Merge pull request galaxyproject#4145 from gallardoalba/Minor_modific…

…ations

Alternative splicing training: minor modifications

news/_posts/2023-04-19-shortlinks.md

@@ -4,7 +4,7 @@ contributors: [hexylena]
 tags: [new feature, gtn]
 layout: news
 cover: "assets/images/purl.png"
-cover_alt: 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
+coveralt: 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
 ---
 
 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.

news/_posts/2023-05-11-ro-crate.md

@@ -6,7 +6,7 @@ contributions:
   editing: [hexylena]
   funding: [by-covid]
 cover: "assets/images/BYCOVID_logo_tagline.png"
-cover_alt: "logo of by covid with subtitle reading beyond covid"
+coveralt: "logo of by covid with subtitle reading beyond covid"
 layout: news
 abbreviations:
   FAIR: Findable Accessible Interoperable Reusable

news/_posts/2023-05-15-isoform-usage-training.md

@@ -0,0 +1,24 @@
+---
+layout: news
+title: "New Galaxy training: Genome-wide alternative splicing analysis"
+contributions:
+  authorship: [gallardoalba]
+
+cover: news/images/isoform_usage_post.jpg
+coveralt: "Schematic of an isoform switch and detection pipeline. Data is annotated and a prediction is made for isoform switch consequences"
+tags: [new tutorial]
+---
+
+The GTN hosts a new training for analyzing alternative splicing at genome-wide scale!
+
+# New Galaxy training: Genome-wide alternative splicing analysis
+
+Isoform switching is a biological phenomenon that plays a crucial role in the regulation and diversity of gene expression. It refers to the process by which alternative splicing of pre-mRNA generates different mRNA isoforms that can produce distinct protein products under different conditions. Despite the fact that alternative splicing has been demonstrated to play a fundamental roles in a wide range of biological contexts, such as tissue-specific expression, disease development and evolutionary adaptation, isoform-based expression anaysis pipelines are still rare when compared with gene-level quantification studies.
+
+This new Galaxy training explores the isoform switching concept and provides a step-by-step guide for analyzing this regulatory mechanism. It makes use of [IsoformSwitchAnalyzeR](https://bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html), a R package which integrates a multi-step analysis for isoform detection and functional prediction.
+
+![Overview of computational pipeline for isoform detection and functional prediction.]({% link news/images/isoform_usage_post.jpg %} "Adapted from Vitting-Seerup et Sandelin, 2017.")
+
+A second important aspect of this pipeline is that it allows to evaluate alternative splicing at two different levels: gene-specific and genome-wide scale. This dual-approach allows not only to indentify specific genes, but also prividing an analytical instrument for the study of genome-wide regulatory networks. Finally, a third important element of this training, directly derived from the operational capabilities of IsoformSwitchAnalyzeR, is that it allows to integrate multiple layers of information in the analysis. Concretely, in order to evaluate the functional consequences of the isoform switching events, IsoformSwitchAnalyzeR allows to integrate information bout coding-potential, protein-domains, signal peptides and instrinsically disordered regions.
+
+[Genome-wide alternative splicing analysis]({% link topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.md %}){: class="btn btn-primary"}