Merge branch 'develop' into 'master'

Regular merge of develop

See merge request R3/school/courses!67

2020/2020-02-17_IT101-DM/slides/img/scripts/ggplot_visualization.R

+
+library(ggplot2)
+library(data.table)
+library(ggpubr)
+data(iris)
+iris <- data.table(iris)
+iris <- iris[c(1:103)]
+
+g1 <- ggplot(iris, aes(x = Species, y = Sepal.Length))+
+  geom_bar(aes(fill = Species),stat="summary", fun.y="mean" ) +guides(fill = F)+
+  ylim(c(0,8))
+
+g2 <- ggplot(iris, aes(x = Species, y = Sepal.Length))+
+  geom_boxplot(aes(fill = Species))+
+  ylim(c(0,8))+guides(fill = F)
+
+g3 <- ggplot(iris, aes(x = Species, y = Sepal.Length))+
+  geom_boxplot(aes(fill = Species))+
+  ylim(c(0,8))+ geom_point( position="jitter")+
+  guides(fill = F)
+
+ggarrange(g1, g2, g3, nrow = 1)+ggsave(filename = "../plot-data.png", device = "png", width =12, height = 6)

2020/2020-02-17_IT101-DM/slides/index.md

+# IT101 - Working with computers
+<br>IT101 - Working with computers<br>
+## February 17th, 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>

2020/2020-02-17_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>
+
+
+
+# Data ingestion/transfer
+## Receiving and sending data 
+
+<img height="450px" 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)
+* AsperaWeb share for sensitive data
+</div>
+</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>

2020/2020-02-17_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>

2020/2020-02-17_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"}
+]

2020/2020-02-17_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

2020/2020-02-17_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 
+
+
+
+# Problem solving
+## Write to the Oracle 
+
+  * The Oracle gives the precise answer to your problems
+    * You have to submit the problem in writing
+    * The Oracle answers a questions only once or if it finds the problem interesting
+    * If you supply a trivial problem, it will stop answering
+    
+  * Available Oracles
+    * Service Now @ [service.uni.lu] (Uni and LCSB helpdesk)
+    * [Stack Overflow](https://stackoverflow.com/) and other online sites
+    * Local experts

2020/2020-02-17_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, 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  - 27th May 2020
+  * 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>