Merge branch '2021-07-27_IT101-DM' into 'develop'

Adding 2021-07-27_IT101-DM slide

See merge request !106

2021/2021-04-20_IT101-DM/slides/data-housekeeping.md

@@ -73,6 +73,13 @@ From Jenny Bryan by CC-BY
 * 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

2021/2021-04-20_IT101-DM/slides/ingestion.md

@@ -4,50 +4,34 @@
 <img src="slides/img/LCSB_storages_full.png" height="750px">
 </div>
 
-<div class='fragment' style="position:absolute">
+<div class='fragment' style="position:relative">
 <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%">
+<div style="position:absolute;left:65%;top:60%">
 
-## 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
+* Unless consortium/project has formally agreed to use a secure commercial cloud
 
 </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>
+<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
+
+# 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">
 
@@ -55,8 +39,8 @@ Data can be corrupted:
 
  * disable write access to the source data
  * generate checksums!
-
-<div style="position:absolute;left:40%">
+ 
+<div style="position:absolute;left:40%;top:30%">
 <img src="slides/img/checksum.png" width="500px">
 </div>
 </div>
@@ -77,3 +61,33 @@ Data can be corrupted:
 <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'>
+
+* Sensitive data protected by encryption
+</div>
+<div class='fragment'>
+
+* Guaranted confidentiality
+</div>
+<div class='fragment'>
+
+* Encryption key which 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>
+
+

2021/2021-04-20_IT101-DM/slides/introduction.md

@@ -24,3 +24,5 @@ Prof. Dr. Rudi Balling, director
    * Technicians
    * Administrators
 </div>
+
+

2021/2021-04-20_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"}
-]
+    { "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

2021/2021-04-20_IT101-DM/slides/reproducibility.md

@@ -94,3 +94,4 @@
 <img src="slides/img/red-cross.png" width="700px"><br>
 </div>
 </div>
+

2021/2021-04-20_IT101-DM/slides/storage_setup.md

@@ -4,12 +4,8 @@
 * Regularly update your SW/OS
 * Encrypt movable media
 
-### Passwords
 
-* Strong passwords
-* Password manager
-* Safe password exchange channels
-* Expiration time on password share
+<div class="fragment" >
 
 ### Backup
   * take care of your own backups!
@@ -24,6 +20,35 @@
 <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

2021/2021-07-27_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>

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

+../../2021-04-20_IT101-DM/slides/code_versioning.md
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2021/2021-07-27_IT101-DM/slides/data-housekeeping.md

+../../2021-04-20_IT101-DM/slides/data-housekeeping.md
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2021/2021-07-27_IT101-DM/slides/data-introduction.md

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

+../../2021-04-20_IT101-DM/slides/data_flow.md
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2021/2021-07-27_IT101-DM/slides/data_life_cycle.md

+
+# Some practical recommandations
+
+* Plan your data walking along the data life cycle
+
+<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 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

2021/2021-07-27_IT101-DM/slides/fair-principles.md

+../../2021-04-20_IT101-DM/slides/fair-principles.md
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2021/2021-07-27_IT101-DM/slides/howtos.md

+../../2021-04-20_IT101-DM/slides/howtos.md
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2021/2021-07-27_IT101-DM/slides/img

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

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

+# IT101 - Working with computers
+<br>IT101 - Working with computers<br>
+## July 27th, 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>
+        Nene Barry<br>
+        Data Steward<br>
+        nene.barry@uni.lu<br>
+        <i>Luxembourg Centre for Systems Biomedicine</i>
+    </h4>
+</div>

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/introduction.md

+../../2021-04-20_IT101-DM/slides/introduction.md
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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/overview.md

+../../2021-04-20_IT101-DM/slides/overview.md
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2021/2021-07-27_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 
+    * Submit the problem in writing
+    * Make the question interesting

2021/2021-07-27_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>
+
+<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
+    * First steps with R (2021-07-27)
+    * Statistical tests and statistical learning for omics data (2021-09-14)
+  * 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">
+
+  * Valentin Grouès</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>

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

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

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

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

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