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

2021 07 27 it101 dm See merge request R3/school/courses!108

Merge branch '2021-07-27_IT101-DM' into 'develop'
2021 07 27 it101 dm See merge request R3/school/courses!108
61b65b0d · Laurent Heirendt · e9435d7e · 10f66eac · 61b65b0d · 61b65b0d
Commit 61b65b0d authored 3 years ago by Laurent Heirendt
--- a/2021/2021-04-20_IT101-DM/slides/data-housekeeping.md
+++ b/2021/2021-04-20_IT101-DM/slides/data-housekeeping.md
@@ -73,13 +73,6 @@ 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

--- a/2021/2021-04-20_IT101-DM/slides/ingestion.md
+++ b/2021/2021-04-20_IT101-DM/slides/ingestion.md
@@ -4,34 +4,50 @@
 <img src="slides/img/LCSB_storages_full.png" height="750px">
 </div>

-<div class='fragment' style="position:relative">
+<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 

-<div style="position:absolute;left:65%;top:60%">
+<img height="400px" style="position:relative;left:10%" src="slides/img/banned_exchange_channels.png"><br>
+<div style="position:absolute; left:10%;width:30%">

-* Unless consortium/project has formally agreed to use a secure commercial cloud
+## 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-02" style="color:grey; font-size:0.8em;">Data Storage and Backup Policy</a>
+<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 and Integrity
-  * When sending data: <font color="red">Do not use emails, use secure platforms (Cloud, Aspera, Atlas share...)!</font>
-
-<div class="fragment">
+# Data ingestion/transfer
 Data can be corrupted:
-
  * (non-)malicious modification
  * faulty file transfer
  * disk corruption
-</div>
  
 <div class="fragment">

@@ -39,8 +55,8 @@ Data can be corrupted:

 * disable write access to the source data
 * generate checksums!
- 
-<div style="position:absolute;left:40%;top:30%">
+
+<div style="position:absolute;left:40%">
 <img src="slides/img/checksum.png" width="500px">
 </div>
 </div>
@@ -61,33 +77,3 @@ 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>
-
-
--- a/2021/2021-04-20_IT101-DM/slides/introduction.md
+++ b/2021/2021-04-20_IT101-DM/slides/introduction.md
@@ -24,5 +24,3 @@ Prof. Dr. Rudi Balling, director
   * Technicians
   * Administrators
 </div>
-
-
--- a/2021/2021-04-20_IT101-DM/slides/list.json
+++ b/2021/2021-04-20_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
+    {"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"}
+]
--- a/2021/2021-04-20_IT101-DM/slides/reproducibility.md
+++ b/2021/2021-04-20_IT101-DM/slides/reproducibility.md
@@ -94,4 +94,3 @@
 <img src="slides/img/red-cross.png" width="700px"><br>
 </div>
 </div>
-
--- a/2021/2021-04-20_IT101-DM/slides/storage_setup.md
+++ b/2021/2021-04-20_IT101-DM/slides/storage_setup.md
@@ -4,8 +4,12 @@
 * Regularly update your SW/OS
 * Encrypt movable media

+### Passwords

-<div class="fragment" >
+* Strong passwords
+* Password manager
+* Safe password exchange channels
+* Expiration time on password share

 ### Backup
  * take care of your own backups!
@@ -20,35 +24,6 @@
 <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

--- a/2021/2021-07-27_IT101-DM/slides/code_versioning.md
+++ b/2021/2021-07-27_IT101-DM/slides/code_versioning.md
-../../2021-04-20_IT101-DM/slides/code_versioning.md
\ No newline at end of file
--- a/2021/2021-07-27_IT101-DM/slides/code_versioning.md
+++ b/2021/2021-07-27_IT101-DM/slides/code_versioning.md
+# Code versioning
+<div style="position:absolute; width:40%">
+
+**git**
+
+  * Current standard for code versioning
+  * Maintain versions of your code as it develops
+  * Local system, which does not require an online repository
+  * Repositories allow distributed development
+
+<img  align="middle" height="300px" src="slides/img/Git-logo.png">
+</div>
+
+<div class="fragment" style="position:absolute; left:50%; width:40%"">
+
+**git@lcsb** 
+* Recommended, supported repository
+* Allows tracking of issues
+* Ready for continous integration - code checked on commits to the repository.
+* [https://git-r3lab.uni.lu](https://git-r3lab.uni.lu)
+
+
+  **Use at LCSB** 
+
+   * All analyses code should be in a repository
+      * Minimally at submission of a manuscript
+      * Better daily
+      * Even better "analyses chunkwise"
+</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-07" style="color:grey; font-size:0.8em;">LCSB-POL-BIC-07 Source Code Management Policy</a>
+</div>
--- a/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
+++ b/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
-../../2021-04-20_IT101-DM/slides/data-housekeeping.md
\ No newline at end of file
--- a/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
+++ b/2021/2021-07-27_IT101-DM/slides/data-housekeeping.md
+# Data housekeeping
+## File names
+<div  style="display:flex; position:static; width:100%">
+<div class="fragment" data-fragment-index="0" style="position:static; width:30%">
+
+### General pricinples  
+  * Machine readable
+  * Human readable
+  * Plays well with default ordering
+</div>
+<div class="fragment" data-fragment-index="1" style="position:absolute; left:33%; width:30%">
+
+### Separators  
+  * No spaces
+  * Underscore to separate
+  * Hyphen to combine
+  
+</div>
+<div class="fragment" data-fragment-index="2" style="position:absolute; left:66%; width:30%">
+
+### Date format follows **ISO 8601**<br>
+
+  2018-12-03<br> 
+  2018-12-06_1700  
+
+</div>
+</div>
+ 
+
+<div class="fragment" data-fragment-index="3" style="width:100%; position:static">
+<div style="position:absolute;width:55%">
+<b>Bad</b> names
+
+```bash
+ PhD-project-Jan19 alldata_final.foo
+ Finacial detailes BIocore 19/11/12.xls
+ ATACseq1Londonmapped.bam
+ Hlad.jez.M-L-průtoky JíObj.z Ohře-od 10-2011.xlsx
+```
+</div>
+<div style="position:relative;width:55%; bottom:20%; left:50%">
+<b>Good</b> names
+
+```bash
+Iris-setosa_samples_1927-05-12.csv
+PI102_Mouse12_EEG_2018-11-03_1245.tsv
+Bioinfiniti_FullProposal_2018-11-15_1655.do
+```
+</div>
+</div>
+<br>
+<br>
+<div class="fragment" data-fragment-index="3" style="width:100%;">
+From Jenny Bryan by CC-BY  
+(https://speakerdeck.com/jennybc/how-to-name-files)
+</div>
+
+
+
+# Data housekeeping
+## File organization
+* Have folder organization conventions for your **group**
+  * Per Paper
+  * Per Study/Project 
+  * Per Collaborator
+* Keep <b>readme files</b> for data  
+  * Title
+  * Date of Creation/Receipt
+  * Instrument or software specific information
+  * People involved
+  * Relations between multiple files/folders 
+
+* 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
+<div style="position:absolute">
+
+## When working 
+  * Clarify and separate source and intermediate data
+  * Keep data copies to a **minimum**
+  * Cleanup post-analysis
+  * Cleanup copies created for presentations or for sharing
+</div> 
+<div style="position:relative;left:50%; width:40%">
+<img src="slides/img/cleaning-table.jpg" height="450px">
+</div>
+
+
+
+# Data housekeeping
+## End of project
+  * handover data to a new responsible when leaving
+  * data should be kept as a single copy on server-side storage 
+    * no copies on desktops and external devices
+  * non-proprietary formats
+  * minimal metadata
+  * sensitive data (e.g. whole genome) **must** be encrypted
+  <br/>
+  <br/>
+  * If not specified otherwise, data must be kept for **10 years** following project end for reproducibility purposes
+<aside class="notes">
+Note: sometimes it is hard to find/understand dataset 10 days old
+</aside>
+ 
+## In doubt on data archival?
+Contact R<sup>3</sup> for support on archival of datasets using tickets:
+  * https://service.uni.lu/sp
+  * Home > Catalog > LCSB > Biocore: Application services > Request for: Support
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right">
+<a href=" https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-03" style="color:grey; font-size:0.8em;">Research Data Retention and Archival Policy</a>
+</div>
+
+
+
+# Data housekeeping - Summary
+## Server is your friend!
+  * Allows a consistent backup policy for your datasets
+  * Keeps number of copies to minimum
+  * Specification of clear access rights
+  * High accessibility
+  * Data are discoverable
+  * Server can't be stolen
+  
+## General guidelines
+  * Use institutional media for storage of **all** data
+  * Research data (particularly sensitive data) should be in a single source location
+  * Enable encryption for data stored on movable media
+  * Clarify and separate source and intermediate data
+  * Disable write access to relevant source data (read-only)
+  * Backup research data!
+  * Download Anti-virus software
+  * Generate checksums 
--- a/2021/2021-07-27_IT101-DM/slides/data-introduction.md
+++ b/2021/2021-07-27_IT101-DM/slides/data-introduction.md
-../../2021-04-20_IT101-DM/slides/data-introduction.md
\ No newline at end of file
--- a/2021/2021-07-27_IT101-DM/slides/data-introduction.md
+++ b/2021/2021-07-27_IT101-DM/slides/data-introduction.md
+# Data and metadata
+<div style="display:grid;grid-gap:100px;grid-template-columns: 40% 40%">
+<div >
+
+## Data
+  * "*information in digital form that can be transmitted or processed*"
+  <p align="right">-- Merriam-Webster dictionary</p>
+  * "*information in an electronic form that can be stored and processed by a computer*"
+  <p align="right">--Cambridge dictionary</p>
+
+</div>
+<div>
+
+## Metadata
+  * data describing other data
+  * information that is given to describe or help you use other information
+  * metadata are data
+    * can be processed and analyzed
+</div>
+</div>
+
+<div class="fragment">
+
+## Metadata examples:
+<div style="position:absolute">
+  <ul>
+    <li> LabBook </li>
+    <li> author/owner of the data</li>
+    <li> origin of the data 
+    <li> data type
+  </ul>
+</div>
+<div style="position:absolute;left:25%">
+  <ul>
+    <li> description of content </li>
+    <li> modification date </li>
+    <li> description of modification </li>
+    <li> location </li>
+  </ul>
+</div> 
+<div style="position:relative;left:50%;top:0.7em">
+  <ul> 
+    <li> calibration readings</li>
+    <li> software/firmware version</li>
+    <li> data purpose</li>
+    <li> means of creation</li>
+  </ul>
+</div>
+</div>
+
+<div class="fragment">
+<br>
+</center>
+<center style="color:red">!Insufficient metadata make the data useless!</center>
+</div>
+<aside class="notes">
+Sometimes metadata collection takes more time than data collection
+</aside>
+
+
+
+# LCSB research data
+three categories:
+  * **Primary data** 
+    * scientific data 
+      * measurements, images, observations, notes, surveys, ...
+      * models, software codes, libraries, ...
+    * metadata directly describing the data
+      * data dictionaries
+      * format, version, coverage descriptions, ...
+
+  * **Research record**
+    * description of the research process, including experiment 
+      * experiment set-up
+      * followed protocols
+      * ...
+    
+  * **Project accompanying documentation** 
+      * ethical approvals, information on the consent
+      * collaboration agreements
+      * intellectual property ownership
+      * other relevant documentation
+
+<div style="position:absolute; width:45%; left:50%; top:28em; text-align:right;">
+<a href="https://howto.lcsb.uni.lu/internal/policies/LCSB-POL-BIC-03/" style="color:grey; font-size:0.8em;">LCSB-POL-BIC-03 Research Data Retention and Archival Policy</a>
+</div>
\ No newline at end of file
--- a/2021/2021-07-27_IT101-DM/slides/data_flow.md
+++ b/2021/2021-07-27_IT101-DM/slides/data_flow.md
-../../2021-04-20_IT101-DM/slides/data_flow.md
\ No newline at end of file
--- a/2021/2021-07-27_IT101-DM/slides/data_flow.md
+++ b/2021/2021-07-27_IT101-DM/slides/data_flow.md
+# Typical flow of data
+
+<div style="display:grid;grid-gap:10px;grid-template-columns: 30% 20% 30%;
+  grid-auto-flow:column;grid-template-rows: repeat(4,auto);position:relative;left:8%">
+  
+<div class="content-box fragment" data-fragment-index="1">
+  <div class="box-title red">Source data</div>
+  <div class="content">
+
+  * Experimental results
+  * Large data sets  
+  * Manually collected data  
+  * External
+
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="2">
+  <div class="box-title yellow">Intermediate</div>
+  <div class="content">
+
+  * Derived data 
+  * Tidy data 
+  * Curated sets
+
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="3">
+  <div class="box-title blue">Analyses</div>
+  <div class="content">
+
+  * Exploratory
+  * Model building
+  * Hypothesis testing
+
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="4">
+  <div class="box-title green">Dissemination</div>
+  <div class="content">
+
+  * Manuscript, report, presentation, ...
+
+  </div>
+</div>
+<center>
+<img src="slides/img/data-flow_sources.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_transformation.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_chart.png" height=60%>
+</center>
+<center>
+<img src="slides/img/data-flow_paper.png" height=60%>
+</center>
+
+<div class="content-box fragment" data-fragment-index="5">
+<div class="box-title red">Preserve</div>
+  <div class="content">
+
+  * Version data sets 
+  * Backup
+  * Protect
+  
+  </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="6">
+  <div class="box-title yellow">Reproduce</div>
+  <div class="content">
+
+  * Automate your builds 
+  * Use workflow tools (e.g. Snakemake)
+  
+  </div>
+</div>
+
+
+<div class="content-box fragment" data-fragment-index="7">
+<div class="box-title blue">Trace</div>
+  <div class="content">
+
+ * Multiple iterations.
+ * Code versioning (Git)
+
+ </div>
+</div>
+
+<div class="content-box fragment" data-fragment-index="8">
+<div class="box-title green">Track</div>
+  <div class="content">
+
+   * Through multiple versions
+ 
+   </div>
+</div>
+
+</div>
+<aside class="notes">
+flow of the data is downstream (mostly), but you are going back and forth
+applies to all data (financial report, lab safety assessment)
+</aside>
--- a/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md
+++ b/2021/2021-07-27_IT101-DM/slides/data_life_cycle.md

 # Some practical recommandations

-* Plan your data walking along the data life cycle
+* Do your data processing according to the data life cycle steps

 <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:
+* Use data management planning 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> 

--- a/2021/2021-07-27_IT101-DM/slides/fair-principles.md
+++ b/2021/2021-07-27_IT101-DM/slides/fair-principles.md
-../../2021-04-20_IT101-DM/slides/fair-principles.md
\ No newline at end of file
--- a/2021/2021-07-27_IT101-DM/slides/fair-principles.md
+++ b/2021/2021-07-27_IT101-DM/slides/fair-principles.md
+# FAIR (meta)data principles
+ * dates back to 2014
+ * well accepted by scientific community
+ * necessity in data driven science
+ * officially embraced by EU and G20
+ * required by funding agencies and journal publishers
+ 
+<center>
+<img src="slides/img/fair-principles.png" height="400px">
+</center>
+<br>
+<br>
--- a/2021/2021-07-27_IT101-DM/slides/howtos.md
+++ b/2021/2021-07-27_IT101-DM/slides/howtos.md
-../../2021-04-20_IT101-DM/slides/howtos.md
\ No newline at end of file
--- a/2021/2021-07-27_IT101-DM/slides/howtos.md
+++ b/2021/2021-07-27_IT101-DM/slides/howtos.md
+# LCSB How-Tos
+<br>
+https://howto.lcsb.uni.lu/
+<center>
+  <img src="slides/img/howtocard.png" width="50%">
+</center>
--- a/2021/2021-07-27_IT101-DM/slides/img
+++ b/2021/2021-07-27_IT101-DM/slides/img
-../../2021-04-20_IT101-DM/slides/img
\ No newline at end of file