Merge pull request #23 from albarema/main

update news

css/materialight.scss

@@ -19,4 +19,4 @@ $footer-bg: #4266A1;
 .layout-border {
   background-color:  #f0f0f0;
   padding: 20px;
-}
+}

css/styles.css

@@ -1,10 +1,45 @@
+.column {
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  justify-content: flex-start;
+  background-color: #f0f0f0;
+  box-sizing: border-box;
+  text-align: center;
+  flex: 1;
+}
+
+.column img {
+  width: 100%;
+  height: 150px; /* Fixed image height */
+  object-fit: cover;
+  border-radius: 8px;
+}
+
+
+.column div {
+  text-align: center;
+  margin-top: 10px;  
+  margin-bottom: 10px;
+  text-align: center;
+  flex-grow: 1;
+}
 
 .grid-cell img {
-    max-width: 50%; /* Make the image responsive */
-    height: 50%; /* Maintain aspect ratio */
-  }
-
-  .layout-border {
-    background-color:  #f0f0f0;
-    padding: 20px;
-  }
+  max-width: 150px; /* Make the image responsive */
+  object-fit: cover; /* Crop to fit while preserving aspect ratio */
+  border-radius: 8px;
+}
+
+.layout-border {
+  background-color:  #f0f0f0;
+  align-items: stretch;  /* Stretch the columns to the same height */
+  display: flex;
+  box-sizing: border-box;         /* Ensure padding/margin does not affect width/height */
+  justify-content: space-evenly;
+  height:100%;
+  width: 100%;
+  gap: 0;  /* Remove extra space between columns */
+  margin: 0;
+  padding: 0;
+}

index.qmd

@@ -9,20 +9,20 @@ bibliography: resources/references.bib
 
 # Welcome to the Health Data Science Sandbox {.centered}
 
-<div style="text-align: center; padding:4px; background-color: #f0f0f0;">
+<div style="text-align: center; padding:4px; background-color: #f0f0f0 ;width: 100%;">
 ### Access our training modules
 </div>
 
 
-::: {layout-nrow=1 layout-ncol=5 .layout-border}
+::: {layout-nrow=1 layout-ncol=5 .grid-cell .layout-border}
 ::: {.column}
 [![HPC Lab](../images/HPC.png){class="hover-target" width="100%"}](https://hds-sandbox.github.io/modules/#sandbox-hpc)
 **<span style="display: block; margin-top:15px; text-align: center; font-size: 1.2em;">HPC Lab</span>**
 
 <div style="text-align: center;">
+    Research Data Management
     HPC launch
     HPC pipes
-    RDM
 </div>
 :::
 

news.qmd

@@ -5,8 +5,8 @@ format:
     page-layout: full
 listing:
   - id: "upcoming_event"
-    image-height: 300px
-    grid-columns: 3
+    image-height: 200px
+    grid-columns: 4
     image-placeholder: "./img/logo.png"
     fields: [image,title, description,categories, date]
     contents: news/upcoming/*.qmd

news/past/2023-11-09-proteomics_biostat_SDU.qmd

@@ -1,5 +1,5 @@
 ---
-title: "Updates from SDU"
+title: "Proteomics App updates"
 description: "Updated Proteomics Sandbox App supporting of a Biostatistics course at SDU"
 Organizers: Jacob Fredegaard Hansen
 date: 2023-11-09

news/past/2024-04-18-sandbox-workshop.qmd

@@ -1,7 +1,7 @@
 ---
 title: "Workshop: Digging into the Health Data Science Sandbox"
 #description: "Data Scientist, Copenhagen University"
-Organizers: Jennifer Bartell
+Organizers: J.Bartell and A.Refoyo
 date: 2024-04-18
 Dates: "18-19 April 2024"
 Location: KU

news/past/2024-07-01-NGS-analysis.qmd

@@ -2,7 +2,7 @@
 title: "Intro to NGS data analysis - Summer School"
 Organizers:  Samuele Soraggi
 date: 2024-07-01
-Dates: "01-05 July 2024"
+Dates: "1-5 July 2024"
 Location: AU
 categories: [Genomics, AU, course]
 ---

news/past/2024-08-21-BinfConference.qmd

@@ -2,7 +2,7 @@
 title: "How I learned to stop worrying and love RDM"
 image: "binfConference_24.png"
 author: "ARM and JB"
-Organizers: "Jennifer Bartell & Alba RM"
+Organizers: "A.Refoyo and J.Bartell"
 date: 2024-08-21
 Dates: "21 August 2024"
 Location: ADBi Conference

news/past/2024-09-01-bioinf-cafe-aarhus.qmd

@@ -4,6 +4,7 @@ image: "https://abc.au.dk/img/ABClogo.png"
 author: Samuele Soraggi
 Organizers: Samuele Soraggi
 date: 2024-09-01
+Dates: "1 September 2024"
 Location: "Aarhus University"
 categories: [coding, bioinformatics, support]
 description: "Bioinformatics Cafe at AU"

news/past/2024-09-10-scverse2024.qmd

@@ -4,6 +4,7 @@ image: "https://images.squarespace-cdn.com/content/v1/65f327a1d63de64385123101/2
 author: Samuele Soraggi
 Organizers: Samuele Soraggi
 date: 2024-09-10
+Dates: "10 September 2024"
 Location: "Technical University of Munich"
 categories: [single cell omics, dimensionality reduction]
 description: "Conference Workshop"

news/past/2024-09-30-hpcLaunch.qmd

@@ -0,0 +1,14 @@
+---
+title: "HPC-Launch"
+image: "../../images/HPC.png"
+Organizers: J.Bartell and A.Refoyo
+date: 2024-09-30
+Dates: "30 September 2024"
+Location: "University of Copenhagen"
+categories: [HPC, RDM, KU, course]
+description: "HPC & RDM intro workshop"
+---
+
+[Sign-up](https://eventsignup.ku.dk/hpc-launch)
+
+The goal of the course HPC-Launch is to support the launch (and/or reconfiguration) of health data projects from an efficient and modern computing and data management perspective. Targeting trainees and researchers in bioinformatics and large-scale health records, the course will consist of two modules: High-Performance Computing (HPC) and Research Data management (RDM). With the HPC module, we want to expand understanding and efficient use of HPC resources for complex health data science projects. We will fill gaps in technical understanding for beginner to intermediate users of supercomputing platforms and share up-to-date information on computing resources available to Danish researchers and how to get access. With the RDM module, we will introduce the importance of research data management practices and demonstrate practical tips and tools for its implementation at a local research group level. Overall, the course will be a mix of theory, discussion of real-world use cases and participant needs, and active practice/exercises conducted on the HPC platform UCloud (SDU) using bash and relevant IDEs.

news/upcoming/2024-11-15-hpcPipes.qmd → news/past/2024-11-04-hpcPipes.qmd

@@ -1,8 +1,10 @@
 ---
-title: "HPC Pipes"
+title: "HPC-Pipes"
 author: "ARM and JB"
-Organizers: Alba
+Organizers: A.Refoyo and J.Bartell
 date: 2024-11-04
+Dates: "4-5 November 2024"
+Location: "University of Copenhagen"
 categories: [snakemake, conda, KU, course]
 description: "Click to sign-up"
 ---

news/upcoming/2025-03-24-genomics.qmd

@@ -0,0 +1,19 @@
+---
+title: "Genomics Sandbox"
+author: "ARM and SS"
+image: "../../images/genomics2.png"
+Organizers: ARM and SS
+date: 2025-03-24
+categories: [genomics, gwas, KU, course]
+description: "Opening for signup soon"
+---
+
+Opening for signup soon.
+
+The Sandbox Genomics course is an intensive four-day program focused on training participants in Population genetics with a focus on Genome-Wide Association Studies (GWAS). The first day covers foundational genetics concepts through lectures and discussions, followed by a step-by-step guide to performing a GWAS study, from data preprocessing to results interpretation. A key feature is a hands-on GWAS case study where participants complete the entire process, including managing missing genotypes, conducting linear regression for association testing, and understanding linkage disequilibrium for fine-mapping. The course emphasizes practical skills, best practices, and common challenges in GWAS, especially when using high-performance computing.
+
+
+
+
+
+

news/upcoming/2024-10-30-hpcLaunch.qmd → news/upcoming/2025-04-7-hpcLaunch.qmd

@@ -1,13 +1,13 @@
 ---
 title: "HPC launch"
 image: "../../images/HPC.png"
-author: JB
+author: JB & ARM 
 Organizers: Jennifer Bartell
-date: 2024-10-30
+date: 2025-05-12
 categories: [HPC, RDM, KU, course]
-description: "Click to sign-up"
+description: "Opening for signup soon"
 ---
 
-[Sign-up](https://eventsignup.ku.dk/hpc-launch)
+Opening for signup soon.
 
 The goal of the course HPC-Launch is to support the launch (and/or reconfiguration) of health data projects from an efficient and modern computing and data management perspective. Targeting trainees and researchers in bioinformatics and large-scale health records, the course will consist of two modules: High-Performance Computing (HPC) and Research Data management (RDM). With the HPC module, we want to expand understanding and efficient use of HPC resources for complex health data science projects. We will fill gaps in technical understanding for beginner to intermediate users of supercomputing platforms and share up-to-date information on computing resources available to Danish researchers and how to get access. With the RDM module, we will introduce the importance of research data management practices and demonstrate practical tips and tools for its implementation at a local research group level. Overall, the course will be a mix of theory, discussion of real-world use cases and participant needs, and active practice/exercises conducted on the HPC platform UCloud (SDU) using bash and relevant IDEs.

news/upcoming/2025-05-12-hpcPipes.qmd

@@ -0,0 +1,14 @@
+---
+title: "HPC Pipes"
+author: "ARM and JB"
+Organizers: A.Refoyo and J.Bartell
+date: 2025-05-12
+categories: [snakemake, conda, KU, course]
+description: "Opening for signup soon"
+---
+
+Opening for signup soon.
+
+The course HPC-Pipes introduces best practices for setting up, running, and sharing reproducible bioinformatics pipelines and workflows, with a strong emphasis on Snakemake for practical exercises. Rather than focusing on specific tools for bioinformatics analysis, we will cover the entire process of building a robust pipeline—applicable to any data type—using workflow languages, environment/package managers, optimized HPC resources, and FAIR principles for data and tool management. By the end of the course, participants will be equipped to design custom pipelines tailored to their analysis needs.
+
+We will guide participants in automating data analysis with popular workflow languages like Snakemake and Nextflow. From there, we’ll explore how to ensure reproducibility within pipelines and the available options for sharing data analysis and software within the research community. Participants will also learn strategies for managing and organizing large datasets, from documentation and processing to storage, sharing, and preservation. We’ll cover tools like Docker and other containers, with demonstrations on using package and environment managers such as Conda to control the software environment within workflows and containers (Docker and Apptainer). Finally, we’ll provide insights into managing and optimizing pipeline projects on HPC platforms, using resources efficiently.

workshop/workshop_april2024.qmd

@@ -85,7 +85,7 @@ Our apps can run on other clusters, simply by pulling a so-called `docker contai
 
 ## Our OMICS apps
 
-The agenda starts with an introduction to High Performance Computing (HPC) and `uCloud`. You will try two apps during the workshop, but we are developing others, and have deployed three apps already.
+The agenda starts with an introduction to High Performance Computing (HPC) and `UCloud`. You will try two apps during the workshop, but we are developing others, and have deployed three apps already.