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GTN Feedback

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Aggregation of feedback submitted since {{ start.month }} using the embed feedback form at the bottom of tutorials. Thank you everyone who submitted feedback!

diff --git a/hall-of-fame.md b/hall-of-fame.md index ec2643af22bf2d..4619cb29b8509f 100644 --- a/hall-of-fame.md +++ b/hall-of-fame.md @@ -1,3 +1,4 @@ --- layout: hall-of-fame +title: "Hall of Fame" --- diff --git a/index.md b/index.md index e4d427d215f4d4..aa6d532dc232d9 100644 --- a/index.md +++ b/index.md @@ -1,3 +1,4 @@ --- layout: home +title: Galaxy Training! --- diff --git a/learning-pathways/index.md b/learning-pathways/index.md index 8c52972c511538..22aa0075ea2090 100644 --- a/learning-pathways/index.md +++ b/learning-pathways/index.md @@ -1,5 +1,6 @@ --- layout: page +title: "Learning Pathways" --- {% assign pathways_science = site.pages | where: "layout", "learning-pathway" | where: "type", "use" | sort: "priority", "last" %} @@ -7,8 +8,6 @@ layout: page {% assign pathways_other = site.pages | where: "layout", "learning-pathway" | where_exp: "item", "item.type != 'use'" | sort: "priority", "last" %} -# Learning Pathways - Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge as you go. We always recommend to follow the tutorials in the order they are listed in the pathway. ## For Scientists diff --git a/news/_posts/2021-03-01-gat.md b/news/_posts/2021-03-01-gat.md index 12ba9c447e792d..e319d5a112e9b5 100644 --- a/news/_posts/2021-03-01-gat.md +++ b/news/_posts/2021-03-01-gat.md @@ -9,6 +9,7 @@ contributions: The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event. -**5 days, 106 registrations, 29 countries, 12.5 hours of video and 100% awesomeness.** +> 5 days, 106 registrations, 29 countries, 12.5 hours of video and 100% awesomeness +{: .quote} Read the full report for all the numbers, details, conclusions and feedback. diff --git a/news/_posts/2021-03-30-tutorial_scrna_plant.md b/news/_posts/2021-03-30-tutorial_scrna_plant.md index 135a7c3ecd6342..2776ba101c2869 100644 --- a/news/_posts/2021-03-30-tutorial_scrna_plant.md +++ b/news/_posts/2021-03-30-tutorial_scrna_plant.md @@ -12,4 +12,4 @@ layout: news 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. -This tutorial replicates the paper ["Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing" (Denyer et al., 2019)](https://doi.org/10.1016/j.devcel.2019.02.022), where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells. +This tutorial replicates the paper {% cite Denyer_2019 %}, where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells. diff --git a/news/_posts/2021-05-25-abbreviations-tag.md b/news/_posts/2021-05-25-abbreviations-tag.md index 5f5295cc244a80..e1d5b853168e71 100644 --- a/news/_posts/2021-05-25-abbreviations-tag.md +++ b/news/_posts/2021-05-25-abbreviations-tag.md @@ -25,13 +25,13 @@ abbreviations: And in your text you can use braces to refer to the term -> > ### {% icon code-in %} Input: Markdown +> > Markdown > > > > The `/jobs` {API} will return {JSON}. When we call the {API} we'll get back this result {JSON}. > > > {: .code-in} > -> > ### {% icon code-out %} Output +> > > > > > The `/jobs` Application Programming Interface (API) will return JavaScript Object Notation (JSON). When we call the API we'll get back this result JSON. > > diff --git a/news/_posts/2021-07-27-a11y.md b/news/_posts/2021-07-27-a11y.md index 2f44cf4fa9b974..8ed850b09e679f 100644 --- a/news/_posts/2021-07-27-a11y.md +++ b/news/_posts/2021-07-27-a11y.md @@ -6,8 +6,6 @@ tags: [new feature] layout: news --- -**Accessibility Improvements** - 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. The rendering is imperfect, due to how our slide deck library handles custom classes within slides, but it should still be an improvement for anyone who wants to scroll through the slides in an alternative format. You can find them linked from the first slide of each slide deck, or from the slides dropdown in the topic pages, *check them out!* diff --git a/news/_posts/2021-09-29-survey.md b/news/_posts/2021-09-29-survey.md index fa7366ed6fb612..0d6c80341ddd31 100644 --- a/news/_posts/2021-09-29-survey.md +++ b/news/_posts/2021-09-29-survey.md @@ -8,13 +8,13 @@ coveralt: "Adversitement for the survey. Written: Got a minute? Did you use Gala layout: news --- -**Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.** +**Do you use Galaxy for Training? Have your say!** Please take a few minutes to let us know about your training experiences. We, the Galaxy Training Network, would like to get feedback from instructors on the use of Galaxy for training, the preparation needed but also on the [Galaxy Training Material](https://training.galaxyproject.org/). This survey should take less than 10 minutes and every questions are optional and can be skipped. It will help us prioritise improvements to the training materials. We're currently focused on making it easier to prepare and give trainings. -[**Fill the survey now**](https://forms.gle/YJq5rTEcdowjBiuh6){:.btn .btn-primary style="color: white; width: 100%; background-color: #528faa;border-color: #528faa;"} +[Fill the survey now](https://forms.gle/YJq5rTEcdowjBiuh6){:.btn .btn-primary style="color: white; width: 100%; background-color: #528faa;border-color: #528faa;"} If you have any questions regarding this survey, please send an email to [galaxytrainingnetwork@gmail.com](mailto:galaxytrainingnetwork@gmail.com) diff --git a/news/_posts/2022-06-02-workflow-reports-tutorial.md b/news/_posts/2022-06-02-workflow-reports-tutorial.md index 630cf50485f222..ea8d084b868d8b 100644 --- a/news/_posts/2022-06-02-workflow-reports-tutorial.md +++ b/news/_posts/2022-06-02-workflow-reports-tutorial.md @@ -11,5 +11,3 @@ layout: news --- 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! - -
diff --git a/news/_posts/2023-02-08-top-tools.md b/news/_posts/2023-02-08-top-tools.md index f3cd6369e319de..89e3c988eb7fac 100644 --- a/news/_posts/2023-02-08-top-tools.md +++ b/news/_posts/2023-02-08-top-tools.md @@ -9,7 +9,7 @@ contributions: layout: news --- -Did you ever wonder which was the number one most used tool in the GTN? There is a new page of [Top Tools]({% link top-tools.html %}) 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. +Did you ever wonder which was the number one most used tool in the GTN? There is a new page of [Top Tools]({% link stats/top-tools.html %}) 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. This list is also [available as a JSON API]({{ site.baseurl }}/api/top-tools.json). And additionally we have exposed them as individual page listings as well, e.g. if you wanted to link to "All GTN Tutorials Using My Tool", you could do that with one of [these pages like Cat1]({{ site.baseurl }}/by-tool/cat1.html), or [iuc/multiqc]({{ site.baseurl }}/by-tool/iuc/multiqc.html) diff --git a/news/_posts/2023-04-19-shortlinks.md b/news/_posts/2023-04-19-shortlinks.md index cc440f70dfc668..a7ae099c7a96b5 100644 --- a/news/_posts/2023-04-19-shortlinks.md +++ b/news/_posts/2023-04-19-shortlinks.md @@ -16,7 +16,7 @@ PURLs are persistent URLs, and can be used to link to a specific version of a tu ## How do I use them? -The PURLs are in the form `gxy.io/GTN:[id]`, where `[id]` is the identifier of the tutorial, slide, or FAQ. For example, the identifier for the [Galaxy Installation with Ansible](https://training.galaxyproject.org/training-material/topics/admin/tutorials/ansible-galaxy/tutorial.html) tutorial is `GTN:T00001`. The PURL for this tutorial is thus [gxy.io/GTN:T00001](https://gxy.io/GTN:T00001). This will always point to the Ansible Galaxy tutorial, no matter what changes are made to the tutorial in the future. +The PURLs are in the form `gxy.io/GTN:[id]`, where `[id]` is the identifier of the tutorial, slide, or FAQ. For example, the identifier for the [Galaxy Installation with Ansible]({% link topics/admin/tutorials/ansible-galaxy/tutorial.md %}) tutorial is `GTN:T00001`. The PURL for this tutorial is thus [gxy.io/GTN:T00001](https://gxy.io/GTN:T00001). This will always point to the Ansible Galaxy tutorial, no matter what changes are made to the tutorial in the future. ## How do I find the PURL for a tutorial? diff --git a/news/_posts/2023-12-18-medchem-user.md b/news/_posts/2023-12-18-medchem-user.md index 57073c876a1e33..d1e41290764114 100644 --- a/news/_posts/2023-12-18-medchem-user.md +++ b/news/_posts/2023-12-18-medchem-user.md @@ -8,7 +8,7 @@ layout: news 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. -Before synthesising any new molecules, it would make sense to check if they correctly dock into the active site. As an enthusiastic user and developer of Galaxy, the idea of using GTN came straight to my mind. Even though molecular docking was beyond the scope of our project, I knew that Galaxy and GTN give such an amazing opportunity to do it in the blink of an eye that I wouldn't be myself if I hadn't tried! Therefore, by using the [tutorial on molecular docking]({% link topics/computational-chemistry/tutorials/cheminformatics/tutorial.md}), I identified the pocket, then I studied the binding of the approved drugs such as Safinamide and Zonisamide and finally I checked how our proposed molecule fits within the pocket. After that, we were ready to synthesise the derivative we came up with! +Before synthesising any new molecules, it would make sense to check if they correctly dock into the active site. As an enthusiastic user and developer of Galaxy, the idea of using GTN came straight to my mind. Even though molecular docking was beyond the scope of our project, I knew that Galaxy and GTN give such an amazing opportunity to do it in the blink of an eye that I wouldn't be myself if I hadn't tried! Therefore, by using the [tutorial on molecular docking]({% link topics/computational-chemistry/tutorials/cheminformatics/tutorial.md %}), I identified the pocket, then I studied the binding of the approved drugs such as Safinamide and Zonisamide and finally I checked how our proposed molecule fits within the pocket. After that, we were ready to synthesise the derivative we came up with! ![Picture of piperine derivative docking into MAO-B pocket.]({% link news/images/2023-12-18-medchem-user.jpg %} "Piperine derivative as a potential inhibitor of MAO-B") diff --git a/short/galaxy.html b/short/galaxy.html index 4ba34bf0072675..a885c0b6a5dc75 100644 --- a/short/galaxy.html +++ b/short/galaxy.html @@ -1,5 +1,6 @@ --- layout: base +title: My Galaxy instance ---

My Galaxy Instance

diff --git a/short/gat.html b/short/gat.html index ac3152b5691286..56e8c35e8046c6 100644 --- a/short/gat.html +++ b/short/gat.html @@ -1,5 +1,6 @@ --- layout: base +title: My GAT Instance ---

My GAT Instance

diff --git a/stats/index.md b/stats/index.md index d99d4ab3b2e5d8..901efb987f684b 100644 --- a/stats/index.md +++ b/stats/index.md @@ -1,5 +1,6 @@ --- layout: base +title: GTN Statistics redirect_from: - /stats --- @@ -42,7 +43,6 @@ redirect_from:

GTN Statistics

-
{% snippet faqs/gtn/gtn_stats.md %} diff --git a/videos/watch.md b/videos/watch.md index a04fe5f86860a0..e24820e95c6ebe 100644 --- a/videos/watch.md +++ b/videos/watch.md @@ -1,5 +1,6 @@ --- layout: base +title: GTN Videos ---