.0: 107 hours of learning across 154 videos
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!

Full Story

Galaxy Administrator Time Burden and Technology Usage
One of the many charts from the report. Histogram of the average duration, in hours, an upgrade takes (excluding DB schema migration). Showing a median of 3 and mean of 4. Mostly under 3, but a few values around 7.
22 July 2024
deploying maintenance survey

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.

Full Story
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External Links

Training Philosophy
hexylena
hexylena:matrix.org
0000-0001-9760-8992
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Stats for materials contributed to by Helena Rasche