diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/best_practices.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/best_practices.md
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index dea55feec7e3ad5a6717044baf28d41001ce6d4d..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/best_practices.md
+++ /dev/null
@@ -1,20 +0,0 @@
-# Best practices
-
-* `pull` before `push`
-* Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
-* Do **not push** to `master`, but **submit a PR**
-* Get your code **reviewed** by your peers (submit a PR!)
-* Submit a PR **often**!
-* `clone` a repository, do not download the `.zip` file.
-* Do **not** combine `git` commands
-   ```bash
-   $ git commit -am "myMessage" # do not do this
-   ```
-* Stage only 1 file at once using
-   ```bash
-   $ git add myFile.md
-   ```
-* Commit **only a few files** at once (after multiple separate `git add` commands)
-* `Push` often - avoid conflicts
-
-Remember: **A `push` a day keeps conflicts away!**
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/branches.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/branches.md
deleted file mode 100644
index 0c91358cb047d118836dd31d9e93cf8655f06601..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/branches.md
+++ /dev/null
@@ -1,98 +0,0 @@
-# Development scheme
-
-
-Generally, in a repository, there are guidelines for contributing.
-
-<div class="fragment">
-
-A common development scheme is dual with a:
-
-- **development** version of the code on `develop`
-- **stable** version of the code on `master`
-
-
-A **version** of the code is referred to as a **branch**.
-
-<div class="fragment">
-
-<img src="slides/img/icon-live-demo.png" height="100px">
-
-
-<font color="red">In the practice repository, the development branch is called `develop`!</font>
-
-<div class="fragment">
-
-![bulb](slides/img/bulb.png) Use this dual development scheme for your own repositories!
-
-
-
-# Branches
-
-A **version** of the code (i.e., a **branch**) is made up of a sequence of code changes.
-
-<div class="fragment">
-
-These individual code changes are called **commits**.
-
-
-For instance, the `master` and `develop` branches can be represented as a timeline:
-<img src="slides/img/branch-master.png" class="branch-master" height="500em"/>
-
-
-
-# Switch between branches
-
-List all branches of the repository with
-```bash
-$ git branch -a
-```
-
-Exit by typing `q`. The branch with the * is the current branch.
-
-<div class="fragment">
-
-Checkout another branch
-```bash
-$ git checkout <branchName>
-```
-
-<div class="fragment">
-
-You can switch to the `develop` branch with
-```bash
-$ git checkout develop
-```
-If the local branch does not exist but the remote does, it is created automatically.
-
-<div class="fragment">
-
-<img src="slides/img/icon-live-demo.png" height="100px">
-
-
-
-# Create your own version
-
-Assume that you want to work on a file:
-
-<div class="fragment">
-
-<font color="red">Create a new **branch**!</font>
-
-```bash
-$ git checkout -b myBranch
-```
-The `-b` flag creates the branch. Locally, you have your own version now:
-<img src="slides/img/branch-create.png" class="branch-create" height="500em"/>
-
-
-
-
-Push your version to your fork:
-```bash
-$ git push origin myBranch
-```
-
-
-<div class="fragment">
-
-<img src="slides/img/icon-live-demo.png" height="100px">
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/cloneRepo.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/cloneRepo.md
deleted file mode 100644
index 887a6e087e73a14ef7ad3790f9e7d0d67ce04b14..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/cloneRepo.md
+++ /dev/null
@@ -1,14 +0,0 @@
-# How do I start working on a repository?
-
-You have to `clone` it first:
-
-```bash
-$ git clone git@github.com:userName/myRepo.git myRepo
-```
-
-If you did not configure your SSH key, clone using HTTPS:
-```bash
-$ git clone https://github.com/userName/myRepo.git myRepo
-```
-
-You will be prompted to enter your credentials.
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/configuration.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/configuration.md
deleted file mode 100644
index 0b07cc4185a35481545f81af5e0f4d8fbc3de063..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/configuration.md
+++ /dev/null
@@ -1,46 +0,0 @@
-# How to configure `git`?
-
-```bash
-$ git config --global user.name "Firstname Lastname"
-$ git config --global user.email "first.last@uni.lu"
-```
-
-Test whether your username and email have been registered
-
-```bash
-$ git config --list
-```
-
-This should list the configuration with `user.name` and `user.email`.
-
-Exit by typing `q`.
-
-
-
-# What is an SSH key?
-
-An SSH key is a secure access credential.
-
-**Principle**: <br><br>
-Communicate **securely** with Github/Gitlab **without** entering the username/password.
-
-
-
-# How do I get and set my SSH key?
-
-Check if you already have an SSH key:
-
-```bash
-$ ls -al ~/.ssh
-```
-
-If there are 2 files named `id_rsa`, you have an SSH key.
-
-If you don’t have yet an SSH key, you have to generate one:
-```bash
-$ ssh-keygen -t rsa # -b 4096
-```
-
-Then, add the SSH key to Github/Gitlab.
-
-<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/essential_commands.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/essential_commands.md
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--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/essential_commands.md
+++ /dev/null
@@ -1,98 +0,0 @@
-# The 5 essential commands
-
-
-**Yes**, you only need 5 commands!
-
-`pull, status, add, commit, push`
-
-or in other words (remember these!):
-```bash
-$ git pull <remote> <branch>
-$ git status
-$ git add myFile.md # example
-$ git commit -m "myMessage" # example
-$ git push <remote> <branch>
-```
-
-
-
-# Pull the latest version of an existing branch
-
-Pull the latest revision on branch `myBranch`:
-```bash
-$ git pull origin myBranch
-# Already up to date
-```
-
-<div class="fragment">
-
-Verify its `status` with:
-```bash
-$ git status
-```
-
-
-
-# Modify a file
-
-Copy the file `template.md` in the folder `_attendees` and rename it with your firstname:
-
-```bash
-$ cd _attendees
-$ cp template.md myName.md
-```
-
-Then, make your changes with your favorite editor!
-
-
-
-# Add your file to the stage
-
-First, check the repository status
-```bash
-$ git status
-# uncommitted changes (displayed in red)
-```
-
-
-<div class="fragment">
-
-Now, add the file (bring it on stage)
-```bash
-$ git add myName.md # replace myName
-$ git status
-# returns the same as before, generally in green (means staged)
-```
-
-<div class="fragment">
-
-**ADVANCED**: If there have been more changes after the file has been added, you can see your changes in the terminal
-```bash
-$ git diff
-```
-exit with `q`
-
-
-
-# Add a commit message
-
-```bash
-$ git commit -m "Add the profile of <myName>"
-$ git status
-```
-
-
-
-# Push your file to your fork
-
-```bash
-$ git push origin myBranch
-```
-
-<div class="fragment">
-
-**ADVANCED**: see the log of all the commits (and your last one) in the terminal
-```bash
-$ git log
-```
-exit by typing `q`.
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/forks.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/forks.md
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--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/forks.md
+++ /dev/null
@@ -1,79 +0,0 @@
-# What is a `fork`?
-
-<img src="slides/img/fork.jpg" class="as-is" height="500em"/>
-<!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
-
-
-
-# Not really ...
-
-<img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
-
-
-
-# What is a `fork`?
-
-In general, when contributing to a repository, you only have **read** access.
-
-In other words, you can only **pull** (unless it is your own repository or access has been granted).
-
-In general, you **cannot write** changes. In other words, you do not have **push** access.
-
-You have to work on your **own copy**.
-
-In other words, you have to work on your own <font color="red">**fork**</font>.
-
-
-
-# How to get a fork?
-
-Browse to the original repository and click on the button `Fork`:
-
-![Fork the repo](https://help.github.com/assets/images/help/repository/fork_button.jpg)
-
-<img src="slides/img/icon-live-demo.png" height="100px">
-
-
-
-# Time to practice!
-
-Fork the practice repository: <br><br>
-https://github.com/LCSB-BioCore/basic-git-practice
-
-Then, clone your fork to your home directory!
-
-<img src="slides/img/icon-live-demo.png" height="100px">
-
-```bash
-$ git clone git@github.com:<yourName>/basic-git-practice.git
-```
-
-Change to the practice directory with:
-```bash
-$ cd basic-git-practice
-```
-
-
-
-# A note on shortcuts ...
-
-<font color="red">
-Any other rudimentary method such as
-
-*'I simply download the `.zip` and unzip it - works like a charm!'*
-
-shall **be avoided**!
-</font>
-
-**Why?**
-
-
-
-# How to update my fork?
-
-As you have your own fork, it will not automatically be updated once the original repository is updated.
-
-![bulb](slides/img/bulb.png) You have to update it yourself!
-
-**More on that later!**
-
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/github_gitlab.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/github_gitlab.md
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+++ /dev/null
@@ -1,18 +0,0 @@
-# GitHub and GitLab
-
-<img src="https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png" alt="GitHub" style="width: 200px;"/>
-<img src="https://gitlab.com/gitlab-com/gitlab-artwork/raw/master/logo/logo-extra-whitespace.png" alt="GitLab" style="width: 200px;"/>
-
-GitHub and GitLab are VCS systems.
-
-GitHub/Gitlab are both **publicly available**, but GitLab can be **on-premise**.
-
-Positive point: GitHub and GitLab are (almost) the same.
-
-
-<img src="slides/img/icon-live-demo.png" height="100px">
-
-
-- **GitHub**: [https://github.com](https://github.com)
-- Public GitLab: [https://gitlab.com](https://gitlab.com)
-- LCSB specific: [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
\ No newline at end of file
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-version https://git-lfs.github.com/spec/v1
-oid sha256:ff78e3c12e93a7548177269db5d4d1e6c0b36cee0802d6a0e02152623287390f
-size 11346236
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@@ -1,19 +0,0 @@
-# R3.school
-
-## June 11th, 2019
-
-<div style="top: 6em; left: 0%; position: absolute;">
-    <img src="theme/img/lcsb_bg.png">
-</div>
-
-<div style="top: 5em; left: 60%; position: absolute;">
-    <img src="slides/img/r3-training-logo.png" height="200px">
-    <br><br><br>
-    <h1>git training for absolute beginners</h1>
-    <br><br><br><br>
-    <h4>
-        Laurent Heirendt, Ph.D.<br><br>
-        laurent.heirendt@uni.lu<br><br>
-        <i>Luxembourg Centre for Systems Biomedicine</i>
-    </h4>
-</div>
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/installation.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/installation.md
deleted file mode 100644
index 506be614073e67dd22fc042230ccb1eb236a9792..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/installation.md
+++ /dev/null
@@ -1,45 +0,0 @@
-# Installation of `git`
-
-<img src="slides/img/github_app.png" class="as-is" height="200" />
-
-**macOS**
-
-Install *Xcode Command Line Tools*
-
-
-**Windows**
-
-Install Git Bash: <br>`https://git-scm.com/download/win`
-
-
-**Linux (Ubuntu)**
-
-```bash
-$ sudo apt-get install git-all
-```
-
-
-
-# How to get started?
-
-**macOS**
-
-Start the `Terminal` or `iTerm`.
-
-
-**Windows**
-
-Start `GUI Bash`.
-
-
-**Linux (Ubuntu)**
-
-Start the `Terminal` or `Terminator`.
-
-
-**Is `git` properly installed?**
-
-```bash
-$ git --version
-# git version 2.10.0
-```
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/list.json b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/list.json
deleted file mode 100644
index e06ee227643e58157bcacd9221c2d00ceff5d03a..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/list.json
+++ /dev/null
@@ -1,65 +0,0 @@
-[
-    {
-        "filename": "index.md"
-    },
-    {
-        "filename": "overview.md"
-    },
-    {
-        "filename": "wheel.md"
-    },
-    {
-        "filename": "repro_crisis.md"
-    },
-    {
-        "filename": "whatiscode.md"
-    },
-    {
-        "filename": "whyCare.md"
-    },
-    {
-        "filename": "qualityCode.md"
-    },
-    {
-        "filename": "what_is_git.md"
-    },
-    {
-        "filename": "the_terminal.md"
-    },
-    {
-        "filename": "the_editor.md"
-    },
-    {
-        "filename": "installation.md"
-    },
-    {
-        "filename": "github_gitlab.md"
-    },
-    {
-        "filename": "configuration.md"
-    },
-    {
-        "filename": "cloneRepo.md"
-    },
-    {
-        "filename": "forks.md"
-    },
-    {
-        "filename": "branches.md"
-    },
-    {
-        "filename": "essential_commands.md"
-    },
-    {
-        "filename": "merge.md"
-    },
-    {
-        "filename": "syncFork.md"
-    },
-    {
-        "filename": "best_practices.md"
-    },
-    {
-        "filename": "thanks.md"
-    }
-]
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/merge.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/merge.md
deleted file mode 100644
index 5b59e684ec66bb668ce48a929608f4de6f238807..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/merge.md
+++ /dev/null
@@ -1,13 +0,0 @@
-# Pull and merge requests
-
-If you want your changes to be reflected on the `develop` or `master` branches,
-**submit a PR** via the Github interface.
-
-Use the **interface** to make use of your peers to review your code!
-<img src="slides/img/branch-merge.png" class="branch-merge" height="500em"/>
-
-Once merged, you can delete the branch via the interface.
-
-<div class="fragment">
-
-<img src="slides/img/icon-live-demo.png" height="100px" >
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/overview.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/overview.md
deleted file mode 100644
index 569ee3789fd8f0a16e39ac938b9f7c5764adce04..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/overview.md
+++ /dev/null
@@ -1,17 +0,0 @@
-# Overview
-
-1. **PART I**: Quality of computer code.
-2. **PART II**: Basic git course
-    1. The terminal
-    2. The editor
-    3. What is `git`? What is the use of `git`? <!--(5 min)//-->
-    4. Installation of `git`
-    5. GitHub and GitLab <!--(5min)//-->
-    6. How do I configure `git`? <!--(5min)//-->
-    7. Where and how to start? <!--(5min)//-->
-    8. What is a fork? <!--(5min)//-->
-    9. What are branches?
-    10. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`)
-    11. What are merge/pull requests? <!--(10 min)//-->
-    12. How do I synchronize my fork?
-    13. Best practices
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/qualityCode.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/qualityCode.md
deleted file mode 100644
index 24abf2c8bba903e0f4e213e3fc049ad7f253636b..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/qualityCode.md
+++ /dev/null
@@ -1,34 +0,0 @@
-# Quality of computer code is relevant for everyone.
-
-`This does not concern me – I am only writing documentation or a script for generating a figure that I want to publish!`
-[Anonymous researcher]
-
-<div class="fragment">
-
-**Great**, but ...
-
-- Figure may not be reproducible
-- Figure looks different when the input data changes
-- Documentation will become outdated
-
-… actually, **EVERYONE** writing documentation, a script, or code is concerned!
-
-<div align="center">
-<img src="slides/img/snoopy.png" height="400px">
-</div>
-
-
-
-# Attributes of high-quality computer code
-
-**Quality** of computer code can be seen as a **group of various attributes**.
-
-High-quality computer code should be:
-
-1. <font color="#A52A2A">**Versioned**</font>: incremental code
-2. <font color="#FFA500">**Well-written**</font> (formatted, documented, commented): easy to read by a human
-3. <font color="#008931">**Tested**</font>: extensively tested code
-
-<div align="center">
-<img src="slides/img/qualitybadge.png">
-</div>
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/repro_crisis.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/repro_crisis.md
deleted file mode 100644
index 8e411c3b8a50de544cdc79ab423a97f97d0407af..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/repro_crisis.md
+++ /dev/null
@@ -1,7 +0,0 @@
-# Reproducibility crisis
-
-<div align="center">
-<img src="slides/img/reproCrisis.png">
-</div>
-
-*Baker, M., <a href="https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970">1,500 scientists lift the lid on reproducibility</a>, Nature 533, 452–454, 2016. doi:10.1038/533452a*
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/syncFork.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/syncFork.md
deleted file mode 100644
index a908869569972adac700f623ec73566b8af5d90c..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/syncFork.md
+++ /dev/null
@@ -1,40 +0,0 @@
-# Synchronize your fork
-
-![bulb](slides/img/bulb.png) Remember, we have to regularly update our own copy of the code.
-
-
-Add the `upstream` address (original/protected repository)
-```bash
-$ git remote add upstream git@github.com:LCSB-BioCore/basic-git-practice.git
-```
-
-![bulb](slides/img/bulb.png) Note the change in the URL.
-
-
-You can then check whether the remote address is set correctly
-```bash
-$ git remote -v
-```
-
-<div class="fragment">
-
-Fetch the changes from upstream (similar to pull)
-```bash
-$ git fetch upstream
-```
-
-
-
-
-Merge the retrieved changes on the `master` branch:
-```bash
-$ git checkout master
-$ git merge upstream/master
-$ git push origin master
-```
-
-<div class="fragment">
-
-Do the same for the `develop` branch.
-
-<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/thanks.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/thanks.md
deleted file mode 100644
index 9f1d826bb46c503b32d1f228512970e726c00618..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/thanks.md
+++ /dev/null
@@ -1,42 +0,0 @@
-# Let's refresh our memories
-
-<div class="fragment">
-
-- What is a **fork**?
-
-<div class="fragment">
-
-- What are **branches**?
-
-<div class="fragment">
-
-- Can I have **multiple branches** in my fork?
-
-<div class="fragment">
-
-- What is a good **development scheme**?
-
-<div class="fragment">
-
-- What are the **5 essential commands**?
-
-
-
-# References & Cheat sheet
-
-[1]: Git Book: https://git-scm.com/book/en/v2
-
-[2]: GitHub training services: https://services.github.com/training/
-
-[3]: Cheat sheet: http://rogerdudler.github.io/git-guide
-
-
-
-# Thank you.
-
-<img src="slides/img/r3-training-logo.png" height="200px">
-
-Contact us if you need help:
-
-r3lab.core@uni.lu
-
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/the_editor.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/the_editor.md
deleted file mode 100644
index bca1b494ce0faed1f5806db841240fd513467d0d..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/the_editor.md
+++ /dev/null
@@ -1,10 +0,0 @@
-# The editor(s)
-
-Recommended editors:
-
-- **Visual Studio Code** (https://code.visualstudio.com)
-- **Atom** (https://atom.io)
-
-*Note*: Other editors such as IntelliJ IDEA (https://www.jetbrains.com/idea) or Sublime Text (https://www.sublimetext.com) can, of course, also be used.
-
-<img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/the_terminal.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/the_terminal.md
deleted file mode 100644
index 32e9979c1fc4d3eeb5286280c4b132bcb4fba8d5..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/the_terminal.md
+++ /dev/null
@@ -1,81 +0,0 @@
-# PART II
-
-<br><br><h1>Basic git course</h1>
-
-
-
-# The terminal (shell)
-
-**macOS users:**
-
-Start the Terminal from your `/Applications` directoy.
-
-![bulb](slides/img/bulb.png) Install iTerm2: `https://www.iterm2.com`
-
-**Windows users:**
-
-Install Git Bash: <br>`https://git-scm.com/download/win`
-
-**Linux users:**
-
-Launch default terminal.<br>
-![bulb](slides/img/bulb.png) Install Terminator: `https://launchpad.net/terminator`
-
-
-
-# First steps in the terminal
-
-Starting the terminal presents itself with a line where you can enter a command
-```bash
-cesar@myComputer>
-```
-
-Often written, for covenience, as
-```bash
-$
-```
-
-When you open your terminal (shell), you are located
-in your home directory (unless otherwise configured), denoted as `~/`.
-
-
-
-# Essential Linux commands
-
-List the contents of a directory
-```bash
-$ ls #-lash
-```
-
-Create a directory
-```bash
-$ mkdir myNewDirectory
-```
-
-Change the directory to a specific folder
-```bash
-$ cd myNewDirectory
-```
-
-Change the directory 1 level and 2 levels up
-```bash
-$ cd ..
-# 1 level up
-
-$ cd ../..
-# 2 levels up
-```
-
-
-
-Move a file or a directory
-```bash
-$ mv myFile.m myNewDirectory/.
-```
-
-
-Rename a file or a directory
-```bash
-$ mv myFile.m myNewFile.m
-$ mv myNewDirectory myDirectory
-```
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/what_is_git.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/what_is_git.md
deleted file mode 100644
index 973cc0593ed0b3b993e870f74c9e0794301e278e..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/what_is_git.md
+++ /dev/null
@@ -1,40 +0,0 @@
-# What is `git`?
-
-<!-- ![](slides/img/git_definition.png) -->
-
-`git` is a **version control system** (VCS) for tracking changes in computer files and coordinating work on those files among multiple people [1].
-
-Designed and implemented in 2005 by **Linus Torvalds**
-
-<div align="center">
-<img src="slides/img/linus.jpg">
-</div>
-
-[1] *https://en.wikipedia.org/wiki/Git*
-
-
-
-# The inventor of `git`
-
-<div align="center">
-<img src="slides/img/git_definition.png">
-</div>
-
-`I'm an egotistical bastard, and I name all my projects after myself.
-First Linux, now git.`
-Linus Torvald (2007-06-14)
-
-
-
-# What is the use of `git`?
-
-* No need to fully rewrite code; **reuse code** and **save time**
-* Keep the changes you made over time (**history**)
-* Allows you to **backtrack** (if necessary) and undo unwanted changes
-* Easily **add contributions** of your collaborators to the main code base
-
-note:
-
-Other points to mention:
-* git shall not be considered as a nuisance, but as a tool that should help to track and trace the code.
-* git is not to track performance. Not using it shows exactly the opposite.
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/whatiscode.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/whatiscode.md
deleted file mode 100644
index 8a7ec810845093821daaaba558c5c1fe777500c1..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/whatiscode.md
+++ /dev/null
@@ -1,15 +0,0 @@
-# What is computer code?
-
-**Computer code**: Set of instructions executed by a computer
-
-**Programming language:**: Style of writing the set of instructions (e.g., C, C++, Fortran, Python, R, Matlab, Julia, …)
-
-**Example:**
-
-<div align="center">
-<img src="slides/img/computerCode.png">
-</div>
-
-<div class="fragment">
-
-<div align="center"><font color="#A52A2A"><span class="fas fa-arrow-right"></span> Maybe this is not so relevant … or even, why should I care?</font></div>
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/wheel.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/wheel.md
deleted file mode 100644
index 789873bca8091e220bf2f81085af88a9ccd66953..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/wheel.md
+++ /dev/null
@@ -1,20 +0,0 @@
-# PART I
-
-<br><br><h1>Quality of computer code.</h1><br>
-<h1>Should you care? What if you didn't?</h1>
-
-
-
-# A true story ...
-
-<div align="center">
-<img src="slides/img/wheel.png">
-</div>
-
-<table style="width:100%">
-  <tr>
-    <th width="33%" align="center">Researcher who cares about<br>quality of his code</th>
-    <th width="33%" align="center">Fellow researcher</th>
-    <th width="33%" align="center">Pi or Manager</th>
-  </tr>
-</table>
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/whyCare.md b/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/whyCare.md
deleted file mode 100644
index 75d3c6b492993927a4d793c470fe5a2996a2f721..0000000000000000000000000000000000000000
--- a/2020/2020-03-30_basicGitTraining/2019-06-11_basicGitTraining/slides/whyCare.md
+++ /dev/null
@@ -1,33 +0,0 @@
-# Why you should care (1)
-
-<div align="center">
-<video width="40%" controls>
-  <source src="slides/img/arianeLaunch.mov" type="video/mp4">
-Your browser does not support the video tag.
-</video>
-</div>
-
-**Aerospace Application**: First launch of Ariane 5, 1996
-
-<font color="#A52A2A"><span class="fas fa-times-circle"></span></font> **Problem**: Rocket exploded shortly after liftoff.
-
-<font color="#FFA500"><span class="fas fa-exclamation-triangle"></span></font> **Root cause of disaster - Software error:**
-
-Horizontal velocity of the rocket exceeded the limits of the 16-bit signed integer value and led to overflow
-Ariane 5 launched with the same software as Ariane 4 - **the code had not been tested**
-
-
-
-# Why you should care (2)
-
-<div align="center">
-<img src="slides/img/therac.png">
-</div>
-
-**Biotechnology Application**: Therac-25 – computer controlled radiation therapy machine
-
-<font color="#A52A2A"><span class="fas fa-times-circle"></span></font> **Problem**: Device malfunctions and delivers a lethal dose of radiation - several patients died.
-
-<font color="#FFA500"><span class="fas fa-exclamation-triangle"></span></font> **Root cause of disaster - Software error:**
-
-**No testing** of software before release, **lack of documentation**
diff --git a/2020/2020-03-30_basicGitTraining/slides/best_practices.md b/2020/2020-03-30_basicGitTraining/slides/best_practices.md
index dea55feec7e3ad5a6717044baf28d41001ce6d4d..13b67fd22c3a360497cef831dc46a8321a6f3833 100644
--- a/2020/2020-03-30_basicGitTraining/slides/best_practices.md
+++ b/2020/2020-03-30_basicGitTraining/slides/best_practices.md
@@ -2,9 +2,9 @@
 
 * `pull` before `push`
 * Work on your <font color="red">own</font> branch (in your own fork), and **not** on `master` and **not** on `develop`
-* Do **not push** to `master`, but **submit a PR**
-* Get your code **reviewed** by your peers (submit a PR!)
-* Submit a PR **often**!
+* Do **not push** to `master`, but **submit a Merge Request (MR)**
+* Get your code **reviewed** by your peers (submit a MR!)
+* Submit a MR **often**!
 * `clone` a repository, do not download the `.zip` file.
 * Do **not** combine `git` commands
    ```bash
diff --git a/2020/2020-03-30_basicGitTraining/slides/cloneRepo.md b/2020/2020-03-30_basicGitTraining/slides/cloneRepo.md
index 887a6e087e73a14ef7ad3790f9e7d0d67ce04b14..c5ded98da9ffaa924e192dd0315c6ab7f893dc42 100644
--- a/2020/2020-03-30_basicGitTraining/slides/cloneRepo.md
+++ b/2020/2020-03-30_basicGitTraining/slides/cloneRepo.md
@@ -3,12 +3,12 @@
 You have to `clone` it first:
 
 ```bash
-$ git clone git@github.com:userName/myRepo.git myRepo
+$ git clone ssh://git@git-r3lab-server.uni.lu:8022/<groupName>/myRepo.git myRepo
 ```
 
 If you did not configure your SSH key, clone using HTTPS:
 ```bash
-$ git clone https://github.com/userName/myRepo.git myRepo
+$ git clone https://git-r3lab.uni.lu/<groupName>/myRepo.git myRepo
 ```
 
 You will be prompted to enter your credentials.
diff --git a/2020/2020-03-30_basicGitTraining/slides/forks.md b/2020/2020-03-30_basicGitTraining/slides/forks.md
index 46abc880bae9f185d52f44d43e6a547ba5a09b27..30ae7dab0d3cbf74b323c45bbcfa5d60b56dd7da 100644
--- a/2020/2020-03-30_basicGitTraining/slides/forks.md
+++ b/2020/2020-03-30_basicGitTraining/slides/forks.md
@@ -1,27 +1,27 @@
 # What is a `fork`?
 
+<center>
 <img src="slides/img/fork.jpg" class="as-is" height="500em"/>
+</center>
 <!--http://www.cndajin.com/data/wls/246/22302193.jpg-->
 
 
 
 # Not really ...
 
+<center>
 <img src="slides/img/fork-crossed.png" class="as-is" height="500em"/>
+</center>
 
 
 
 # What is a `fork`?
 
-In general, when contributing to a repository, you only have **read** access.
-
-In other words, you can only **pull** (unless it is your own repository or access has been granted).
-
-In general, you **cannot write** changes. In other words, you do not have **push** access.
-
-You have to work on your **own copy**.
-
-In other words, you have to work on your own <font color="red">**fork**</font>.
+- In general, when contributing to a repository, you only have **read** access.
+- In other words, you can only **pull** (unless it is your own repository or access has been granted).
+- In general, you **cannot write** changes. In other words, you do not have **push** access.
+- You have to work on your **own copy**.
+- In other words, you have to work on your own <font color="red">**fork**</font>.
 
 
 
@@ -38,19 +38,20 @@ Browse to the original repository and click on the button `Fork`:
 # Time to practice!
 
 Fork the practice repository: <br><br>
-https://github.com/LCSB-BioCore/basic-git-practice
+https://git-r3lab.uni.lu/R3/school/git/basic-practice-pages<br><br>
+
 
 Then, clone your fork to your home directory!
 
 <img src="slides/img/icon-live-demo.png" height="100px">
 
 ```bash
-$ git clone git@github.com:<yourName>/basic-git-practice.git
+$ git clone ssh://git@git-r3lab-server.uni.lu:8022/<yourName>/basic-practice-pages.git
 ```
 
 Change to the practice directory with:
 ```bash
-$ cd basic-git-practice
+$ cd basic-practice-pages
 ```
 
 
@@ -75,5 +76,7 @@ As you have your own fork, it will not automatically be updated once the origina
 
 ![bulb](slides/img/bulb.png) You have to update it yourself!
 
+<br>
+
 **More on that later!**
 
diff --git a/2020/2020-03-30_basicGitTraining/slides/img/Git-Logo-Black.png b/2020/2020-03-30_basicGitTraining/slides/img/Git-Logo-Black.png
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--- a/2020/2020-03-30_basicGitTraining/slides/img/arianeLaunch.mov
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:ff78e3c12e93a7548177269db5d4d1e6c0b36cee0802d6a0e02152623287390f
-size 11346236
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deleted file mode 100644
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diff --git a/2020/2020-03-30_basicGitTraining/slides/overview.md b/2020/2020-03-30_basicGitTraining/slides/overview.md
index 4c6c9585aa04265ab3cb087b3c0d35a250dd7a5e..1cb37bc5db07b75083e2a83b13b2ba306549a8ab 100644
--- a/2020/2020-03-30_basicGitTraining/slides/overview.md
+++ b/2020/2020-03-30_basicGitTraining/slides/overview.md
@@ -1,10 +1,10 @@
 # Overview
 
-1. The terminal
-2. The editor
-3. What is `git`? What is the use of `git`?
+1. What is `git`? What is the use of `git`?
+2. GitHub and GitLab
+3. The terminal
 4. Installation of `git`
-5. GitHub and GitLab
+5. The editor
 6. How do I configure `git`?
 7. Where and how to start?
 8. What is a fork?
diff --git a/2020/2020-03-30_basicGitTraining/slides/syncFork.md b/2020/2020-03-30_basicGitTraining/slides/syncFork.md
index a908869569972adac700f623ec73566b8af5d90c..b773cd1fbebba6cc901be3010729d6a8c95b7111 100644
--- a/2020/2020-03-30_basicGitTraining/slides/syncFork.md
+++ b/2020/2020-03-30_basicGitTraining/slides/syncFork.md
@@ -5,7 +5,8 @@
 
 Add the `upstream` address (original/protected repository)
 ```bash
-$ git remote add upstream git@github.com:LCSB-BioCore/basic-git-practice.git
+$ URL=ssh://git@git-r3lab-server.uni.lu:8022/R3/school/git/basic-practice-pages.git
+$ git remote add upstream $URL
 ```
 
 ![bulb](slides/img/bulb.png) Note the change in the URL.
@@ -35,6 +36,12 @@ $ git push origin master
 
 <div class="fragment">
 
-Do the same for the `develop` branch.
+Do the same for the `develop` branch:
+
+```bash
+$ git checkout develop
+$ git merge upstream/develop
+$ git push origin develop
+```
 
 <img src="slides/img/icon-live-demo.png" height="100px">
\ No newline at end of file
diff --git a/2020/2020-03-30_basicGitTraining/slides/thanks.md b/2020/2020-03-30_basicGitTraining/slides/thanks.md
index 9f1d826bb46c503b32d1f228512970e726c00618..249286cd0efdd99d8da09fc7cbb07dded88932b9 100644
--- a/2020/2020-03-30_basicGitTraining/slides/thanks.md
+++ b/2020/2020-03-30_basicGitTraining/slides/thanks.md
@@ -38,5 +38,5 @@
 
 Contact us if you need help:
 
-r3lab.core@uni.lu
+lcsb-r3@uni.lu