2021/2021-10-20_basicGitTraining/slides/forks.md

+# 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`:
+
+![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<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
+```
+
+Change to the practice directory with:
+```bash
+$ cd basic-git-practice
+```
+
+<img src="slides/img/icon-live-demo.png" height="100px">
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/<yourName>/basic-git-practice.git
+```
+
+
+
+# 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>
+
+<br>
+
+**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!
+
+<br>
+
+**More on that later!**

2021/2021-10-20_basicGitTraining/slides/github_gitlab.md

+# 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://gitlab.lcsb.uni.lu](https://gitlab.lcsb.uni.lu)

2021/2021-10-20_basicGitTraining/slides/img

+../../2021-03-18_basicGitTraining/slides/img
\ No newline at end of file

2021/2021-10-20_basicGitTraining/slides/index.md

+# Elixir-LU training (R3.school)
+
+## October 20th, 2021
+
+<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/elixir.png" height="200px">
+    <img src="slides/img/r3-training-logo.png" height="200px">
+    <br><br><br><br>
+    <h1>Basic git training</h1>
+    <br><br><br><br>
+    <h4>
+        Laurent Heirendt, Ph.D.<br>
+        laurent.heirendt@uni.lu<br>
+        <i>ELIXIR/LU, Luxembourg Centre for Systems Biomedicine</i>
+    </h4>
+</div>
+

2021/2021-10-20_basicGitTraining/slides/installation.md

+# The terminal (shell)
+
+**macOS users:**
+
+> Start the Terminal from your `/Applications` directoy.
+
+![bulb](slides/img/bulb.png) 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>
+![bulb](slides/img/bulb.png) 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`.

2021/2021-10-20_basicGitTraining/slides/list.json

+[
+    { "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" }
+]

2021/2021-10-20_basicGitTraining/slides/merge.md

+# Pull (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

2021/2021-10-20_basicGitTraining/slides/overview.md

+# 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

2021/2021-10-20_basicGitTraining/slides/syncFork.md

+# 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:
+
+```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

2021/2021-10-20_basicGitTraining/slides/thanks.md

+# 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.
+
+<br>
+<center>
+<img src="slides/img/elixir.png" height="200px">
+<img src="slides/img/r3-training-logo.png" height="200px">
+
+<br><br>
+Contact us if you need help:
+<br><br>
+lcsb-r3@uni.lu
+<br><br>
+We'd appreciate feedback: https://bit.ly/elixirgit202110
+<br><br>
+Next course: `Data processing with R tidyverse - November 11-16, 2021`
+
+</center>
\ No newline at end of file

2021/2021-10-20_basicGitTraining/slides/the_editor.md

+# 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 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">

2021/2021-10-20_basicGitTraining/slides/the_terminal.md

+# 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 2.33.1
+```
+
+
+
+# Essential Linux commands
+
+List the contents of a directory
+```bash
+$ ls
+```
+
+You can list more details with:
+```bash
+$ ls -lah
+```
+
+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

2021/2021-10-20_basicGitTraining/slides/what_is_git.md

+# 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.

2022/2022-02-22_IT101-DM/slides/access_management.md

+# Access Management
+<div style="display:grid;grid-gap:100px;grid-template-columns: 40% 40%">
+<div >
+
+## UNI-LU Account
+  * Mails services including web mail: <a href="https://owa.uni.lu" style="color:blue; font-size:0.8em;">owa.uni.lu</a>
+  * Microsoft Office & Teams: <a href="https://service.uni.lu" style="color:blue; font-size:0.8em;">service.uni.lu</a>
+  * SAP services: <a href="https://fiori.uni.lu/fiori" style="color:blue; font-size:0.8em;">fiori.uni.lu/fiori</a>
+  * University's Intranet: <a href="https://intranet.uni.lux" style="color:blue; font-size:0.8em;">intranet.uni.lux</a>
+  * All remote work services : Webex, Slack...
+  
+
+</div>
+<div>
+<div class="fragment">
+
+## LUMS Account
+  * go to <a href="https://service.uni.lu" style="color:blue; font-size:0.8em;">service.uni.lu</a>: make a request and  go to <a href="https://lcsb-cdc-lums-02.uni.lu" style="color:blue; font-size:0.8em;">lums.uni.lu</a> to activate your account upon receiving credentials 
+
+  <div style="position:absolute;left:20%;top:90%">
+  <img src="slides/img/access.png" height="400px">
+  </div>
+
+  <div style="position:absolute;left:60%;top:90%">
+  <img src="slides/img/lums.png" height="400px">
+  </div>  
+<div class="fragment">  
+
+    * Owncloud: <a href="http://owncloud.lcsb.uni.lu" style="color:blue; font-size:0.8em;">owncloud.lcsb.uni.lu</a>
+    * R3 Gitlab: <a href="https://gitlab.lcsb.uni.lu" style="color:blue; font-size:0.8em;">gitlab.lcsb.uni.lu</a>
+    * Private Bin: <a href="https://privatebin.lcsb.uni.lu" style="color:blue; font-size:0.8em;">privatebin.lcsb.uni.lu</a> 
+    * LCSB Wiki page, Webdav, LCSB Analytics page
+
+
+</div>
+</div>

2022/2022-02-22_IT101-DM/slides/code_versioning.md

+# Code versioning
+<div style="position:absolute; width:40%">
+
+**git**
+
+  * Current standard for code versioning
+  * Maintain versions of your code as it develops
+  * Local system, which does not require an online repository
+  * Repositories allow distributed development
+
+<img  align="middle" height="300px" src="slides/img/Git-logo.png">
+</div>
+
+<div class="fragment" style="position:absolute; left:50%; width:40%"">
+
+**git@lcsb** 
+* Recommended, supported repository
+* Allows tracking of issues
+* Ready for continous integration - code checked on commits to the repository.
+* [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
+
+
+  **Use at LCSB** 
+
+   * All analyses code should be in a repository
+      * Minimally at submission of a manuscript
+      * Better daily
+      * Even better "analyses chunkwise"
+</div>
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
+<a href="https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-07" style="color:grey; font-size:0.8em;">LCSB-POL-BIC-07 Source Code Management Policy</a>
+</div>

2022/2022-02-22_IT101-DM/slides/data-housekeeping.md

+# Data housekeeping
+## File names
+<div  style="display:flex; position:static; width:100%">
+<div class="fragment" data-fragment-index="0" style="position:static; width:30%">
+
+### General pricinples  
+  * Machine readable
+  * Human readable
+  * Plays well with default ordering
+</div>
+<div class="fragment" data-fragment-index="1" style="position:absolute; left:33%; width:30%">
+
+### Separators  
+  * No spaces
+  * Underscore to separate
+  * Hyphen to combine
+  
+</div>
+<div class="fragment" data-fragment-index="2" style="position:absolute; left:66%; width:30%">
+
+### Date format follows **ISO 8601**<br>
+
+  2018-12-03<br> 
+  2018-12-06_1700  
+
+</div>
+</div>
+ 
+
+<div class="fragment" data-fragment-index="3" style="width:100%; position:static">
+<div style="position:absolute;width:55%">
+<b>Bad</b> names
+
+```bash
+ PhD-project-Jan19 alldata_final.foo
+ Finacial detailes BIocore 19/11/12.xls
+ ATACseq1Londonmapped.bam
+ Hlad.jez.M-L-průtoky JíObj.z Ohře-od 10-2011.xlsx
+```
+</div>
+<div style="position:relative;width:55%; bottom:20%; left:50%">
+<b>Good</b> names
+
+```bash
+Iris-setosa_samples_1927-05-12.csv
+PI102_Mouse12_EEG_2018-11-03_1245.tsv
+Bioinfiniti_FullProposal_2018-11-15_1655.do
+```
+</div>
+</div>
+<br>
+<br>
+<div class="fragment" data-fragment-index="3" style="width:100%;">
+From Jenny Bryan by CC-BY  
+(https://speakerdeck.com/jennybc/how-to-name-files)
+</div>
+
+
+
+# Data housekeeping
+## File organization
+* Have folder organization conventions for your **group**
+  * Per Paper
+  * Per Study/Project 
+  * Per Collaborator
+* Keep <b>readme files</b> for data  
+  * Title
+  * Date of Creation/Receipt
+  * Instrument or software specific information
+  * People involved
+  * Relations between multiple files/folders 
+
+* Separate files you are actively working from the old ones  
+* Orient newcomers to the group's conventions
+
+<div style="position:absolute;left:43%;top:10%">
+<img src="slides/img/folder_structure.png" height="700px">
+</div>
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
+<a href="https://riojournal.com/article/56508/" style="color:grey; font-size:0.8em;">Foundational Practices of Research Data Management</a>
+</div>
+
+
+
+# Data housekeeping
+<div style="position:absolute">
+
+## When working 
+  * Clarify and separate source and intermediate data
+  * Keep data copies to a **minimum**
+  * Cleanup post-analysis
+  * Cleanup copies created for presentations or for sharing
+</div> 
+<div style="position:relative;left:50%; width:40%">
+<img src="slides/img/cleaning-table.jpg" height="450px">
+</div>
+
+
+
+# Data housekeeping
+## End of project
+  * handover data to a new responsible when leaving
+  * data should be kept as a single copy on server-side storage 
+    * no copies on desktops and external devices
+  * non-proprietary formats
+  * minimal metadata
+  * sensitive data (e.g. whole genome) **must** be encrypted
+  <br/>
+  <br/>
+  * If not specified otherwise, data must be kept for **10 years** following project end for reproducibility purposes
+<aside class="notes">
+Note: sometimes it is hard to find/understand dataset 10 days old
+</aside>
+ 
+## In doubt on data archival?
+Contact R<sup>3</sup> for support on archival of datasets using tickets:
+  * https://service.uni.lu/sp
+  * Home > Catalog > LCSB > Biocore: Application services > Request for: Support
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
+<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-03" style="color:grey; font-size:0.8em;">Research Data Retention and Archival Policy</a>
+</div>
+
+
+
+# Data housekeeping - Summary
+## Server is your friend!
+  * Allows a consistent backup policy for your datasets
+  * Keeps number of copies to minimum
+  * Specification of clear access rights
+  * High accessibility
+  * Data are discoverable
+  * Server can't be stolen
+  
+## General guidelines
+  * Use institutional media for storage of **all** data
+  * Research data (particularly sensitive data) should be in a single source location
+  * Enable encryption for data stored on movable media
+  * Clarify and separate source and intermediate data
+  * Disable write access to relevant source data (read-only)
+  * Backup research data!
+  * Download Anti-virus software
+  * Generate checksums 

2022/2022-02-22_IT101-DM/slides/data-introduction.md

+# Data and metadata
+<div style="display:grid;grid-gap:100px;grid-template-columns: 40% 40%">
+<div >
+
+## Data
+  * "*information in digital form that can be transmitted or processed*"
+  <p align="right">-- Merriam-Webster dictionary</p>
+  * "*information in an electronic form that can be stored and processed by a computer*"
+  <p align="right">--Cambridge dictionary</p>
+
+</div>
+<div>
+
+## Metadata
+  * data describing other data
+  * information that is given to describe or help you use other information
+  * metadata are data
+    * can be processed and analyzed
+</div>
+</div>
+
+<div class="fragment">
+
+## Metadata examples:
+<div style="position:absolute">
+  <ul>
+    <li> LabBook </li>
+    <li> author/owner of the data</li>
+    <li> origin of the data 
+    <li> data type
+  </ul>
+</div>
+<div style="position:absolute;left:25%">
+  <ul>
+    <li> description of content </li>
+    <li> modification date </li>
+    <li> description of modification </li>
+    <li> location </li>
+  </ul>
+</div> 
+<div style="position:relative;left:50%;top:0.7em">
+  <ul> 
+    <li> calibration readings</li>
+    <li> software/firmware version</li>
+    <li> data purpose</li>
+    <li> means of creation</li>
+  </ul>
+</div>
+</div>
+
+<div class="fragment">
+<br>
+</center>
+<center style="color:red">!Insufficient metadata make the data useless!</center>
+</div>
+<aside class="notes">
+Sometimes metadata collection takes more time than data collection
+</aside>
+
+
+
+# LCSB research data
+three categories:
+  * **Primary data** 
+    * scientific data 
+      * measurements, images, observations, notes, surveys, ...
+      * models, software codes, libraries, ...
+    * metadata directly describing the data
+      * data dictionaries
+      * format, version, coverage descriptions, ...
+
+  * **Research record**
+    * description of the research process, including experiment 
+      * experiment set-up
+      * followed protocols
+      * ...
+    
+  * **Project accompanying documentation** 
+      * ethical approvals, information on the consent
+      * collaboration agreements
+      * intellectual property ownership
+      * other relevant documentation
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right;">
+<a href="https://howto.lcsb.uni.lu/internal/policies/LCSB-POL-BIC-03/" style="color:grey; font-size:0.8em;">LCSB-POL-BIC-03 Research Data Retention and Archival Policy</a>
+</div>
\ No newline at end of file

2022/2022-02-22_IT101-DM/slides/data_flow.md

+# Typical flow of data
+
+<div style="display:grid;grid-gap:10px;grid-template-columns: 30% 20% 30%;
+  grid-auto-flow:column;grid-template-rows: repeat(4,auto);position:relative;left:8%">
+  
+<div class="content-box fragment" data-fragment-index="1">
+  <div class="box-title red">Source data</div>
+  <div class="content">
+
+  * Experimental results
+  * Large data sets  
+  * Manually collected data  
+  * External
+
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="2">
+  <div class="box-title yellow">Intermediate</div>
+  <div class="content">
+
+  * Derived data 
+  * Tidy data 
+  * Curated sets
+
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="3">
+  <div class="box-title blue">Analyses</div>
+  <div class="content">
+
+  * Exploratory
+  * Model building
+  * Hypothesis testing
+
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="4">
+  <div class="box-title green">Dissemination</div>
+  <div class="content">
+
+  * Manuscript, report, presentation, ...
+
+  </div>
+</div>
+<center>
+<img src="slides/img/data-flow_sources.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_transformation.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_chart.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_paper.png" height=60%>
+</center>
+
+<div class="content-box fragment" data-fragment-index="5">
+<div class="box-title red">Preserve</div>
+  <div class="content">
+
+  * Version data sets 
+  * Backup
+  * Protect
+  
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="6">
+  <div class="box-title yellow">Reproduce</div>
+  <div class="content">
+
+  * Automate your builds 
+  * Use workflow tools (e.g. Snakemake)
+  
+  </div>
+</div>
+
+
+<div class="content-box fragment" data-fragment-index="7">
+<div class="box-title blue">Trace</div>
+  <div class="content">
+
+ * Multiple iterations.
+ * Code versioning (Git)
+
+ </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="8">
+<div class="box-title green">Track</div>
+  <div class="content">
+
+   * Through multiple versions
+ 
+   </div>
+</div>
+
+</div>
+<aside class="notes">
+flow of the data is downstream (mostly), but you are going back and forth
+applies to all data (financial report, lab safety assessment)
+</aside>

2022/2022-02-22_IT101-DM/slides/data_life_cycle.md

+
+# Some practical recommandations
+
+* Do your data processing according to the data life cycle steps
+
+<div class='fragment' style="position:relative;left:25%;top:60%">
+<img  align="middle" height="300px" src="slides/img/rdm-cycle.png">
+</div>
+<div class="fragment">
+
+* Use data management planning tools:
+  * DMPonline <a href="https://dmponline.elixir-luxembourg.org/" style="color:blue; font-size:0.8em;">https://dmponline.elixir-luxembourg.org/</a>
+   <img  src="slides/img/dmponline_logo.png" height="50px">
+  * DS Wizard <a href="https://learning.ds-wizard.org/" style="color:blue; font-size:0.8em;">https://learning.ds-wizard.org/</a> 
+  <img  src="slides/img/dsw_logo.png" height="100px">
+  
+<div>
+
+<div class="fragment">
+
+* Annotate your data and code using Ontologies and standardised metadata
+
+</div>
\ No newline at end of file

2022/2022-02-22_IT101-DM/slides/fair-principles.md

+# FAIR (meta)data principles
+ * dates back to 2014
+ * well accepted by scientific community
+ * necessity in data driven science
+ * officially embraced by EU and G20
+ * required by funding agencies and journal publishers
+ 
+<center>
+<img src="slides/img/fair-principles.png" height="400px">
+</center>
+<br>
+<br>