.ci/analytics/gdpr-banner.html

+<div id="lap-cookies-banner" class="presentation-banner">
+    <div class="banner-intro">
+        <div class="close-button">
+            <a class="lap-refuse">
+                <i class="fa fa-times" aria-hidden="true"></i>
+            </a>
+        </div>
+        <div class="banner-img">
+            <img src="https://analytics.lcsb.uni.lu/lap/static/logos/r3-logo.svg" type="image/svg+xml"/>
+        </div>
+        <div class="banner-title">This website needs some cookies and similar means to function.</div>
+        <div class="banner-text">If you permit us, we will use those means to collect data on your visits for aggregated
+            statistics to improve our service.
+        </div>
+    </div>
+
+    <div class="banner-buttons">
+        <a class="btn lap-accept">Accept cookies for aggregated statistics</a>
+        <a class="btn lap-refuse">No thanks, only technically necessary cookies</a>
+        <a class="btn lap-cookies-more" href="https://courses.lcsb.uni.lu/privacy-policy">More information</a>
+    </div>
+</div>
\ No newline at end of file

.ci/analytics/head.html

+<script>
+    const settings = {
+        expires: "180",
+        matomoURL: "https://analytics.lcsb.uni.lu/hub/",
+        siteID: "8", //you get this siteID by sending an email to lcsb-r3@uni.lu
+        accept_all_text: "Aggregate statistics cookies accepted",
+        only_necessary_text: "Only necessary cookies accepted",
+        doNotTrack_text: "Do Not Track is enabled",
+        cookieName: "lap",
+        bots: /bot|crawler|spider|crawling/i,
+        timeout_hidebanner: "500",
+        cookieDomain: "courses.lcsb.uni.lu"
+    };
+</script>
+<script src="https://analytics.lcsb.uni.lu/lap/static/js/jquery.min.js"></script>
+<script src="https://analytics.lcsb.uni.lu/lap/static/js/lap.js"></script>
+
+<link rel="stylesheet" type="text/css" href="https://analytics.lcsb.uni.lu/lap/static/css/lap.css" />

.ci/analytics/policy.html

+<div class="bottomPrivacy">
+    <a href="https://courses.lcsb.uni.lu/privacy-policy">Privacy Policy</a>
+    (<span id="doNotTrack-text"><span id="gdpr-result-text"></span> - <a href="javascript: showBanner();">change</a></span>)
+</div>
\ No newline at end of file

.ci/deploy.sh

 #!/bin/bash
 
-PAGEURL="https://r3.pages.uni.lu/school/courses"
+PAGEURL="https://courses.lcsb.uni.lu"
 
 rootDir=$(pwd)
 echo $rootDir
 
 # clean previous builds
 rm -rf $rootDir/public
+rm -rf $rootDir/theme
 mkdir $rootDir/public
 
+if [[ $CI_COMMIT_REF_NAME == "develop" ]]; then
+    version="latest";
+elif [[ $CI_COMMIT_REF_NAME == "master" ]]; then
+    version="stable";
+else
+    version="unstable";
+fi
+
+# build the unstable version - can be optimized
+git submodule update --init --recursive
+
+# add matomo
+sed -i "/matomohead/r./.ci/analytics/head.html" theme/templates/_index.html
+sed -i "/matomopolicy/r./.ci/analytics/policy.html" theme/templates/_index.html
+sed -i "/matomobanner/r./.ci/analytics/gdpr-banner.html" theme/templates/_index.html
+
+echo " > LAP included"
+
 # loop through all the presentations
 nBlades=0
 for d in $(find . -maxdepth 1 -type d)
 do
     if [[ "${d}" == *20* ]]; then
-        cd "${d}"
+        pushd "${d}"
         echo "changed to ${d}"
         for d1 in $(find . -maxdepth 1 -type d)
         do
             if [[ ${#d1} -ge 2 ]]; then
                 let "nBlades+=1"
-                #blades[$nBlades]="$tutorial"
                 BLADE=${d1:2}
                 echo " > -----------------------------------------------------"
                 echo "Building ... ${d1}"
 
                 # create the required folders in public
-                mkdir $rootDir/public/$BLADE
-                mkdir $rootDir/public/$BLADE/unstable
-                mkdir $rootDir/public/$BLADE/latest
-                mkdir $rootDir/public/$BLADE/stable
-
-                # change to the blade directory to be built
-                cd $BLADE
+                mkdir -p $rootDir/public/$BLADE/$version
 
-                # build the unstable version - can be optimized
-                git config submodule.theme.url https://$CI_DEPLOY_USER:$CI_DEPLOY_PASSWORD@git-r3lab.uni.lu/R3-core/outreach/theme.git
-                git submodule update --recursive --init
+                echo "going to $BLADE..."
+                pushd $BLADE
 
                 # run contribute
-                cp ../../template/Gruntfile.coffee .
-                ln -s ../../theme/package.json package.json
-                ln -s ../../theme theme
+                cp -v ../../template/Gruntfile.coffee .
+                ln -sv ../../theme/package.json package.json
+                ln -sv ../../theme theme
 
                 # install npm
-                #npm install -g npm@latest yo grunt-cli generator-reveal
-                #npm install
-                yarn global add grunt-cli generator-reveal
+                echo "installing deps"
+                yarn add grunt-cli generator-reveal grunt
                 yarn install
 
-                grunt dist
-                mv public/* $rootDir/public/$BLADE/unstable/.
-                echo " > unstable built for file set ${BLADE}"
-
-                # build the master version into stable
-                git fetch --tags
-                latestTag=$(git describe --tags `git rev-list --tags --max-count=1`)
-                git stash
-                git checkout $latestTag
-                git submodule update --init
-                grunt dist
-                mv public/* $rootDir/public/$BLADE/stable/.
-                echo " > stable built for file set ${BLADE}"
-
-                # build the develop version into latest
-                git stash
-                git checkout -f develop
-                git fetch origin develop
-                git reset --hard origin/develop
-                git submodule update --init
-                grunt dist
-                mv public/* $rootDir/public/$BLADE/latest/.
+                echo "running dist"
+                yarn exec grunt dist
+                echo "copying to common public dir"
+                cp -rLv public/* $rootDir/public/$BLADE/$version/.
+
                 echo " > latest built for file set ${BLADE}"
 
                 # auto redirect file to the stable version
@@ -85,9 +78,10 @@ do
                 echo "autoredirect file set"
 
                 # move back out
-                cd ..
+                popd
                 echo " > -----------------------------------------------------"
             fi
         done
+        popd
     fi
 done

.ci/generateIndex.py

+import os, re
+from os import path
+
+def build_link(title, href):
+    return f'- <a href="{href}">{title}</a>\n'
+
+def build_section_start(title):
+    return f'\n' #<h3>{title}</h3>\n
+
+def build_section_end():
+    return "" #\t\t</ul>\n\t</div>
+
+def camel_to_snake(name):
+  name = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
+  return re.sub('([a-z0-9])([A-Z])', r'\1_\2', name).lower()
+
+# loop through the entire internal tree
+localroot = os.getcwd()
+
+
+# generate the index properly speaking
+cardDirs = ["2023", "2022", "2021", "2020", "2019"]
+index=''
+
+# determine first the directories
+for direct in cardDirs:
+    if path.isdir(direct):
+        dirs = os.listdir(direct)
+        dirs.sort(reverse=True);
+        index += "\n# " + direct + "\n\n"
+        for d in dirs:
+            if d[0] != ".":
+                href = 'https://courses.lcsb.uni.lu/'+d
+                linkText = camel_to_snake(d)
+                linkText = linkText.replace("_", " ")
+                linkText = linkText.title()
+
+                # special rules
+                linkText = linkText.replace("Dm", "Data Management")
+                linkText = linkText.replace("It", "IT")
+                linkText = linkText.replace("Siu", "SIU")
+
+                index += build_link(linkText, href)
+
+# output the index
+print(index)
+
+
+# Read in the file
+repoName = "courses.lcsb.uni.lu"
+os.chdir(repoName)
+indexFile = "index.md"
+filedata = ""
+with open(indexFile, 'r') as file :
+    for line in file:
+        filedata += line
+
+        # stop reading once the index place holder has been reached
+        if re.search("<!-- index -->", line):
+            filedata += "[[ index ]]"
+            break
+
+# Replace the target string
+filedata = filedata.replace('[[ index ]]', index)
+
+# Write the file out again
+with open(indexFile, 'w') as file:
+  file.write(filedata)
+
+print("\n > New index generated and saved in " + indexFile)
+os.chdir("..")

.gitignore

+*.ai
+site/
+courses.lcsb.uni.lu
 index.html
 package-lock.json
 dist/
@@ -20,3 +23,4 @@ package.json
 ./theme/package.json
 __pycache__/
 contribute.egg-info/
+.*.swp

.gitlab-ci.yml

-image: digitallyseamless/nodejs-bower-grunt
+stages:
+  - retrieve
+  - generate
+  - build
+  - deploy
 
-pages:
-  stage: deploy
+retrieve:repo:
+  image:
+    name: alpine/git:latest
+    entrypoint: [""]
+  stage: retrieve
   script:
-    - bash .ci/deploy.sh
+    - git clone https://$CI_DEPLOY_TOKEN:$CI_DEPLOY_PASSWORD@git-r3lab.uni.lu/R3/school/courses.lcsb.uni.lu.git
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - courses.lcsb.uni.lu
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
 
+generate:index:
+  image: python
+  stage: generate
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  script:
+    - python .ci/generateIndex.py
+  artifacts:
+    expire_in: 1 day
+    paths:
+      - courses.lcsb.uni.lu
+
+build:website:
+  image: git-r3lab.uni.lu:4567/r3/docker/jekyll-lcsb
+  stage: build
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  before_script:
+    - cd courses.lcsb.uni.lu
+    - gem install bundler -v2.0.2
+    - bundle install && bundle update jekyll-theme-lcsb-default && bundle update jekyll-theme-lcsb-frozen-components
+    - cd ..
+  script:
+    - cd courses.lcsb.uni.lu
+    - bundle exec jekyll build -d site --config "_config.yml"
+    - mv site ../.
+    - cd ..
   artifacts:
-    expire_in: 1 week
+    expire_in: 1 day
+    paths:
+      - site
+  variables:
+    JEKYLL_ENV: production
+
+build:courses:
+  image: node:19-bullseye
+  stage: build
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  script:
+    - bash .ci/deploy.sh
+  artifacts:
+    expire_in: 1 day
     paths:
       - public
+
+upload:
+  stage: deploy
+  image: alpine
+  before_script:
+    - apk add rsync
+    - 'which ssh-agent || ( apk add --update openssh )'
+    - eval $(ssh-agent -s)
+    - echo "$B64SSHPRIVKEY" | base64 -d | tr -d '\r' | ssh-add - > /dev/null
+    - mkdir -p ~/.ssh && chmod 700 ~/.ssh
+    - 'echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config'
+    - echo "$KNOWNHOSTS" > ~/.ssh/known_hosts
+    - chmod 644 ~/.ssh/known_hosts
+  rules:
+    - if: $CI_COMMIT_BRANCH == "develop"
+    - if: $CI_COMMIT_BRANCH == "master"
+  script:
+    - rsync -ravu --info=progress2 -e "ssh -p $SSHPORT" site/* $SSHCONNECT:~/web/latest
+    - rsync -ravu --info=progress2 -e "ssh -p $SSHPORT" public/* $SSHCONNECT:~/web/latest

.gitmodules

 [submodule "theme"]
 	path = theme
-	url = https://git-r3lab.uni.lu/R3/outreach/theme.git
+	url = https://gitlab.lcsb.uni.lu/R3/outreach/theme.git
 
 

2019/2019-06-11_basicGitTraining/slides/forks.md

@@ -71,7 +71,7 @@ shall **be avoided**!
 
 # How to update my fork?
 
-As you have your own fork, it will not automatically update once the original repository is update.
+As you have your own fork, it will not automatically be updated once the original repository is updated.
 
 ![bulb](slides/img/bulb.png) You have to update it yourself!
 

2019/2019-06-11_basicGitTraining/slides/thanks.md

@@ -38,5 +38,5 @@
 
 Contact us if you need help:
 
-r3lab.core@uni.lu
+lcsb-r3@uni.lu
 

2019/2019-08-22_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>
+<aside class="notes">
+Policy! - code in central repository
+</aside>

2019/2019-08-22_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:40%">
+<b>Bad</b> names
+
+ ```
+ PhD-project-Jan19 alldata_final.foo
+ Finacial detailes BIocore 19/11/12.xls
+ ATACseq1Londonmapped.bam
+ ```
+</div>
+<div style="position:relative;width:40%; bottom:20%; left:50%">
+<b>Good</b> names
+
+```
+Iris-setosa_samples_1927-05-12.csv
+PI102_Mouse12_EEG_2018-11-03_1245.tsv
+Bioinfiniti_FullProposal_2018-11-15_1655.do
+```
+</div>
+</div>
+<div class="fragment" data-fragment-index="3" style="width:100%; position:static">
+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 
+  
+* 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
+  * Handover data to a new responsible when leaving
+</div> 
+<div style="position:relative;left:50%; width:40%">
+<img src="slides/img/cleaning-table.jpg" height="450px">
+</div>
+
+
+
+# Data housekeeping
+## End of project
+  * data should be kept as a single copy on server-side storage
+  * non-proprietary formats
+  * minimal metadata:
+    * source
+    * context of generation
+    * data structure
+    * content
+  * sensitive data (e.g. whole genome) **must** be encrypted
+  * remove all other copies from desktops and external devices
+  
+  
+  * 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
+
+
+
+# Data housekeeping - Summary
+
+* 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 
+
+<div class="fragment">
+
+## Server is your friend!
+
+</div>

2019/2019-08-22_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

2019/2019-08-22_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>

2019/2019-08-22_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>

2019/2019-08-22_IT101-DM/slides/howtos.md

+# LCSB How-Tos
+<br>
+https://howto.lcsb.uni.lu/
+<center>
+  <img src="slides/img/howtocard.png" width="50%" style="border: 1px solid #555;">
+</center>