2021/2021-07-27_IT101-DM/slides/img/scripts

+../../../2021-04-20_IT101-DM/slides/img/scripts
\ No newline at end of file

2021/2021-07-27_IT101-DM/slides/img/undraw_secure_server_s9u8.png

+../../../2021-04-20_IT101-DM/slides/img/undraw_secure_server_s9u8.png
\ No newline at end of file

2021/2021-07-27_IT101-DM/slides/img/wordcloud.png

+../../../2021-04-20_IT101-DM/slides/img/wordcloud.png
\ No newline at end of file

2021/2021-07-27_IT101-DM/slides/ingestion.md

-../../2021-04-20_IT101-DM/slides/ingestion.md
\ No newline at end of file

2021/2021-07-27_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:relative">
+<img src="slides/img/LCSB_storages_personal-crossed.png" height="750px">
+
+<div style="position:absolute;left:65%;top:60%">
+
+* Unless consortium/project has formally agreed to use a secure commercial cloud
+
+</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-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
+</div>
+
+
+
+
+# Data ingestion: Transfer and Integrity
+  * When sending data: <font color="red">Do not use emails, use secure platforms (Cloud, Aspera, Atlas share...)!</font>
+
+<div class="fragment">
+Data can be corrupted:
+
+  * (non-)malicious modification
+  * faulty file transfer
+  * disk corruption
+</div>
+  
+<div class="fragment">
+
+### Solution
+
+ * disable write access to the source data
+ * generate checksums!
+ 
+<div style="position:absolute;left:40%;top:30%">
+<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>
+
+
+
+# Data ingestion/Integrity
+## Encryption
+<div class='fragment' style="position:relative;left:25%;top:60%">
+<img  align="middle" height="300px" src="slides/img/encryption.png">
+</div>
+
+<div class='fragment'>
+
+* Guaranted confidentiality
+</div>
+<div class='fragment'>
+
+* Encryption key need to be kept safe
+</div>
+<div class='fragment'>
+
+* <font color= red>Loosing your encryption key means loosing your data!</font>
+</div>
+<div class='fragment'>
+
+* Make a off-site backup of your data
+</div>
+
+

2021/2021-07-27_IT101-DM/slides/introduction.md

-../../2021-04-20_IT101-DM/slides/introduction.md
\ No newline at end of file

2021/2021-07-27_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>
+
+

2021/2021-07-27_IT101-DM/slides/list.json

-../../2021-04-20_IT101-DM/slides/list.json
\ No newline at end of file

2021/2021-07-27_IT101-DM/slides/list.json

+[
+    { "filename": "index.md" },
+    { "filename": "introduction.md" },
+    { "filename": "access_management.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": "data_life_cycle.md" },
+    { "filename": "problem_solving.md" },
+    { "filename": "fair-principles.md" },
+    { "filename": "r3_group.md" },
+    { "filename": "thanks.md" }
+]
\ No newline at end of file

2021/2021-07-27_IT101-DM/slides/overview.md

-../../2021-04-20_IT101-DM/slides/overview.md
\ No newline at end of file

2021/2021-07-27_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

2021/2021-07-27_IT101-DM/slides/reproducibility.md

-../../2021-04-20_IT101-DM/slides/reproducibility.md
\ No newline at end of file

2021/2021-07-27_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
+ 
+</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>
+

2021/2021-07-27_IT101-DM/slides/storage_setup.md

-../../2021-04-20_IT101-DM/slides/storage_setup.md
\ No newline at end of file

2021/2021-07-27_IT101-DM/slides/storage_setup.md

+# Storage set-up
+
+* Download Anti-virus software
+* Regularly update your SW/OS
+* Encrypt movable media
+
+
+<div class="fragment" >
+
+### 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>
+
+</div>
+
+<div class="fragment">
+
+### Passwords
+
+* Strong passwords
+* Password manager
+* Safe password exchange channels
+* Expiration time on password share
+</div>
+
+
+
+# Storage set-up
+## Password exchange channels
+<div style="position:relative">
+<img src="slides/img/privateBin.png" height="350px">
+</div>
+<div style="position:absolute;left:65%;top:85%">
+
+
+* Free service provided by LSCB at <a href="https://privatebin.lcsb.uni.lu" style="color:blue; font-size:0.8em;">privatebin.lcsb.uni.lu</a> 
+* **LUMS** account is required
+* Set expiry period
+* Can expire upon first access
+* Password only accessible by sender and recipient
+</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>

2021/2021-07-27_IT101-DM/slides/thanks.md

-../../2021-04-20_IT101-DM/slides/thanks.md
\ No newline at end of file

2021/2021-07-27_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>
+<div style="position:absolute">
+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://gitlab.lcsb.uni.lu/
+
+HPC: https://hpc.uni.lu/
+
+Service Portal: https://service.uni.lu/sp
+
+LCSB intranet: https://intranet.uni.lux
+</div>
+<div style="position:relative;top:1.5em;left:55%;width:45%">
+Avalable SW and tools:
+<div style="margin-left: 20px;">
+SIU managed:
+
+&ensp; - Service Portal > All Catalogs > IT > Softwares
+</div>
+<div style="margin-left: 20px;">
+LCSB managed:
+
+&ensp; - Service Portal > Knowledge > FAQ - Corporate Software\
+&ensp; - LCSB intranet > Science tab > Tools
+</div>
+</div>

2021/2021-07-27_IT101-DM/slides/visualization.md

-../../2021-04-20_IT101-DM/slides/visualization.md
\ No newline at end of file

2021/2021-07-27_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>

2021/2021-10-20_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!**