galaxyproject · bgruening · Jul 7, 2023 · Jul 7, 2023 · Jul 7, 2023 · Jul 7, 2023
diff --git a/content/news/2021-03-01-gat/index.md b/content/news/2021-03-01-gat/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-01"
+tags: [training, gtn-news]
+title: "[GTN news] Galaxy Admin Training Success"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/01/gat.html'
+---
+
+The Galaxy Admins and the GTN instructors community has just run the largest-ever Galaxy Admin training event.
+
diff --git a/content/news/2021-03-16-slides_to_videos/index.md b/content/news/2021-03-16-slides_to_videos/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-16"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: Automatic Slides-to-video conversion"
+authors: "Helena Rasche, Delphine Lariviere"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/16/slides_to_videos.html'
+---
+
+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.
+
diff --git a/content/news/2021-03-17-galaxy_release/index.md b/content/news/2021-03-17-galaxy_release/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-17"
+tags: [training, gtn-news]
+title: "[GTN news] Galaxy 21.01 released!"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/17/galaxy_release.html'
+---
+
+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.
+
diff --git a/content/news/2021-03-17-smorgasbord_report/index.md b/content/news/2021-03-17-smorgasbord_report/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-17"
+tags: [training, gtn-news]
+title: "[GTN news] Report on the GTN Smörgåsbord event"
+authors: "Saskia Hiltemann, Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/17/smorgasbord_report.html'
+---
+
+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.
+
diff --git a/content/news/2021-03-18-gcc2021-virtual-edition/index.md b/content/news/2021-03-18-gcc2021-virtual-edition/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-18"
+tags: [training, gtn-news]
+title: "[GTN news] Galaxy Community Conference 2021"
+authors: "Saskia Hiltemann"
+external: 'https://training.galaxyproject.orghttps://www.vibconferences.be/events/gcc2021-virtual-edition'
+---
+
+This is an external post, please follow the link to read it.
+
diff --git a/content/news/2021-03-18-gtn_cofest_may/index.md b/content/news/2021-03-18-gtn_cofest_may/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-18"
+tags: [training, gtn-news]
+title: "[GTN news] Next GTN CoFest May 20, 2021"
+authors: "Saskia Hiltemann, Helena Rasche, Bérénice Batut, Jennifer Hillman-Jackson, Delphine Lariviere, Anna Syme, Maria Doyle"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/18/gtn_cofest_may.html'
+---
+
+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!
+
diff --git a/content/news/2021-03-18-tutorial_imaging_cell_profiler/index.md b/content/news/2021-03-18-tutorial_imaging_cell_profiler/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-18"
+tags: [training, gtn-news]
+title: "[GTN news] New Tutorial: Object tracking using CellProfiler"
+authors: "Beatriz Serrano-Solano, Yi Sun, Jean-Karim Hériché"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/18/tutorial_imaging_cell_profiler.html'
+---
+
+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.
+
diff --git a/content/news/2021-03-24-faqs/index.md b/content/news/2021-03-24-faqs/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-24"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: FAQs"
+authors: "Saskia Hiltemann, Helena Rasche, Bérénice Batut"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/24/faqs.html'
+---
+
+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.
+
diff --git a/content/news/2021-03-24-tutorial_assembly_mrsa/index.md b/content/news/2021-03-24-tutorial_assembly_mrsa/index.md
@@ -0,0 +1,17 @@
+        ---
+        site: [all]
+        date: "2021-03-24"
+        tags: [training, gtn-news]
+        title: "[GTN news] New Tutorials: Genome assembly of a MRSA genome"
+        authors: "Bazante Sanders, Miaomiao Zhou, Helena Rasche, Saskia Hiltemann"
+        external: 'https://training.galaxyproject.org/training-material/news/2021/03/24/tutorial_assembly_mrsa.html'
+        ---
+
+        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.
+
diff --git a/content/news/2021-03-30-tutorial_scrna_plant/index.md b/content/news/2021-03-30-tutorial_scrna_plant/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-03-30"
+tags: [training, gtn-news]
+title: "[GTN news] New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy"
+authors: "Mehmet Tekman, Beatriz Serrano-Solano"
+external: 'https://training.galaxyproject.org/training-material/news/2021/03/30/tutorial_scrna_plant.html'
+---
+
+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.
+
diff --git a/content/news/2021-04-06-new-video-player/index.md b/content/news/2021-04-06-new-video-player/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-04-06"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: Video Player"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2021/04/06/new-video-player.html'
+---
+
+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.
+
diff --git a/content/news/2021-04-10-tutorial_plant_transcriptomics/index.md b/content/news/2021-04-10-tutorial_plant_transcriptomics/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-04-10"
+tags: [training, gtn-news]
+title: "[GTN news] New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana"
+authors: "Cristóbal Gallardo, Pavankumar Videm, Beatriz Serrano-Solano"
+external: 'https://training.galaxyproject.org/training-material/news/2021/04/10/tutorial_plant_transcriptomics.html'
+---
+
+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.
+
diff --git a/content/news/2021-09-24-jupyter/index.md b/content/news/2021-09-24-jupyter/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-09-24"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: Automatic Jupyter Notebooks"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2021/09/24/jupyter.html'
+---
+
+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.
+
diff --git a/content/news/2021-09-29-survey/index.md b/content/news/2021-09-29-survey/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-09-29"
+tags: [training, gtn-news]
+title: "[GTN news] Got a minute? Take our survey about Galaxy for training and have your say!"
+authors: "Bérénice Batut"
+external: 'https://training.galaxyproject.org/training-material/news/2021/09/29/survey.html'
+---
+
+Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.
+
diff --git a/content/news/2021-10-12-speed/index.md b/content/news/2021-10-12-speed/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-10-12"
+tags: [training, gtn-news]
+title: "[GTN news] Attention Contributors: GTN Performance Enhancements"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2021/10/12/speed.html'
+---
+
+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.
+
diff --git a/content/news/2021-11-10-api/index.md b/content/news/2021-11-10-api/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2021-11-10"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: GTN API with OpenAPI 3 specification"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2021/11/10/api.html'
+---
+
+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.
+
diff --git a/content/news/2022-05-20-schema/index.md b/content/news/2022-05-20-schema/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2022-05-20"
+tags: [training, gtn-news]
+title: "[GTN news] GTN Metadata Schemas"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2022/05/20/schema.html'
+---
+
+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.
+
diff --git a/content/news/2022-06-02-workflow-reports-tutorial/index.md b/content/news/2022-06-02-workflow-reports-tutorial/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2022-06-02"
+tags: [training, gtn-news]
+title: "[GTN news] New Tutorial: Workflow Reports"
+authors: "Saskia Hiltemann"
+external: 'https://training.galaxyproject.org/training-material/news/2022/06/02/workflow-reports-tutorial.html'
+---
+
+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/content/news/2022-09-11-data-manipulation-tutorial/index.md b/content/news/2022-09-11-data-manipulation-tutorial/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2022-09-11"
+tags: [training, gtn-news]
+title: "[GTN news] New Tutorial: Data Manipulation"
+authors: "Saskia Hiltemann"
+external: 'https://training.galaxyproject.org/training-material/news/2022/09/11/data-manipulation-tutorial.html'
+---
+
+Many analyses in Galaxy require small data manipulations in between tools as a sort of “glue” between analysis steps. For example, you may need to change the file format, re-order columns in a table, replace certain values, or perform some filtering operation, before you can proceed to the next step of your analysis. Galaxy offers a wide range of tools that can perform such generic data manipulation tasks, and mastering these types of operations in Galaxy can help you streamline your analysis and get the most out of Galaxy.
+
diff --git a/content/news/2022-11-18-singlecell/index.md b/content/news/2022-11-18-singlecell/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2022-11-18"
+tags: [training, gtn-news]
+title: "[GTN news] New Topic: Single Cell Analysis!"
+authors: "Wendi Bacon, Mehmet Tekman"
+external: 'https://training.galaxyproject.org/training-material/news/2022/11/18/singlecell.html'
+---
+
+Single-cell analysis now has it’s own topic! These tutorials were previously part of the transcriptomics topic, but due to the amazing efforts byWendi Bacon,Mehmet Tekmanand others, we now have so many single-cell analysis tutorials that they deserve their own dedicated topic! From introductory slides and practicals, to case study tutorials generating cell clusters and trajectories from raw sequencing files, and even a growing subtopic of smaller tips and tricks for adapting analysis to user needs, the single cell topic either has what you need or is working on it. Come learn or get involved!
+
diff --git a/content/news/2022-11-29-deconvolution/index.md b/content/news/2022-11-29-deconvolution/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2022-11-29"
+tags: [training, gtn-news]
+title: "[GTN news] New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!"
+authors: "Mehmet Tekman, Wendi Bacon"
+external: 'https://training.galaxyproject.org/training-material/news/2022/11/29/deconvolution.html'
+---
+
+The still new and shiny single-cell analysis topic now boasts a deconvolution tutorial suite! What does deconvolution do you ask? Well, in this context, it infers cell proportions from bulk RNA-seq data. You heard that correctly - instead of expensive new single-cell experiments, you can re-analyse old bulk RNA-seq data and estimate cell proportions. All you need is a reasonably good single cell dataset to use as a reference and you’re good to go! The tutorial suite shows you how to build your reference from publicly available single cell data, and apply analysis to some publicly available bulk RNA-seq data.
+
diff --git a/content/news/2023-01-23-new-covid19-topic/index.md b/content/news/2023-01-23-new-covid19-topic/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2023-01-23"
+tags: [training, gtn-news]
+title: "[GTN news] New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic"
+authors: "Helena Rasche, Wolfgang Maier"
+external: 'https://training.galaxyproject.org/training-material/news/2023/01/23/new-covid19-topic.html'
+---
+
+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.
+
diff --git a/content/news/2023-01-24-prometheus/index.md b/content/news/2023-01-24-prometheus/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2023-01-24"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: Prometheus Metrics endpoint"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2023/01/24/prometheus.html'
+---
+
+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.
+
diff --git a/content/news/2023-01-26-pathogen-detection-tutorial/index.md b/content/news/2023-01-26-pathogen-detection-tutorial/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2023-01-26"
+tags: [training, gtn-news]
+title: "[GTN news] New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition"
+authors: "Bérénice Batut, Engy Nasr"
+external: 'https://training.galaxyproject.org/training-material/news/2023/01/26/pathogen-detection-tutorial.html'
+---
+
+Food contamination with pathogens are a major burden on our society. Globally, they affect an estimated 600 million people a year and impact socioeconomic development at different levels. These outbreaks are mainly due to Salmonella spp. followed by Campylobacter spp. and Noroviruses.
+
diff --git a/content/news/2023-02-02-black-history-month/index.md b/content/news/2023-02-02-black-history-month/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2023-02-02"
+tags: [training, gtn-news]
+title: "[GTN news] GTN Celebrates Black History Month"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2023/02/02/black-history-month.html'
+---
+
+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.
+
diff --git a/content/news/2023-02-08-top-tools/index.md b/content/news/2023-02-08-top-tools/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2023-02-08"
+tags: [training, gtn-news]
+title: "[GTN news] What are the most used tools in the GTN?"
+authors: "Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2023/02/08/top-tools.html'
+---
+
+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.
+
diff --git a/content/news/2023-03-21-galaxy-trainer-directory/index.md b/content/news/2023-03-21-galaxy-trainer-directory/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2023-03-21"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: Trainer Directory! (Add yourself today!)"
+authors: "Helena Rasche, Lucille Delisle"
+external: 'https://training.galaxyproject.org/training-material/news/2023/03/21/galaxy-trainer-directory.html'
+---
+
+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.
+
diff --git a/content/news/2023-04-13-learning-pathways/index.md b/content/news/2023-04-13-learning-pathways/index.md
@@ -0,0 +1,11 @@
+---
+site: [all]
+date: "2023-04-13"
+tags: [training, gtn-news]
+title: "[GTN news] New Feature: Learning Pathways!"
+authors: "Saskia Hiltemann, Helena Rasche"
+external: 'https://training.galaxyproject.org/training-material/news/2023/04/13/learning-pathways.html'
+---
+
+Introducing Learning Pathways in the GTN! 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 step by step.
+