Built a minimal repository with gh-pages based on Henry's template

about.md

@@ -3,3 +3,40 @@
 > More information about your (your team) and your work.
 
 Some text about you here.
+# About
+
+## The course 
+
+## Objectives
+
+In this course you will learn:
+
+- What is Docker and why is needed?
+
+- How to install it - Requirements, best practices.
+
+- Run, pull or login interactively in your container.
+
+- Creating your first Dockerfile and adding some software (rnaseq realeted).
+
+- File system mounts.
+
+- Uploading the container imagein Docker hub.
+
+## Data Science platform
+
+Data Science has become an essential piece both in academia and industry to accelerate gaining insights into the generated datasets. As a strategy to integrate high-level analytics in [DTU - Biosustain](https://www.biosustain.dtu.dk/) we created a centralized [Data Science platform (DSP)](https://www.biosustain.dtu.dk/technologies/informatics/data-science-platform) that provides support to our researchers while promoting standardized data and data processes.
+
+The DSP team aims to make data science more accessible and inclusive not only at DTU Biosustain but also across the DTU Community. The platform follows a data-centric approach that focuses on data infrastructure, processes, and outputs as ongoing, evolving products rather than one-time projects. Each data product is designed as a multidisciplinary collaboration involving the entire data lifecycle and pursuing standardization and automation, and with data usage and reusage in mind. 
+
+The DSP is based on four pillars: 
+
+– Support: our research fellows on Statistics, Programming, Data analytics, and Machine learning
+
+– Education: coorganizing Data club with DTU - Bioengineering and organizing Data Science workshops
+
+– Innovation: introducing researchers to new computational biology methods and technologies  
+
+– Tooling: implementing open-sourced standard tools 
+
+You can contact us at [Data Science platform email](mailto:[email protected]).

conf.py

@@ -6,9 +6,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "Data Science Platform notes template"
-copyright = "2024, DTU Biosustain, Informatics Platform, DSP"
-author = "Henry Webel"
+project = "Data Club Feb 2025: Docker Introduction"
+copyright = "2025, DTU Biosustain, Informatics Platform, DSP"
+author = "Albert Palleja"
 
 
 # -- General configuration ---------------------------------------------------

course_contents/DockerIntro.md

@@ -0,0 +1,20 @@
+# Docker Introduction
+
+Docker is a handy management tool to build, run and share container images.
+
+Differences between a container and a container image?
+
+Docker is widely used in bioinformatics because it addresses several challenges that are common in this field:
+
+- Reproducibility
+- Portability
+- Sofware dependency management
+- Scalability
+- Collaboration
+- Version control of environments
+- Integration with other bioinformatics tools (e.g. Nextflow)
+
+When you install Docker Desktop (is it mandatory, worth),... where are the images saved, are they occupying a lot? Things to take into account in the maintenance ...
+
+These container images can be uploaded and published in a centralized repository known as [Docker Hub](https://hub.docker.com/), or hosted by other parties, such as [Quay](https://quay.io/).
+

course_contents/HandsOn.md

@@ -0,0 +1,4 @@
+# Docker Hands-on beginners training
+
+Inspired on Nextflow training: <https://training.nextflow.io/basic_training/containers/>
+

index.md

@@ -1,6 +1,10 @@
-# Static website Template
+# Docker Introduction
 
-This is a template for a static website using Sphinx and GitHub Pages.
+What if reviewer number 2 tells you that it is impossible to reproduce your results? Ups! Figuring out all software versions and dependencies in your machine and in the reviewer's machine and compare them sounds like very tedious work! Wouldn't it be nice to send him/her your pipeline in a Docker container with the needed software pre-installed and all the dependencies in place?
+
+Docker simplifies bioinformatics workflows by ensuring reproducibility, portability, and dependency management, which makes it essential in computational biology.
+
+And remember to ask questions during the Data Club or over lunch, you can always contact us at [Data Science platform email](mailto:[email protected]).
 
 ```{toctree}
 :maxdepth: 2
@@ -12,8 +16,16 @@ about
 ```{toctree}
 :maxdepth: 2
 :hidden:
-:caption: A topic
+:caption: Course contents
+
+course_contents/DockerIntro.md
+course_contents/HandsOn.md
+```
+
+```{toctree}
+:maxdepth: 2
+:hidden:
 
-folder_topic/article_topic
+resources
 ```
 

resources.md

@@ -0,0 +1,9 @@
+# Resources
+
+## Docker desktop installation link
+
+## Container images repositories
+
+[Docker Hub](https://hub.docker.com/)
+
+[Quay](https://quay.io/)