diff --git a/2020/2020-03-30_basicGitTraining/slides/best_practices.md b/2020/2020-03-30_basicGitTraining/slides/best_practices.md new file mode 100644 index 0000000000000000000000000000000000000000..13b67fd22c3a360497cef831dc46a8321a6f3833 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/best_practices.md @@ -0,0 +1,20 @@ +# 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 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 + $ 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/slides/branches.md b/2020/2020-03-30_basicGitTraining/slides/branches.md new file mode 100644 index 0000000000000000000000000000000000000000..0c91358cb047d118836dd31d9e93cf8655f06601 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/branches.md @@ -0,0 +1,98 @@ +# 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"> + + 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/slides/cloneRepo.md b/2020/2020-03-30_basicGitTraining/slides/cloneRepo.md new file mode 100644 index 0000000000000000000000000000000000000000..c5ded98da9ffaa924e192dd0315c6ab7f893dc42 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/cloneRepo.md @@ -0,0 +1,14 @@ +# How do I start working on a repository? + +You have to `clone` it first: + +```bash +$ 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://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/configuration.md b/2020/2020-03-30_basicGitTraining/slides/configuration.md new file mode 100644 index 0000000000000000000000000000000000000000..6217c28d6a1e061695cc8ca48f250ea6c449d6d0 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/configuration.md @@ -0,0 +1,52 @@ +# 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 +``` + +If you set a password to your key (recommended), add it to the `ssh-agent`: +```bash +$ eval "$(ssh-agent -s)" +$ ssh-add -K ~/.ssh/id_rsa +``` + +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/slides/essential_commands.md b/2020/2020-03-30_basicGitTraining/slides/essential_commands.md new file mode 100644 index 0000000000000000000000000000000000000000..2753772cf5ed9390a003e0654b9664f0c6e16462 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/essential_commands.md @@ -0,0 +1,98 @@ +# 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 firstnameLastname.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/slides/forks.md b/2020/2020-03-30_basicGitTraining/slides/forks.md new file mode 100644 index 0000000000000000000000000000000000000000..30ae7dab0d3cbf74b323c45bbcfa5d60b56dd7da --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/forks.md @@ -0,0 +1,82 @@ +# 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>. + + + +# How to get a fork? + +Browse to the original repository and click on the button `Fork`: + + + +<img src="slides/img/icon-live-demo.png" height="100px"> + + + +# Time to practice! + +Fork the practice repository: <br><br> +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 ssh://git@git-r3lab-server.uni.lu:8022/<yourName>/basic-practice-pages.git +``` + +Change to the practice directory with: +```bash +$ cd basic-practice-pages +``` + + + +# 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. + + You have to update it yourself! + +<br> + +**More on that later!** + diff --git a/2020/2020-03-30_basicGitTraining/slides/github_gitlab.md b/2020/2020-03-30_basicGitTraining/slides/github_gitlab.md new file mode 100644 index 0000000000000000000000000000000000000000..84930c3922e96a6f2bb75d3ed85881aa19c2e2de --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/github_gitlab.md @@ -0,0 +1,18 @@ +# 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 diff --git a/2020/2020-03-30_basicGitTraining/slides/img b/2020/2020-03-30_basicGitTraining/slides/img new file mode 120000 index 0000000000000000000000000000000000000000..b1bf666f8728acd0582537911f968789b8f1ac9a --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/img @@ -0,0 +1 @@ +../../../2019/2019-06-11_basicGitTraining/slides/img \ No newline at end of file diff --git a/2020/2020-03-30_basicGitTraining/slides/index.md b/2020/2020-03-30_basicGitTraining/slides/index.md new file mode 100644 index 0000000000000000000000000000000000000000..3ce684cec9d9d0c51881eade69a326512399b687 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/index.md @@ -0,0 +1,19 @@ +# R3.school + +## March 30th, 2020 + +<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 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/slides/installation.md b/2020/2020-03-30_basicGitTraining/slides/installation.md new file mode 100644 index 0000000000000000000000000000000000000000..731b4e823deb56000b71acfa54ce9758773ed458 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/installation.md @@ -0,0 +1,64 @@ +# The terminal (shell) + +**macOS users:** + +> Start the Terminal from your `/Applications` directoy. + + Install iTerm2: [https://www.iterm2.com](https://www.iterm2.com) + +<br> + +**Windows users:** + +> Install Git Bash: [https://git-scm.com/download/win](https://git-scm.com/download/win) + +<br> + +**Linux users:** + +> Launch default terminal.<br> + Install Terminator: [https://launchpad.net/terminator](https://launchpad.net/terminator) + + + +# Installation of `git` + +<img src="slides/img/github_app.png" class="as-is" height="200" /> + +**macOS** + +> Install *Xcode Command Line Tools* + +<br> + +**Windows** + +> Install Git Bash: <br>`https://git-scm.com/download/win` + +<br> + +**Linux (Ubuntu)** + +```bash +$ sudo apt-get install git-all +``` + + + +# How to get started? + +**macOS** + +> Start the `Terminal` or `iTerm`. + +<br> + +**Windows** + +> Start `GUI Bash`. + +<br> + +**Linux (Ubuntu)** + +> Start the `Terminal` or `Terminator`. diff --git a/2020/2020-03-30_basicGitTraining/slides/list.json b/2020/2020-03-30_basicGitTraining/slides/list.json new file mode 100644 index 0000000000000000000000000000000000000000..5794aa1399df46ac7386b3684c0a3c442e7cc74c --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/list.json @@ -0,0 +1,18 @@ +[ + { "filename": "index.md" }, + { "filename": "overview.md" }, + { "filename": "what_is_git.md" }, + { "filename": "github_gitlab.md" }, + { "filename": "installation.md" }, + { "filename": "the_terminal.md" }, + { "filename": "the_editor.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/slides/merge.md b/2020/2020-03-30_basicGitTraining/slides/merge.md new file mode 100644 index 0000000000000000000000000000000000000000..277081385008051a73a55357e5fe75c197505b81 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/merge.md @@ -0,0 +1,13 @@ +# Merge (pull) requests + +If you want your changes to be reflected on the `develop` or `master` branches, +**submit a merge request (MR)** via the git-r3lab 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/slides/overview.md b/2020/2020-03-30_basicGitTraining/slides/overview.md new file mode 100644 index 0000000000000000000000000000000000000000..1cb37bc5db07b75083e2a83b13b2ba306549a8ab --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/overview.md @@ -0,0 +1,15 @@ +# Overview + +1. What is `git`? What is the use of `git`? +2. GitHub and GitLab +3. The terminal +4. Installation of `git` +5. The editor +6. How do I configure `git`? +7. Where and how to start? +8. What is a fork? +9. What are branches? +10. The 5 essential commands (`pull` / `status` / `add` / `commit` / `push`) +11. What are merge/pull requests? +12. How do I synchronize my fork? +13. Best practices \ No newline at end of file diff --git a/2020/2020-03-30_basicGitTraining/slides/syncFork.md b/2020/2020-03-30_basicGitTraining/slides/syncFork.md new file mode 100644 index 0000000000000000000000000000000000000000..b773cd1fbebba6cc901be3010729d6a8c95b7111 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/syncFork.md @@ -0,0 +1,47 @@ +# Synchronize your fork + + Remember, we have to regularly update our own copy of the code. + + +Add the `upstream` address (original/protected repository) +```bash +$ URL=ssh://git@git-r3lab-server.uni.lu:8022/R3/school/git/basic-practice-pages.git +$ git remote add upstream $URL +``` + + Note the change in the URL. + + +You can then check whether the remote address is set correctly +```bash +$ 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: + +```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 new file mode 100644 index 0000000000000000000000000000000000000000..27802556cea3d6135766db521b8e8e8ad4e669c9 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/thanks.md @@ -0,0 +1,40 @@ +# 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. 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: + +lcsb-r3@uni.lu + diff --git a/2020/2020-03-30_basicGitTraining/slides/the_editor.md b/2020/2020-03-30_basicGitTraining/slides/the_editor.md new file mode 100644 index 0000000000000000000000000000000000000000..dfa94339c3fd33f17e15bc874574bda652526a15 --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/the_editor.md @@ -0,0 +1,12 @@ +# The editor(s) + +Recommended editors: + +- **Visual Studio Code** [https://code.visualstudio.com](https://code.visualstudio.com) +- **Atom** [https://atom.io](https://atom.io) + +*Note*: Other editors such as can, of course, also be used. Examples: +- IntelliJ IDEA [https://www.jetbrains.com/idea](https://www.jetbrains.com/idea) +- Sublime Text [https://www.sublimetext.com](https://www.sublimetext.com) + +<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/the_terminal.md b/2020/2020-03-30_basicGitTraining/slides/the_terminal.md new file mode 100644 index 0000000000000000000000000000000000000000..0abe54183778dc4ff637384cc65fedfc0fdc147a --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/the_terminal.md @@ -0,0 +1,65 @@ +# 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 `~/`. + +<br> + +**Is `git` properly installed?** + +```bash +$ git --version +# git version 2.10.0 +``` + + + +# 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/slides/what_is_git.md b/2020/2020-03-30_basicGitTraining/slides/what_is_git.md new file mode 100644 index 0000000000000000000000000000000000000000..973cc0593ed0b3b993e870f74c9e0794301e278e --- /dev/null +++ b/2020/2020-03-30_basicGitTraining/slides/what_is_git.md @@ -0,0 +1,40 @@ +# What is `git`? + +<!--  --> + +`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/2020/2020-05-12_IT101-DM/slides/DinoSequentialSmaller.gif b/2020/2020-05-12_IT101-DM/slides/DinoSequentialSmaller.gif new file mode 120000 index 0000000000000000000000000000000000000000..4fb59b8ec20821cb388d6e77f8e39c3af85effe8 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/DinoSequentialSmaller.gif @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/img/DinoSequentialSmaller.gif \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/cleaning-table.jpg b/2020/2020-05-12_IT101-DM/slides/cleaning-table.jpg new file mode 120000 index 0000000000000000000000000000000000000000..54f672eed344d52553dd73254926b8bcbcfb8a2d --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/cleaning-table.jpg @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/img/cleaning-table.jpg \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/code_versioning.md b/2020/2020-05-12_IT101-DM/slides/code_versioning.md new file mode 120000 index 0000000000000000000000000000000000000000..7cb1342ad9a15a80d7d07ef6b7a9499dea9a6fec --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/code_versioning.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/code_versioning.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/data-housekeeping.md b/2020/2020-05-12_IT101-DM/slides/data-housekeeping.md new file mode 120000 index 0000000000000000000000000000000000000000..747c3cef7d05e92b2f04f268f5164fac261c2514 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/data-housekeeping.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/data-housekeeping.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/data-introduction.md b/2020/2020-05-12_IT101-DM/slides/data-introduction.md new file mode 120000 index 0000000000000000000000000000000000000000..b8befc2396f2eebb4ebbcf2666eaa97805b3e6e9 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/data-introduction.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/data-introduction.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/data_flow.md b/2020/2020-05-12_IT101-DM/slides/data_flow.md new file mode 120000 index 0000000000000000000000000000000000000000..860b2b2a3187d8a82c2c5c7310269c24cdd69007 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/data_flow.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/data_flow.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/excel_analyses-sheet.jpeg b/2020/2020-05-12_IT101-DM/slides/excel_analyses-sheet.jpeg new file mode 120000 index 0000000000000000000000000000000000000000..6de93190d2cca1590e987dfc67efe92f99beca1e --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/excel_analyses-sheet.jpeg @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/img/excel_analyses-sheet.jpeg \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/fair-principles.md b/2020/2020-05-12_IT101-DM/slides/fair-principles.md new file mode 120000 index 0000000000000000000000000000000000000000..614979ebc89a9b0bf04cf6cb21f4dc31116fb19d --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/fair-principles.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/fair-principles.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/favicon.ico b/2020/2020-05-12_IT101-DM/slides/favicon.ico new file mode 120000 index 0000000000000000000000000000000000000000..d661e6729facc9bb5b8f8840a45da88f2254fd71 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/favicon.ico @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/img/favicon.ico \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/howtos.md b/2020/2020-05-12_IT101-DM/slides/howtos.md new file mode 120000 index 0000000000000000000000000000000000000000..67e07850c4e13871d231fdc4749a2774cf65fd3c --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/howtos.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/howtos.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/img b/2020/2020-05-12_IT101-DM/slides/img new file mode 120000 index 0000000000000000000000000000000000000000..49a2865eced6b1922a9fb4f1c5cf8065f1f10c86 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/img @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/img/ \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/index.md b/2020/2020-05-12_IT101-DM/slides/index.md new file mode 100644 index 0000000000000000000000000000000000000000..c16924c26b3fe1d4064dfd044f760ec08fa51acf --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/index.md @@ -0,0 +1,20 @@ +# IT101 - Working with computers +<br>IT101 - Working with computers<br> +## May 12th, 2020 + +<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><br> + <h3></h3> + <br><br><br> + <h4> + Vilem Ded<br> + Data Steward<br> + vilem.ded@uni.lu<br> + <i>Luxembourg Centre for Systems Biomedicine</i> + </h4> +</div> diff --git a/2020/2020-05-12_IT101-DM/slides/ingestion.md b/2020/2020-05-12_IT101-DM/slides/ingestion.md new file mode 120000 index 0000000000000000000000000000000000000000..05eea4bb716157d10f0da6a03388def8ec26bbc0 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/ingestion.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/ingestion.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/introduction.md b/2020/2020-05-12_IT101-DM/slides/introduction.md new file mode 120000 index 0000000000000000000000000000000000000000..4b28996cbc4a67efe217f4e8faf785179bb2c93a --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/introduction.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/introduction.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/list.json b/2020/2020-05-12_IT101-DM/slides/list.json new file mode 120000 index 0000000000000000000000000000000000000000..1302be9d4466a9f5a41e41f83ae03619362a702b --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/list.json @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/list.json \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/overview.md b/2020/2020-05-12_IT101-DM/slides/overview.md new file mode 120000 index 0000000000000000000000000000000000000000..db510e2e96f4ef9708e8b5f919169676dfd6e0cb --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/overview.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/overview.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/problem_solving.md b/2020/2020-05-12_IT101-DM/slides/problem_solving.md new file mode 120000 index 0000000000000000000000000000000000000000..66f58da4e55d13355d6a8064319e2b934dc5b551 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/problem_solving.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/problem_solving.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/r3_group.md b/2020/2020-05-12_IT101-DM/slides/r3_group.md new file mode 100644 index 0000000000000000000000000000000000000000..f9281d78398689f2ea662aa1878f480eecd6d81d --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/r3_group.md @@ -0,0 +1,133 @@ +# Responsible and Reproducible Research (R<sup>3</sup>) +## What is R<sup>3</sup>? + + +A multi-facetted change management +process built on 3 pillars: + +- R3 pathfinder + +- R3 school + +- R3 accelerator + +Common link module: R3 clinic + +<div style="top: -1em; left: 50%; position: absolute;"> + <img src="slides/img/3pillars-full.png"> +</div> + +<br> +<br> +<br> +<br> + +<aside class="notes"> +Pathfinder - policies, data management changes<br> +School - courses, howtos, trainnings<br> +Accelerator - advanced teams and their boost/support, CI/CD setup<br> +Clinic - hands-on, meetings in groups, code review + suggestions<br> +</aside> + +## R<sup>3</sup> Training + * LCSB's Monthly Data Management and Data Protection training + * ELIXIR Luxembourg's Best practices in research data management and stewardship <br> + start on 19th May 2020 - 3 x 2 day sessions <br> https://elixir-luxembourg.org/training + * R<sup>3</sup> school Git basics - every 4 months + <aside class="notes"> + Direct newcommers to this monthly training + </aside> + + + +# Responsible and Reproducible Research (R<sup>3</sup>) +<center><img src="slides/img/r3-training-logo.png" height="200px"></center> + +Your R<sup>3</sup> contacts: +<div style="display:block;text-align:center;position:relative"> +<div class="profile-container"> + + * Christophe Trefois + * <img src="slides/img/R3_profile_pictures/christophe_trefois.png"> + * R<sup>3</sup> coordination + +</div> +<div class="profile-container"> + + * Venkata Satagopam + * <img src="slides/img/R3_profile_pictures/venkata_satagopam.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Reinhard Schneider + * <img src="slides/img/R3_profile_pictures/reinhard_schneider.png"> + * Head of Bioinformatics Core + +</div> +<div class="profile-container"> + + * Pinar Alper + * <img src="slides/img/R3_profile_pictures/pinar_alper.png"> + * Data steward + +</div> +<div class="profile-container"> + + * Yohan Yarosz</li> + * <img src="slides/img/R3_profile_pictures/yohan_yarosz.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Laurent Heirendt</li> + * <img src="slides/img/R3_profile_pictures/laurent_heirendt.png"> + * Git, CI + +</div> +<div class="profile-container"> + + * Wei Gu</li> + * <img src="slides/img/R3_profile_pictures/wei_gu.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Sarah Peter</li> + * <img src="slides/img/R3_profile_pictures/sarah_peter.png"> + * HPC + +</div> +<div class="profile-container"> + + * Vilem Ded</li> + * <img src="slides/img/R3_profile_pictures/vilem_ded.png"> + * Data steward + +</div> +<div class="profile-container"> + + * Noua Toukourou</li> + * <img src="slides/img/R3_profile_pictures/noua_toukourou.png"> + * R<sup>3</sup> Core + +</div> +<div class="profile-container"> + + * Alexey Kolodkin</li> + * <img src="slides/img/R3_profile_pictures/alexey_kolodkin.png"> + * Data steward + +</div> +<div class="profile-container"> + + * Maharshi Vyas</li> + * <img src="slides/img/R3_profile_pictures/maharshi_vyas.png"> + * R<sup>3</sup> Core + +</div> + +</div> diff --git a/2020/2020-05-12_IT101-DM/slides/reproducibility.md b/2020/2020-05-12_IT101-DM/slides/reproducibility.md new file mode 120000 index 0000000000000000000000000000000000000000..3c2445cfaf26dcb66e8ee207dd6465699625e33e --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/reproducibility.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/reproducibility.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/rudi_balling.jpg b/2020/2020-05-12_IT101-DM/slides/rudi_balling.jpg new file mode 120000 index 0000000000000000000000000000000000000000..94f5ee71a64577ee592b5f9ea00ccd20a51ba60c --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/rudi_balling.jpg @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/img/rudi_balling.jpg \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/storage_setup.md b/2020/2020-05-12_IT101-DM/slides/storage_setup.md new file mode 120000 index 0000000000000000000000000000000000000000..d5363b000cd021c4ab72a4a9eeb90d77f304ed47 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/storage_setup.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/storage_setup.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/thanks.md b/2020/2020-05-12_IT101-DM/slides/thanks.md new file mode 120000 index 0000000000000000000000000000000000000000..c81123046f3344f76f0902b149a4d9d7c070c184 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/thanks.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/thanks.md \ No newline at end of file diff --git a/2020/2020-05-12_IT101-DM/slides/visualization.md b/2020/2020-05-12_IT101-DM/slides/visualization.md new file mode 120000 index 0000000000000000000000000000000000000000..82924b907833767bbd9460a245902e36775084a6 --- /dev/null +++ b/2020/2020-05-12_IT101-DM/slides/visualization.md @@ -0,0 +1 @@ +../../2020-03-12_IT101-DM/slides/visualization.md \ No newline at end of file