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2021/2021-03-09_IT101-DM/slides/index.md

+# IT101 - Working with computers
+<br>IT101 - Working with computers<br>
+## March 09th, 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/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>

2021/2021-03-09_IT101-DM/slides/ingestion.md

+# Data housekeeping
+## Available data storage
+<div class='fragment' style="position:absolute">
+<img src="slides/img/LCSB_storages_full.png" height="750px">
+</div>
+
+<div class='fragment' style="position:absolute">
+<img src="slides/img/LCSB_storages_personal-crossed.png" height="750px">
+</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-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
+</div>
+
+
+
+# Data ingestion/transfer
+## Receiving and sending data 
+
+<img height="400px" style="position:relative;left:10%" src="slides/img/banned_exchange_channels.png"><br>
+<div style="position:absolute; left:10%;width:30%">
+
+## E-mail is not for data transfer
+
+* Avoid transfer of any data by e-mail
+* E-mail is a poor repository
+* Data can be read on passage
+
+</div>
+<div class="fragment" style="left:50%; width:30%; position:absolute">
+
+## Exchanging data
+* Share on Atlas server
+* OwnCloud share (LCSB - BioCore)
+* DropIt service (SIU)
+* LFT (IBM Aspera) share for sensitive data
+</div>
+</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-05" style="color:grey; font-size:0.8em;">Research Human Data Sharing Policy</a>
+</div>
+
+
+
+# Data ingestion/transfer
+Data can be corrupted:
+  * (non-)malicious modification
+  * faulty file transfer
+  * disk corruption
+  
+<div class="fragment">
+
+### Solution
+
+ * disable write access to the source data
+ * generate checksums!
+
+<div style="position:absolute;left:40%">
+<img src="slides/img/checksum.png" width="500px">
+</div>
+</div>
+
+<div class="fragment" style="position:relative; left:0%">
+
+
+## When to generate checksums?
+* before data transfer
+  - new dataset from collaborator
+  - upload to remote repository
+
+* long term storage
+  - master version of dataset
+  - snapshot of data for publication
+</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-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
+</div>

2021/2021-03-09_IT101-DM/slides/introduction.md

+# Introduction
+<div  class="fragment" style="position:absolute">
+<img   height="450px" src="slides/img/wordcloud.png"><br>
+
+## Learning objectives
+
+  * How to manage your data
+  * How to look and analyze your data
+  * Solving issues with computers
+  * Reproduciblity in the research data life cycle
+
+</div>
+<div  class="fragment" style="position:relative;left:50%; width:40%">
+<div >
+<center>
+<img   height="405px" src="slides/img/rudi_balling.jpg"><br>
+Prof. Dr. Rudi Balling, director
+</center>
+</div>
+
+## Pertains to practically all people at LCSB
+   * Scientists
+   * PhD candidates
+   * Technicians
+   * Administrators
+</div>

2021/2021-03-09_IT101-DM/slides/list.json

+[
+    {"filename": "index.md"},
+    {"filename": "introduction.md"},
+    {"filename": "data-introduction.md"},
+    {"filename": "data_flow.md"},
+    {"filename": "ingestion.md"},
+    {"filename": "storage_setup.md"},
+    {"filename": "data-housekeeping.md"},
+    {"filename": "howtos.md"},
+    {"filename": "reproducibility.md"},
+    {"filename": "code_versioning.md"},
+    {"filename": "visualization.md"},
+    {"filename": "problem_solving.md"},
+    {"filename": "fair-principles.md"},
+    {"filename": "r3_group.md"},
+    {"filename": "thanks.md"}
+]

2021/2021-03-09_IT101-DM/slides/overview.md

+## Overview
+
+0. Introduction - learning objectives + targeted audience
+1. Data workflow
+1. Ingestion:
+    * receiving/sending/sharing data
+    * file naming
+    * checksums
+    * backup
+ 1. making data tidy 
+    * what is table 
+    * 
+ 1. Learning to code workflows and analyses - excel files, coding
+ 1. Code versioning and reproducibility
+ 1. Visualization
+  * see the data
+ 1. problem solving
+    * guide
+    * rubberducking
+    * google for help
+    * oracle
+  1. R3 team
+  1. Acknowledgment
+  
+  1. data minimization

2021/2021-03-09_IT101-DM/slides/problem_solving.md

+# Problem solving
+A guide for solving computing issues
+
+1. Express the problem 
+  * Write down what you want to achieve
+2. Search for help 
+  * Read **FAQs**, **help pages** and the **official documentation** well before turning to Google
+  * Use stack exchange, forums and related resources carefully
+3. Ask an expert 
+    * You have to submit the problem in writing
+    * Make the question interesting
+    * If you supply a trivial problem, it will stop answering

2021/2021-03-09_IT101-DM/slides/r3_group.md

+# 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, finding optimal 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 trainings <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>)
+<section data-transition="none" data-background-image="slides/img/r3-training-logo.png" data-background-size="1000px" data-background-opacity="0.1">
+</section>
+<div style="display:block;text-align:center;position:relative;" >
+<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">
+  * Datasteward
+
+</div>
+<div class="profile-container">
+
+  * Yohan Yarosz</li>
+  * <img src="slides/img/R3_profile_pictures/yohan_yarosz.png">
+  * Development
+
+</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">
+
+  * Sarah Peter</li>
+  * <img src="slides/img/R3_profile_pictures/sarah_peter.png">
+  * Infrastructure
+
+</div>
+<div class="profile-container">
+
+  * Valentine Groues</li>
+  * <img src="slides/img/R3_profile_pictures/valentine_groues.png">
+  * Development
+  
+</div>
+<div class="profile-container">
+
+  * Vilem Ded</li>
+  * <img src="slides/img/R3_profile_pictures/vilem_ded.png">
+  * Datasteward
+  
+</div>
+<div class="profile-container">
+
+  * Noua Toukourou</li>
+  * <img src="slides/img/R3_profile_pictures/noua_toukourou.png">
+  * Infrastructure
+  
+</div>
+<div class="profile-container">
+
+  * Alexey Kolodkin</li>
+  * <img src="slides/img/R3_profile_pictures/alexey_kolodkin.png">
+  * Datasteward
+  
+</div>
+<div class="profile-container">
+
+  * Maharshi Vyas</li>
+  * <img src="slides/img/R3_profile_pictures/maharshi_vyas.png">
+  * Infrastructure
+  
+</div>
+
+<div class="profile-container">
+
+  * Nene Barry</li>
+  * <img src="slides/img/R3_profile_pictures/nene_barry.png">
+  * Datasteward
+  
+</div>
+
+<div class="profile-container">
+
+  * Karim Chaouch</li>
+  * <img src="slides/img/R3_profile_pictures/karim_chaouch.png">
+  * Development
+  
+</div>
+<div class="profile-container">
+
+  * Christophe Trefois
+  * <img src="slides/img/R3_profile_pictures/christophe_trefois.png">
+  * R<sup>3</sup> team lead
+
+</div>
+</div>

2021/2021-03-09_IT101-DM/slides/reproducibility.md

+# Reproducibility
+* ensures credibility
+* key requirement for follow-up and collaborative studies
+
+<div style="position:absolute">
+<img src="slides/img/reproducibility_nature.png" height="650px">
+</div>
+
+<div class="fragment" style="position:relative;left:50%">
+
+## Why is our workflow not reproducible?
+
+ Lack of provenance:
+  * Input data downloaded from “some website”
+  * Copy & paste operations
+  * Manual text entry
+  * Analysis not coded
+  * Intermediate and final data not generated by deterministic processes
+</div>
+
+
+
+# Reproducibility
+## Learning to code workflows and analyses
+<div style="display:inline-grid;grid-gap: 40px;grid-template-columns: auto auto;position:relative;left:12%">
+<div class="fragment">
+<div class="content-box">
+<div class="box-title red">Spreadsheets alone</div>
+<div class="content">
+
+  * Is great for looking at data.
+  * Data entry is fast.
+  * Analysis flow is hidden and not in focus.
+  
+</div>
+</div>
+<div style="text-align:center">
+<img src="slides/img/excel_data-sheet.png" height="280px">
+</div>
+</div>
+
+<div class="fragment">
+<div class="content-box">
+<div class="box-title">Coding</div>
+<div class="content">
+
+  * Is great for controlling analysis
+  * Data is hidden.
+  * Flow is visible.
+</div> 
+</div> 
+<img src="slides/img/code-example.png"  height="280px">
+</div>
+</div>
+
+<div class="content-box fragment" style="left:15%;width:60%;position:relative">
+<div class="box-title green">Develop data science skills</div>
+<div class="content">
+
+  * Develop good data management and analysis habits.
+  * Start coding your analysis within spreadsheets.
+  * Make yourself familiar with a statistics environment such as R, Python or Matlab
+  * No need to learn a high level programming language such as C++ or Java.
+
+</div>
+</div>
+
+</div>
+
+
+
+# Table
+<div style="position:absolute">
+"Tabular format of data"
+
+### Header
+
+ * one line!
+ * **good** names of columns
+ 
+### Rows
+ * represent observations/entities
+ 
+### Columns
+  * represent property of the observations
+  * one data type
+</div>
+<div style="left:50%; position:relative; top:-2em">
+<img src="slides/img/excel_data-sheet.png" width="700px">
+<div class="fragment" data-fragment-index="3" style="position:absolute">
+<img src="slides/img/excel_analyses-sheet.jpeg" width="700px"><br>
+</div>
+<div class="fragment" data-fragment-index="4" style="position:relative">
+<img src="slides/img/red-cross.png" width="700px"><br>
+</div>
+</div>

2021/2021-03-09_IT101-DM/slides/storage_setup.md

+# Storage set-up
+
+* Download Anti-virus software
+* Regularly update your SW/OS
+* Encrypt movable media
+
+### Passwords
+
+* Strong passwords
+* Password manager
+* Safe password exchange channels
+* Expiration time on password share
+
+### Backup
+  * take care of your own backups!
+  * don't work on your backup copy!
+  * minimum is <b>3-2-1 backup rule</b>
+
+
+<div style="position:absolute;right:10%;top:10%">
+<img src="slides/img/undraw_secure_server_s9u8.png" height="750px">
+</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-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
+</div>
+
+
+
+# Storage set-up
+## Backup - Central IT/LCSB
+<div style="position:relative">
+<img src="slides/img/LCSB_storages_backed-up.png" height="750px">
+</div>
+<div style="position:absolute;left:65%;top:60%">
+
+Server administrators take care of:
+* server backups
+* LCSB OwnCloud backups
+* group/application server backups (not always)
+
+</div>
+
+
+
+# Storage set-up
+## Backup - personal research data
+<div style="position:relative">
+<img src="slides/img/LCSB_storages_backup.png" height="750px">
+</div>
+<div style="position:absolute;left:55%;top:70%">
+
+<font color="red">One version should reside on Atlas!</font>
+
+</div>

2021/2021-03-09_IT101-DM/slides/thanks.md

+# Thank you.<sup> </sup>
+<center><img src="slides/img/r3-training-logo.png" height="200px"></center>
+<br>
+<br>
+<br>
+<br>
+<center>
+Contact us if you need help:
+
+<a href="mailto:lcsb-r3@uni.lu">lcsb-r3@uni.lu</a>
+</center>
+
+Links:
+
+HowTo Cards / Policies: https://howto.lcsb.uni.lu/
+
+Course Slides: https://courses.lcsb.uni.lu/
+
+Internal Presentations: https://presentations.lcsb.uni.lu/
+
+LCSB GitLab: https://git-r3lab.uni.lu/
+
+HPC: https://hpc.uni.lu/
+
+Service Portal: https://service.uni.lu/sp

2021/2021-03-09_IT101-DM/slides/visualization.md

+# Visualization
+<center>
+
+**Plot your data!**
+<figure>
+  <img src="slides/img/DinoSequentialSmaller.gif" height="500px">
+  <blockquote>"never trust summary statistics alone; always visualize your data"</blockquote>
+  <figcaption>--Alberto Cairo</figcaption>
+</figure> 
+</center>
+
+
+
+# Visualization
+<center>
+
+**Plot your data!**
+<figure>
+  <img src="slides/img/plot-data.png" height="800px">
+</figure> 
+</center>

2021/2021-03-18_basicGitTraining/slides/best_practices.md

+# Best practices
+
+* `pull` before `push` and, generally, before starting to work
+* 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 Pull Request (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!**

2021/2021-03-18_basicGitTraining/slides/branches.md

+# 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">

2021/2021-03-18_basicGitTraining/slides/cloneRepo.md

+# How do I start working on a repository?
+
+You have to `clone` it first:
+
+```bash
+$ git clone git@github.com:LCSB-BioCore/basic-git-practice.git
+```
+
+If you did not configure your SSH key, clone using HTTPS:
+```bash
+$ git clone https://github.com/LCSB-BioCore/basic-git-practice.git
+```
+
+You will be prompted to enter your credentials.