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2021/2021-03-18_basicGitTraining/slides/the_terminal.md

@@ -28,7 +28,12 @@ $ git --version
 
 List the contents of a directory
 ```bash
-$ ls #-lash
+$ ls
+```
+
+You can list more details with:
+```bash
+$ ls -lah
 ```
 
 Create a directory
@@ -36,6 +41,8 @@ Create a directory
 $ mkdir myNewDirectory
 ```
 
+
+
 Change the directory to a specific folder
 ```bash
 $ cd myNewDirectory
@@ -50,8 +57,6 @@ $ cd ../..
 # 2 levels up
 ```
 
-
-
 Move a file or a directory
 ```bash
 $ mv myFile.m myNewDirectory/.

2021/2021-04-20_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>

2021/2021-04-20_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
+
+
+
+# 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 

2021/2021-04-20_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

2021/2021-04-20_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>

2021/2021-04-20_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>

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

+# LCSB How-Tos
+<br>
+https://howto.lcsb.uni.lu/
+<center>
+  <img src="slides/img/howtocard.png" width="50%">
+</center>