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# IT101 - Working with computers
<br>IT101 - Working with computers<br>
## April 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/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>
# 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>
# 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>
[
{"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"}
]
## 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
# 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
# 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>
# 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>
# 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>
# 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://git-r3lab.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>
# 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>
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