Merge branch 'develop' into 'master'

[release] Regular merge of develop

See merge request !305

.ci/generateIndex.py

 import os, re
 from os import path
 from natsort import natsorted
+from pathlib import Path
 
 def line_prepender(filename, line):
     with open(filename, 'r+') as f:
@@ -33,7 +34,7 @@ def build_section_start(title, shortcut):
     title = title.replace("Covid 19", "COVID-19")
     title = title.replace("Ppc", "PPC")
 
-    return f'\n\t<div class="index-box noborderbox" id="{shortcut}">\n\t\t<h3>{title}</h3>\n\t\t<ul>\n'
+    return f'\n\t<div class="index-box noborderbox" id="{shortcut}-card">\n\t\t<h3>{title}</h3>\n\t\t<ul>\n'
 
 def build_section_end():
     return "\t\t</ul>\n\t</div>"
@@ -100,6 +101,7 @@ sections = natsorted(sections)
 # Index contains the generated content, init it with an empty container
 index = ''
 index += '\n<div class="index-box-container">\n'
+whiteList = ''
 
 localIndexArr = [[]] * len(sections)
 for folder in cardDirs:
@@ -157,6 +159,12 @@ for folder in cardDirs:
                                 header += "  - /" + folder + "/cards/" + shortcut + "\n"
                                 header += "---"
 
+                                # add autogenerated links to whitelist
+                                whiteList += permalink + "\n"
+                                whiteList += "/?" + shortcut + "\n"
+                                whiteList += "/cards/" +shortcut + "\n"
+                                whiteList += "/" + folder + "/cards/" + shortcut + "\n"
+
                                 # add the header properly speaking
                                 line_prepender(fileName, header)
 
@@ -197,7 +205,7 @@ for s in sections:
     index += build_section_end()
     k += 1
 
-# Close the container
+# close the container
 index += "\n</div>"
 
 ## add link to return to main index
@@ -226,3 +234,13 @@ with open(indexFile, 'w') as file:
   file.write(filedata)
 
 print("\n > New index generated and saved in " + indexFile)
+
+# write link whitelist out
+whiteListFile = ".ci/whitelist.txt"
+if Path(whiteListFile).exists():
+    with open(whiteListFile, 'r') as file :
+        for line in file:
+            whiteList += line
+
+with open(whiteListFile, 'w') as file:
+    file.write(whiteList)

.ci/whitelist.txt

+/privacy-policy
+/search
+https://www.dev47apps.com/
+https://www.dev47apps.com/droidcam/connect/
+https://cerbere.uni.lu/
+http://iptel.uni.lux/
+javascript:%20showBanner();
+javascript:showBanner();
+media/7zip-encryption-windows.mp4?width=400
+media/Get_MD5_checksum_windows.mp4
+https://intranet.uni.lux
+https://intranet.uni.lux/the_university/lcsb/lscb_internal/
+https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Godparent%20Checklist%20-%20newcomers.pdf
+https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20Before%20Arriving%20in%20Luxembourg.pdf
+https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20upon%20Arrival%20in%20Luxembourg.pdf
+https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx
+https://intranet.uni.lux/the_university/sc/Lists/Policies%20%20Procedures/DispForm.aspx?ID=9
+https://intranet.uni.lux/the_university/siu/Documents/Dropit%20client%20-%20configuration%20guide.pdf#search=dropit
+https://intranet.uni.lux/the_university/siu/Pages/siu-guides.aspx
\ No newline at end of file

.gitignore

@@ -42,4 +42,6 @@ handbook/
 internal/handbook
 internal/handbook-additional
 internal/handbook-annexes
-!internal/covid-19/exit-strategy/*.pdf
+!internal/covid-19/exit-strategy/*.pdf
\ No newline at end of file
+checkFolder
+.cache/

.gitlab-ci.yml

+
+
 stages:
   - prepare
   - save
   - build
+  - check
   - generate
   - deploy
   - trigger
@@ -26,6 +29,7 @@ prepare:index:
     - python .ci/generateIndex.py
     - mkdir .tmp
     - cp cards.md .tmp/.
+    - cp .ci/whitelist.txt .tmp/.
   artifacts:
     expire_in: 1 day
     paths:
@@ -77,27 +81,49 @@ build:pages:
     expire_in: 1 day
     paths:
       - build
+      - .tmp
   rules:
     - if: $CI_COMMIT_REF_NAME
-    - if: $CI_MERGE_REQUEST_ID
   before_script:
     - apt-get -qq update
     - apt-get install -y -qq git-lfs
     - gem install bundler:$BUNDLER_VERSION && bundle install
   script:
     # Generate the configuration for forks (will use Gitlab Pages on personal namespaces)
-    - 'echo "url: https://$CI_PROJECT_NAMESPACE.$CI_PAGES_DOMAIN" >> .ci/_config_gitlab_pages.yml'
-    - 'echo "baseurl: /$CI_PROJECT_NAME" >> .ci/_config_gitlab_pages.yml'
-
-    # If there is no config for the current branch, use the one for Gitlab Pages
-    - 'if [ ! -f ".ci/_config_$CI_COMMIT_REF_NAME.yml" ]; then mv .ci/_config_gitlab_pages.yml .ci/_config_$CI_COMMIT_REF_NAME.yml; fi'
-
+    - |
+      if [ $CI_MERGE_REQUEST_ID ]; then
+          export CI_COMMIT_REF_NAME="develop";
+      else
+          echo "url: https://$CI_PROJECT_NAMESPACE.$CI_PAGES_DOMAIN" >> .ci/_config_gitlab_pages.yml;
+          echo "baseurl: /$CI_PROJECT_NAME" >> .ci/_config_gitlab_pages.yml;
+          # If there is no config for the current branch, use the one for Gitlab Pages
+          if [ ! -f ".ci/_config_$CI_COMMIT_REF_NAME.yml" ]; then
+              mv .ci/_config_gitlab_pages.yml .ci/_config_$CI_COMMIT_REF_NAME.yml;
+          fi
+      fi
     # Display, which configuration is used
-    - 'echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"'
-
+    - |
+      echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"
     # Run Jekyll with custom configuration
     - bundle exec jekyll build -d build --config "_config.yml,.ci/_config_$CI_COMMIT_REF_NAME.yml"
 
+# check
+# ------------------------------------------------------------------------------------
+
+check:links:
+   stage: check
+   image: $CI_REGISTRY/r3/apps/tailorbird/linkchecker
+   rules:
+     - if: $CI_COMMIT_REF_NAME
+     - if: $CI_MERGE_REQUEST_ID
+   allow_failure: true
+   before_script:
+     - cp .tmp/whitelist.txt build/.
+     - cp -r build /check
+     - cd /
+   script:
+     - python link_check.py
+
 # generate
 # ------------------------------------------------------------------------------------
 
@@ -163,4 +189,4 @@ trigger:
   tags:
     - privileged
   script:
-    - curl --silent --output /dev/null -X POST -F token=$INTERNAL_TRIGGER_TOKEN -F ref=$CI_COMMIT_BRANCH $INTERNAL_REPO
+    - curl --silent --output /dev/null -X POST -F token=$INTERNAL_TRIGGER_TOKEN -F ref=$CI_COMMIT_BRANCH $INTERNAL_REPO
\ No newline at end of file

_config.yml

@@ -19,8 +19,8 @@ description: >- # this means to ignore newlines until "baseurl:"
   This page is an index for lab cards  that are intended to provide practical guidance  in  implementing Data Management, Data Protection and IT setup.
 
 # URL settings (the most difficult part, please refer to the guide)
-baseurl: "/"  # the subpath of your site, e.g. /gitlab-repository-name
-url: "https://localhost"  # the base hostname & protocol for your site, e.g. http://gitlab-namespace-name.pages.uni.lu/
+baseurl: "/howto-cards"  # the subpath of your site, e.g. /gitlab-repository-name
+url: "https://howto.lcsb.uni.lu"  # the base hostname & protocol for your site, e.g. http://gitlab-namespace-name.pages.uni.lu/
 
 # Banner settings
 banner: howto-card  # When you have custom images, change this setting's value to the name of the folder containing them

assets/js/box_hider.js

-/** 
+/**
  * This is used to hide the sections of the index page
  * based on the URL fragment (a.k.a. "hash")
  */
 window.boxHider = (function() {
     function GetSelectedId() {
-        var boxId = window.location.hash;
+        var boxId = window.location.hash + '-card';
         if (boxId.length > 0) {
             return boxId.substring(1);
         }
@@ -24,10 +24,10 @@ window.boxHider = (function() {
     function GetSelectedBoxElement(id) {
         var allBoxesArray = GetAllBoxElementsArray();
         var element = document.getElementById(id);
-        
+
         if (allBoxesArray.includes(element)) {
             return element;
-        } 
+        }
 
         return false;
     }
@@ -61,7 +61,7 @@ window.boxHider = (function() {
         var boxId = GetSelectedId();
         if (boxId.length == 0) {
             // If there is no hash in the URL, just show all the boxes
-            ShowAllBoxes(); 
+            ShowAllBoxes();
             return;
         }
         // Otherwise, proceed to getting the corresponding div element

cards.md

@@ -31,17 +31,25 @@ order: -1
 
 <div class="index-box-container">
 
-	<div class="index-box noborderbox" id="access">
+	<div class="index-box noborderbox" id="access-card">
 		<h3>Access</h3>
 		<ul>
 			<li><a href="{{ 'external/access/harrenhal-access' | relative_url }}">HARRENHAL access</a></li>
 			<li><a href="{{ 'external/access/lums-passwords' | relative_url }}">LUMS account</a></li>
 			<li><a href="{{ 'external/access/passwords' | relative_url }}">Managing your passwords</a></li>
 			<li><a href="{{ 'external/access/vpn-cerbere-access' | relative_url }}">VPN/CERBERE connection</a></li>
+			<li><a href="{{ 'external/access/wifiNetworkAccessGuests' | relative_url }}">WiFi network access for guests</a></li>
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="contribute">
+	<div class="index-box noborderbox" id="backup-card">
+		<h3>Backup</h3>
+		<ul>
+			<li><a href="{{ 'external/backup/computer' | relative_url }}">Staff Computer</a></li>
+
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="contribute-card">
 		<h3>Contribute</h3>
 		<ul>
 			<li><a href="{{ 'external/contribute/git-clients' | relative_url }}">Git clients</a></li>
@@ -53,7 +61,7 @@ order: -1
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="exchange-channels">
+	<div class="index-box noborderbox" id="exchange-channels-card">
 		<h3>Exchange channels</h3>
 		<ul>
 			<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
@@ -62,15 +70,20 @@ order: -1
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="general">
+	<div class="index-box noborderbox" id="general-card">
 		<h3>General</h3>
 		<ul>
+			<li><a href="{{ 'external/general/BelvalCampusMap' | relative_url }}">Belval Campus Map</a></li>
 			<li><a href="{{ 'external/general/attend-webex' | relative_url }}">Attend the LCSB Team Meeting online (webex)</a></li>
+			<li><a href="{{ 'external/general/getToLCSB' | relative_url }}">How to get to the Luxembourg Centre for Systems Biomedicine</a></li>
+			<li><a href="{{ 'external/general/glossary' | relative_url }}">Glossary</a></li>
+			<li><a href="{{ 'external/general/links' | relative_url }}">Important websites</a></li>
 			<li><a href="{{ 'external/general/remote-working' | relative_url }}">Work remotely</a></li>
+			<li><a href="{{ 'external/general/usefulLinks' | relative_url }}">Useful links for living in Luxemburg</a></li>
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="integrity">
+	<div class="index-box noborderbox" id="integrity-card">
 		<h3>Integrity</h3>
 		<ul>
 			<li><a href="{{ 'external/integrity/checksum' | relative_url }}">Ensuring Integrity of Data Files with Checksums</a></li>
@@ -79,11 +92,12 @@ order: -1
 			<li><a href="{{ 'external/integrity/encryption/file' | relative_url }}">Encrypting Files and Folders</a></li>
 			<li><a href="{{ 'external/integrity/naming' | relative_url }}">Naming files</a></li>
 			<li><a href="{{ 'external/integrity/organization' | relative_url }}">Organization</a></li>
+			<li><a href="{{ 'external/integrity/sanitisation' | relative_url }}">Sanitising Data Files</a></li>
 			<li><a href="{{ 'external/integrity/spreadsheets' | relative_url }}">Working with spreadsheets</a></li>
 
 		</ul>
 	</div>
-	<div class="index-box noborderbox" id="lab">
+	<div class="index-box noborderbox" id="lab-card">
 		<h3>Lab</h3>
 		<ul>
 			<li><a href="{{ 'external/lab/book-lab-equipment' | relative_url }}">How to book a Lab Equipment in Quarks</a></li>
@@ -92,10 +106,38 @@ order: -1
 			<li><a href="{{ 'external/lab/lab-coats' | relative_url }}">Lab coats</a></li>
 			<li><a href="{{ 'external/lab/maintenance_of_cold_traps' | relative_url }}">Maintenance of cold traps  </a></li>
 			<li><a href="{{ 'external/lab/personal-alert-safety-system' | relative_url }}">Personal alert safety system (PASS)</a></li>
-			<li><a href="{{ 'external/lab/quarks-chemical-platform' | relative_url }}">Quarks - Chemical platform</a></li>
+			<li><a href="{{ 'external/lab/quarks-general' | relative_url }}">Quarks - General information</a></li>
 			<li><a href="{{ 'external/lab/utilization-of-balances' | relative_url }}">Utilization of balances</a></li>
 			<li><a href="{{ 'external/lab/utilization-of-pH-meter' | relative_url }}">Utilization of pH meter</a></li>
 
 		</ul>
 	</div>
+	<div class="index-box noborderbox" id="on-offboarding-card">
+		<h3>On offboarding</h3>
+		<ul>
+			<li><a href="{{ 'external/on-offboarding/checklistArrival' | relative_url }}">Checklist upon arrival in Luxemburg</a></li>
+			<li><a href="{{ 'external/on-offboarding/checklistBeforeArriving' | relative_url }}">Newcomer Checklist before Arriving in Luxembourg</a></li>
+			<li><a href="{{ 'external/on-offboarding/checklistGetStarted' | relative_url }}">Newcomer's checklist</a></li>
+			<li><a href="{{ 'external/on-offboarding/checklistGodparent' | relative_url }}">Checklist for godparents</a></li>
+			<li><a href="{{ 'external/on-offboarding/godparent' | relative_url }}">Godparents for Newcomers</a></li>
+			<li><a href="{{ 'external/on-offboarding/onboarding' | relative_url }}">Onboarding new members at the LCSB</a></li>
+
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="ppc-card">
+		<h3>PPC</h3>
+		<ul>
+			<li><a href="{{ 'external/ppc/add-gitignore' | relative_url }}">Add a .gitignore to your repository</a></li>
+			<li><a href="{{ 'external/ppc/publish-repo' | relative_url }}">Publish a repository</a></li>
+
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="publication-card">
+		<h3>Publication</h3>
+		<ul>
+			<li><a href="{{ 'external/publication/10WaysImproveEnglish' | relative_url }}">10 ways to improve your English</a></li>
+			<li><a href="{{ 'external/publication/publishInBiotools' | relative_url }}">Publishing a tool in *bio.tools*</a></li>
+
+		</ul>
+	</div>
 </div><br><center><a href="{{ '/' | relative_url }}">go back</a></center><br><center><a href="{{ '/cards' | relative_url }}">Overview of all HowTo cards</a></center>
\ No newline at end of file

external/access/lums-passwords/lums-passwords.md

@@ -31,7 +31,7 @@ In case you are not a member of the university, please ask your collaborator at
 
 ## (Re-)Activating LUMS account upon receiving credentials or after password reset
 
-The password you will receive from the system administrators is temporary and **it will expire after one month**, so you have to reset it as soon as possible. It is usually sent as a link to [PrivateBin](https://howto.lcsb.uni.lu/?passwords). **This link is valid for one week and is deleted after you see it once**, thus you need to keep it open until you have followed these steps to reset your password:
+The password you will receive from the system administrators is temporary and **it will expire after one month**, so you have to reset it as soon as possible. It is usually sent as a link to [PrivateBin]({{ '/?access:passwords' | relative_url }}). **This link is valid for one week and is deleted after you see it once**, thus you need to keep it open until you have followed these steps to reset your password:
 
   1. Go to [lums.uni.lu](https://lums.uni.lu) and login with your LUMS username and the temporary password you received.<br>**NOTE:** If you experience any issues at this step, try to use *Chrome* browser for this procedure.<br/><img src="img/lums_login.png" height="200px"><br/>
   Should the login look different from this, e.g. like a pop-up, click on **x** or **Cancel** to close it.
@@ -43,7 +43,7 @@ The password you will receive from the system administrators is temporary and **
   5. Enter a new password of your choice in the field **"New Password"** and repeat the same password in the field **"Verify Password"**. This is the actual password you need to use from now on, so make sure to remember it.
   6. Click on **"Reset Password and Login"**.
 
-It is a good practice to use a password manager which will not only help you to keep track of your passwords so you will never forget it, but it will also help you to generate passwords which are very safe (see [HowTo card](https://howto.lcsb.uni.lu/?passwords) on password management for more detail).
+It is a good practice to use a password manager which will not only help you to keep track of your passwords so you will never forget it, but it will also help you to generate passwords which are very safe (see [HowTo card]({{ '/?access:passwords' | relative_url }}) on password management for more detail).
 
 ## Changing password for LUMS accounts
 If you want to change your password for the LUMS account, you can:

external/access/wifiNetworkAccessGuests/wifiNetworkAccessGuests.md

+---
+layout: page
+permalink: /external/access/wifiNetworkAccessGuests/
+shortcut: access:wifiNetworkAccessGuests
+redirect_from:
+  - /cards/access:wifiNetworkAccessGuests
+  - /external/cards/access:wifiNetworkAccessGuests
+---
+# WiFi network access for guests
+
+- Each UL staff member can provide wireless network access for her/his visitors by creating an account on the [Guest Sponsor Portal](https://sponsor.uni.lux:8443/sponsorportal/PortalSetup.action?portal=06f49c40-ad3a-11e4-ba4b-0050568059d7)
+- In order to create the guest account, you must log in with your normal UL username and password
+- Please also refer to the [process for visitor rules](https://howto.lcsb.uni.lu/?hr:visitorsRules)
+- Such a visitor account has a lifetime of maximum 5 days. If you need accounts for people staying longer, please open a [ticket via the SIU helpdesk](https://service.uni.lu/sp)
+- Guests will only have access to the internet and public services but not to internal resources
+
+Other documentations on how to use the SIU systems can be found on the [UL intranet (section SIU-SIU-Guides-Wireless Network)](https://intranet.uni.lux/the_university/siu/Pages/siu-guides.aspx).
+
+For any questions please open a [ticket via the SIU helpdesk](https://service.uni.lu/sp).
+
+<!--Process owner: Julia Kessler-->
+

external/backup/computer/computer.md

+---
+layout: page
+permalink: /external/backup/computer/
+shortcut: backup:computer
+redirect_from:
+  - /cards/backup:computer
+  - /external/cards/backup:computer
+---
+# Staff Computer
+
+## Backup to External Disk
+
+### macOS
+
+macOS platform comes with Time Machine, a very easy to use backup feature. Time Machine backups can be set up as follows:
+
+1. Connect an external disk to your computer.
+2. Using Finder open up  **/Applications/System Preferences** and Select **Time Machine**.  <br/>  ![Alt](img/mac_tm_1.png "Title")
+3. From the **Time Machine** main screen click **Select Backup Disk**  &nbsp;  ![Alt](img/mac_tm_2.png "Title")
+4. From the list select your external disk. It is also recommended that you select the option to **encrypt backups**.   <br/>  ![Alt](img/mac_tm_3.png "Title")
+5. If you opt for encryption you will be asked for an encryption password. You will need this password whenever you re-connect the disk to your computer or whenever you restart your Mac. You should keep this password safe using [Password Management software]({{ 'external/access/passwords' | relative_url }}). <br/>  ![Alt](img/mac_tm_4.png "Title")
+6. Time Machine requires an apple-specific disk format to work. Your external disk may not be in this format (e.g. may be in exFAT format which is accessible both by Windows and Mac). In such a case Time Machine will prompt you to approve the erasure and re-formatting of your external disk (see below). If you do not want to re-format, you may [create a disk image]({{ 'external/integrity/encryption/file' | relative_url }}) on your external disk and then point Time Machine to this image.  <br/>  ![Alt](img/mac_tm_5.png "Title")
+7. After you select a backup disk, provide password and confirm disk format (if applicable), Time Machine will automatically start the backup process in the background. You may continue to work. You will receive a notification, when the first backup is complete.  <br/>  ![Alt](img/mac_tm_6.png "Title")
+8. If you want to initiate another backup manually, click the Time Machine logo in your menu bar and select **Back Up Now**. It is recommended that you enable the automatic backup feature of Time Machine. To do so,  go to  **/Applications/System Preferences/Time Machine** and select the option **Back Up Automatically**.   <br/>  ![Alt](img/mac_tm_7.png "Title")
+
+Official instructions for restoring your Mac using a Time Machine backup can be found [here](https://support.apple.com/en-us/HT201250)
+
+### Windows
+
+Windows's offerings for backup has different names in different versions.
+
+* _Microsoft Backup and Restore_, which is available in [Windows 7](http://windows.microsoft.com/en-US/windows7/Back-up-your-files) and [Windows 10](https://support.microsoft.com/en-us/help/17143/windows-10-back-up-your-files), allows backup of your entire system or selected folders/files on your computer.
+* _File History_, which is is available in [Windows 8 and 10](http://windows.microsoft.com/en-us/windows-8/set-drive-file-history), provides an easy to use option with which you can backup select files/folders. _File History_ runs periodically, tracks versions of your files, and allows you to go back older versions.
+
+Before creating a backup, make sure that your backup drive is encrypted as a safety measure in case of disk loss or theft (see [howto page on disk encryption]({{ 'external/integrity/encryption/disk' | relative_url }})).
+
+The steps to switch **File History** on your computer is as follows:
+
+1. Connect an external disk to your computer.
+2. From the **Start** menu select **Settings/Update & Security/Backup**.  <br/> ![Alt](img/win_fh_1.png "Title")
+3. Click the "+" next to Add a drive. You'll see a prompt to choose an external drive, choose the disk you have connected.
+4. File History has now started archiving your data. An on/off slider will now appear under a new heading called **Automatically back up my files.** <br/> ![Alt](img/win_fh_2.png "Title")
+5. By default, Windows 10's File History will back-up all the folders in the **User** folder. And it will run the backup on an hourly schedule. To change any of those settings click on More options under the on/off slider (see below). <br/> ![Alt](img/win_fh_2_2.png "Title")
+6. In the **Backup Options** dialog, under the  **Back up these folders.** you can remove existing folders and add new ones. **Important Note:** Make sure that any application that read/write your data files/folder are closed, when you're making this _File History_ configuration.  <br/>
+<img src="img/win_fh_3.png" height="200em"/>
+
+
+The instructions for restoring your files from **File History** can be found [here](https://it.nmu.edu/docs/backup-using-windows-file-history)
+
+
+## Backup to dropit.uni.lu
+
+The University of Luxembourg's cloud service [DropIt](https://dropit.uni.lu/) provides all staff with 100GB of storage.
+
+To use this service, first, visit [dropit.uni.lu](https://dropit.uni.lu/). You should be able to login with your university credentials. In case of login problems, request IT support using [ServiceNow](https://service.uni.lu/).
+
+Second, in order to create backups of your computer on DropIt cloud, you need to install a client application. The University IT Guideline [here](https://intranet.uni.lux/the_university/siu/Documents/Dropit%20client%20-%20configuration%20guide.pdf#search=dropit) provides the details on how to install this client application for macOS, Windows and Linux platforms, and also, how to configure the backup process on your computer.

external/contribute/git-clients/git-clients.md

@@ -8,7 +8,7 @@ redirect_from:
 ---
 # Git clients
 
-Installation instructions are provided [here](https://howto.lcsb.uni.lu/?contribute:install-git).
+Installation instructions are provided [here]({{ '/?contribute:install-git' | relative_url }}).
 
 ## GUI clients
 

external/contribute/install-git/install-git.md

@@ -9,7 +9,7 @@ redirect_from:
 
 # Installation of Git
 
-Several git clients are presented [here](https://howto.lcsb.uni.lu/?contribute:git-clients).
+Several git clients are presented [here]({{ '/?contribute:git-clients' | relative_url }}).
 
 For most of the git clients, `git` is actually required to be installed on the system. You can find installers for Windows, MacOS and Linux on the [Git webpage](https://git-scm.com/downloads).
 
@@ -17,4 +17,4 @@ If you are using Visual Studio Code, and if you want to contribute to a reposito
 ```bash
 ssh git@gitlab.lcsb.uni.lu -p8022
 ```
-Then, press Enter and type `yes`. This will add the git-r3lab server to the known hosts on your system.
+Then, press Enter and type `yes`. This will add the Gitlab server to the known hosts on your system.
\ No newline at end of file

external/contribute/markdown/markdown.md

@@ -132,4 +132,4 @@ Markdown file can be written in any text editor. There are many editors supporti
   * ByWord
 * Online
   * [GitHub pages](https://pages.github.com/)
-  * [stackedit.io](stackedit.io)
+  * [stackedit.io](https://stackedit.io)

external/contribute/vscode/vscode.md

@@ -59,7 +59,7 @@ For each how-to card, it is strongly recommended to create a new branch.
 
 ## Step 4: Write the procedure in Markdown
 
-If you need more details on how to do this, refer to the [corresponding howto-card](.../write-markdown).
+If you need more details on how to do this, refer to the [corresponding howto-card](/?contribute:markdown).
 
 ## Step 5: Commit your changes
 

external/contribute/web-ide/web-ide.md

@@ -13,7 +13,10 @@ This shows how to use Gitlab Web IDE to add or edit a howto-card:
 
 Before you start, please make sure that you have the correct access rights to edit the repository.
 
-*Note: If you do not have the rights to edit the repository, you can either ask for permissions by contacting the repository maintainers, or use your own copy of the repository (called a `fork`). Please follow [these instructions](https://docs.gitlab.com/ee/user/project/repository/forking_workflow.html#creating-a-fork) to obtain your copy (fork). You can then [mirror the fork automatically](/cards/contribute:mirror-fork) to keep in sync.*
+*Note: If you do not have the rights to edit the repository, you can either ask for permissions by contacting
+the repository maintainers, or use your own copy of the repository (called a `fork`).
+Please follow [these instructions](https://docs.gitlab.com/ee/user/project/repository/forking_workflow.html#creating-a-fork) to
+obtain your copy (fork). You can then [mirror the fork automatically]({{ '/?contribute:mirror-fork' | relative_url }}) to keep in sync.*
 
 A clear difference between editing a file in a git-tracked repository compared to a live document is that you can make an edit directly, and then suggesting the change. You can make this edit on your own version (called a `branch`), and then request to merge your changes into the main repository (through opening a `merge request`).
 

external/exchange-channels/asperaweb/asperaweb.md

@@ -85,7 +85,7 @@ You can use the official [IBM Aspera Diagnostic Tool](https://test-connect.asper
 
 ### **Using Microsoft Edge browser**
 
-Microsoft Edge browser requires to download and install [IBM Aspera Connect for Edge](https://www.microsoft.com/store/productId/9N6XL57H8BMG).
+Microsoft Edge browser requires to download and install [IBM Aspera Connect for Edge](https://microsoftedge.microsoft.com/addons/detail/ibm-aspera-connect/kbffkbiljjejklcpnfmoiaehplhcifki).
 
 ### **UDP/TCP port and firewall**
 

external/exchange-channels/owncloud/owncloud.md

@@ -44,7 +44,7 @@ When sharing research data, one should observe the following guidance using Ownc
 
 ## Installing Owncloud Desktop Client
 
-**Important:** OwnCloud is fetching information from LUMS, therefore changes like a password reset (see How-to cards [Changing password for LUMS accounts](https://howto.lcsb.uni.lu/?lums-passwords)) should be performed **only** via LUMS!
+**Important:** OwnCloud is fetching information from LUMS, therefore changes like a password reset (see How-to cards [Changing password for LUMS accounts]({{ '/?lums-passwords' | relative_url }}) should be performed **only** via LUMS!
 
 1. Please try following link to download the owncloud desktop client depending on your operating system (this is an example for Windows, similar steps for other OS) -
 

external/general/BelvalCampusMap/BelvalCampusMap.md

+---
+layout: page
+permalink: /external/general/BelvalCampusMap/
+shortcut: general:BelvalCampusMap
+redirect_from:
+  - /cards/general:BelvalCampusMap
+  - /external/cards/general:BelvalCampusMap
+---
+
+# Belval Campus Map
+
+![](img/BelvalCampusMap.png)

external/general/getToLCSB/getToLCSB.md

+---
+layout: page
+permalink: /external/general/getToLCSB/
+shortcut: general:getToLCSB
+redirect_from:
+  - /cards/general:getToLCSB
+  - /external/cards/general:getToLCSB
+---
+# How to get to the Luxembourg Centre for Systems Biomedicine
+
+![](img/LCSB.jpg)
+
+
+### 1. Arriving by plane at Luxembourg airport:
+The Luxembourg airport, called Findel, is 34 km away from the University Campus BELVAL where LCSB is located.
+You can take either taxi or public transport to reach LCSB.
+- **Via Taxi (110€ one way)**
+
+From Luxembourg airport you can take a taxi to BELVAL near the city Esch-sur-Alzette.
+Trustworthy taxi services: coluxtaxi (colux.lu; tel: +352 48 22 33); webtaxi (webtaxi.lu; tel: +352 27 515)
+*Price: ca 110€ one way (in Luxembourg taxis are very expensive!)*
+*Duration: 30 minutes (during rush hour 45-60 min)*
+
+Benelux taxi: the price from/to airport is about 85€. To take advantage of this offer, the taxi has to be booked in advance.
+www.beneluxtaxi.lu / +352 40 38 40 / reservation@beneluxtaxi.lu (please ask confirmation of the price)
+A map of the Campus BELVAL and how to find both LCSB buildings is shown below.
+
+- **Via public transport (free)**
+
+From Luxembourg airport you can take the bus to Luxembourg central train station using bus line 29 or line 16 and
+stop at "Central station (Gare Centrale)". For the timetable check the following links:
+line 29: http://www.vdl.lu/autobus_ligne29.html
+line 16: http://www.vdl.lu/autobus_ligne16.html
+
+From Luxembourg’s central train station, you will get a train every 20 minutes to BELVAL-Université where LCSB
+is located. Please see below "Arriving by Train" for all details.
+
+*Public transportation is free in Luxemburg!*
+*Duration: 45-60 minutes (including bus, train and walk)*
+
+- **Arriving by train from Luxembourg central station:**
+
+Take the train in direction of "Rodange" or "Petange".
+Your stop is called: "Belval-Université" station
+*Please note that public transportation is free in Luxemburg!*
+Duration: 35 minutes (including train and walk)
+A map of the Campus BELVAL and how to find both LCSB buildings is shown below. From Belval train station it's about a 5
+minutes-walk to either of our locations.
+
+### 2. Arriving by car:
+If you travel by car, please take the highway A4 in direction Esch-sur-Alzette, and stay on that road until it ends at the
+roundabout called "Raemerich". Do not leave the A4 too early! Simply follow the A4 until it ends, then follow the signs to
+"Belval" at the large roundabout. On the campus, unfortunately, there are no signs leading the way to the LCSB.
+Please use the following plan to orientate on the campus. The House of Biomedicine (LCSB I) is directly next to the old blast
+furnace site, close to the red Dexia buildings. The building is a bit hidden. It is a six floor modern white building. Biotech II
+(LCSB II) is behind the big outdoor parking, right next to ADEM (Agence pour le développement de l'emploi / Employment
+Development Agency) and across the street from Southlane Towers.
+*Duration: about 20 minutes from Luxembourg City or 30 minutes from Luxembourg Airport (without traffic jam).*
+
+##### Parking at Campus BELVAL
+Since Campus Belval is foreseen to be a green car-free Campus, parking may not be easy. Due to the constructions around
+our buildings, we currently cannot offer visitor parking. To park your car we recommend using one of the following. From
+either site it is less than five minute walk to either of our buildings.
+- Parking Square Mile
+Price: 0.70€/hour
+- Belval Plaza parking garage
+Price: first 3 hours free, afterwards 3€/hour (from 07:00 to 20:00) and 1€/hour (from 20:00 to 07:00)
+
+### 3. Arriving by bus:
+You can also arrive by bus from Esch-sur-Alzette or from Luxembourg City. Please visit www.mobiliteit.lu to select your
+travelling options.
+*Please note, however, that if you travel from Luxembourg City, the train is the preferred option.*
+
+
+
+![](img/map.jpg)

external/general/glossary/glossary.md

+---
+layout: page
+permalink: /external/general/glossary/
+shortcut: general:glossary
+redirect_from:
+  - /cards/general:glossary
+  - /external/cards/general:glossary
+---
+# Glossary
+
+Are you sometimes confused with all the abbreviations and names in and around the LCSB? Here you find an overview of the most common names abbreviation you may come across during your time at the LCSB.
+
+
+|Short|Full name|What is it?|
+|------|--------|---------|
+|AsperaWeb|-|Software for end-to-end encrypted data transfer at the LCSB|
+|Atlas|-|Server of the LCSB|
+|BT1 & BT2|House of Biomedicine/Biotech 1&2|Indication of the different buildings of the LCSB|
+|CFL|Chemins de Fer Luxembourgeois|Operator for public transport (train, bus) in Luxemburg|
+|CHL|Centre Hospitalier de Luxembourg|Central Hospital in Luxemburg city – also collaborating with the LCSB|
+|CNER|Comité National d’Ethique de Recherche|National committee for ethical approval or research projects|
+|CNS|Caissee Nationale de Santé|National health insurance company in Luxemburg|
+|DAISY|DAta Information SYstem  |Comprehensive tool to manage your research data in a GDPR-compliant manner. For access, [login with you UNI.LU-account at DAISY](https://daisy.lcsb.uni.lu).|
+|DLSM|Department of Life Science and Medicine|Department of the FSTM, formerly called LSRU|
+|DTU|Doctoral Training Unit|Umbrella for organization of PhD students from different groups working on a common project|
+|Docebo|-|Internal learning platform of the LCSB. [Visit Docebo](https://unisupport.docebosaas.com/learn/signin)|
+|ESS|Employee Self-Service|Platform to change your personal data and view your employee profile. Accessible via the intranet |
+|Fiori|-|View your payslips and request holidays. Only accessible when logged into the internal network: [click here](https://fiori.uni.lu/fiori/)|
+|FNR|Fonds National de la Recherche|Main funder of research activities in Luxemburg investing both public funds and private donations|
+|FSTM|Faculty of Science, Technology and Medicine|One of the three faculties at the University of Luxemburg|
+|GitLab|-|Web-based application for implementation and management of software |
+|KTT/KT4|Building where Ketterthill is located|Indication of the different buildings of the LCSB|
+|LIH|Luxembourg Institute of Health|Public biomedical research organisation. Works closely together with the LCSB|
+|LIMS|Laboratory Information Management System|Software to manage samples and associated data|
+|LIST|Luxembourg Institute of Science and Technology|Research Institute at Belval Campus developing market-oriented services and prototypes|
+|LSRU|Life Science Research Unit|Former name for a department of the FSTM. Now called DLSM|
+|LUMS|LCSB User Management System|Provides you access to most LCSB internal software. **Requires an additional account besides your UNI.LU-login!**|
+|MSA|Maison du Savoir|Central building of the University of Luxemburg also hosting administration|
+|OWA|Outlook Web Access|To check your emails from anywhere via a web-browser. Login with you UNI.LU-credentials at [owa.uni.lu](https://owa.uni.lu)|
+|R3|Responsible and Reproducible Research|Initiative of the Bioinformatics Core group to raise research quality|
+|SAP|Systeme, Anwendungen und Produkte|Software for data management and information exchange|
+|SIL|Service of Infrastructure and Logistics|Support for workplace and transportation. You can contact them via the online ticketing system at [service.uni.lu](https://service.uni.lu)|
+|SIU|Service Informatique de l’Université|Unit that organizes, administrates and develops IT platforms & systems at the University of Luxemburg|
+|Slack|-|Online-based instant messaging platform to organize and work on projects together|
+|SOP|Standard Operation Procedure|Internal guideline how common tasks should be executed|
+|VM|Virtual Machine|Entire operating system running inside another operating system.|
+|VPN|Virtual Private Network|Allows you to connect to the internal university pages, services and servers via a program (client) upon login with your university credentials|
+
+
+
+
+

external/general/links/important_links.md

+---
+layout: page
+permalink: /external/general/links/
+shortcut: general:links
+redirect_from:
+  - /cards/general:links
+  - /external/cards/general:links
+---
+# Important websites
+
+This is an overview on websites to manage work and help you with the navigation on work-related matters at the University of Luxemburg.
+
+
+| Link | Description |
+| :------ | :------ |
+|[www.uni.lu](https://www.uni.lu)|General website of the University. You can find general information as well as specific information on the faculties and institutes here.|
+|[intranet.uni.lux](https://intranet.uni.lux)|The internal platform of the University. Here you find internal information and have access to different services such as the HR Employee Self-Service (ESS). By clicking on ‘My LCSB’ next to your name in the top right corner, you are directed to the LCSB Intranet with information on upcoming presentations, science tools and social events. **Please note:** This site can only be accessed when you are logged into the university network, either in your office or via a VPN client from elsewhere. See also the [corresponding How-to Card](https://howto.lcsb.uni.lu/?access:vpn-cerbere-access)|
+|[service.uni.lu](https://service.uni.lu/sp)|Here you find service and support from the university. You can create tickets on all regulatory and legal issues as well as on IT-related topics, e.g. to get access to specific folders and software.|
+|[lums.uni.lu](https://lums.uni.lu)|The LUMS (LCSB User Management System) allows you to get access to internal resources such as software provided and/or hosted by the LCSB. **Please note:** You need to request an additional account to be able to log in as your usual UNI.LU-credentials will **not do the job.** The LUMS-accounts can also be created for external researchers and collaborators.|
+|[howto.lcsb.uni.lu](https://howto.lcsb.uni.lu/)|This is where the How-to Cards are deposited and constantly updated. You can find answers on administrative as well as on lab-related procedures here. For complex instructions, a step-by-step tutorial with corresponding screenshots or examples is provided. We encourage you to bookmark this page as many answers to your questions might be covered by a card. If you have any suggestions for improvements on existing or additional How-to Cards, just contact the R3 department.|
+|[owncloud.lcsb.uni.lu](https://owncloud.lcsb.uni.lu/)|LCSB ownCloud is a private cloud storage service for the use of LCSB staff and collaborators. It is suitable for exchanging small-sized files (up to 1-2 gigabyte, all SSL encrypted). You need a [LUMS account](https://howto.lcsb.uni.lu/?access:lums-passwords) for using this platform. The LUMS accounts can also be provided to external collaboration partners and can be requested at the [Service Portal](https://service.uni.lu/sp). For more information see also the [User’s Guide for ownCloud](https://howto.lcsb.uni.lu/?exchange-channels:owncloud).|
+|[daisy.lcsb.uni.lu](https://daisy.lcsb.uni.lu/)|The DAta Information SYstem (DAISY) is a comprehensive tool to manage your research data in a GDPR-compliant manner. You can create projects & datasets and share them with your collaboration partners. For more information and detailed description on DAISY, please refer to the [corresponding How-to Card](https://howto.lcsb.uni.lu/?daisy).|
+|[owa.uni.lu](https://owa.uni.lu/)|The Outlook Web Application to access your mail account via any web browser. Login with you UNI.LU-credentials.|
+|[fiori.uni.lu](https://fiori.uni.lu/fiori/)|Upon login with your UNI.LU-credentials, this site provides you information on your employee profile. You can submit leave requests via this portal and also view your payslips.|
+|[llcreservation.uni.lu](http://llcreservation.uni.lu)|Booking a room in the Luxemburg Learning Centre at the University Campus in Belval. Login with your staff/student credentials.|
+|[gitlab.lcsb.uni.lu](https://gitlab.lcsb.uni.lu/)|A developer’s platform operated by the R3-team where you can contribute to publish and develop public protocols/procedures, etc.  For instance, these How-to-cards can be created there. So also the corresponding card on [how to contribute](https://howto.lcsb.uni.lu/?contribute:add-edit-card).|

external/general/remote-working/remote-working.md

@@ -11,7 +11,7 @@ redirect_from:
 In case you need to work remotely, there are several tools and services that you can use to
 stay connected and continue your work.
 
-An important reference is the [list of important links](https://howto.lcsb.uni.lu/?general:links).
+An important reference is the [list of important links]({{ '/?general:links' | relative_url }}).
 
 <p style="color:grey"><b>Note:</b> If the link does not work, please refer to the section <b>Connecting to the university network</b> since you are most probably not connected to the university internal network.</p>
 
@@ -20,12 +20,12 @@ There is also a set of [tutorials](https://remote.uni.lu/) prepared by the unive
 ## Connecting to the university network
 
 If you want to access the university infrastructure, such as the servers or storage, you can do so by connecting
-via [Virtual Private Network (VPN)](http://vpn.uni.lu). All details are given [here](https://howto.lcsb.uni.lu/?access:vpn-cerbere-access).
+via [Virtual Private Network (VPN)](http://vpn.uni.lu). All details are given [here]({{ '/?access:vpn-cerbere-access' | relative_url }}).
 
 ## Instant messaging
 
 One of the recommended tools to communicate is Slack. Each research group can sign up for free and
-create their own Slack instance on [slack.com](www.slack.com).
+create their own Slack instance on [slack.com](https://www.slack.com).
 
 ## Video conferencing and virtual meetings
 
@@ -43,7 +43,7 @@ In case you want to do video conferences, but do not have a webcam, you can use
 
 For Android phones you can use [DroidCam Wireless Webcam](http://www.dev47apps.com/). It comes with a desktop client for Windows and Linux, but also works on MacOS without the client.
 
-On Apple iPhones (and Android as well) you can use [EpocCam](http://www.kinoni.com/). This requires you to install drivers on your computer as well.
+On Apple iPhones (and Android as well) you can use [EpocCam](https://www.elgato.com/en/epoccam). This requires you to install drivers on your computer as well.
 
 Both apps support connecting to your computer either via WiFi or USB. EpocCam supports USB connection only for iOS, though. With DroidCam, you need to [install ADB, enable developer options and USB debugging](http://www.dev47apps.com/droidcam/connect/), if you want to connect your phone via USB.
 
@@ -65,8 +65,8 @@ You can use the following tools to take notes or writing manuscripts together:
 
 When on-the-go or working remotely, the [LCSB ownCloud](https://owncloud.lcsb.uni.lu) is the best way to share and work collaboratively on files.
 
-More details on how to set up ownCloud are provided [here](https://howto.lcsb.uni.lu/?exchange-channels:owncloud). You can share your files and folders
-directly with your collaborators by following [these instructions](https://howto.lcsb.uni.lu/?exchange-channels:owncloud:share-files).
+More details on how to set up ownCloud are provided [here]({{ '/?exchange-channels:owncloud' | relative_url }}). You can share your files and folders
+directly with your collaborators by following [these instructions]({{ '/?exchange-channels:owncloud:share-files' | relative_url }}).
 
 ## Development of code
 

external/general/usefulLinks/usefulLinks.md

+---
+layout: page
+permalink: /external/general/usefulLinks/
+shortcut: general:usefulLinks
+redirect_from:
+  - /cards/general:usefulLinks
+  - /external/cards/general:usefulLinks
+---
+# Useful links for living in Luxemburg
+Here, we compiles a few resources that might facilitate your start in Luxemburg - or also inspire you if you are already living here for a while.
+Please note that those are external link and thus the LCSB has no control of the integrity of the content.
+
+- [JustArrived](https://www.justarrived.lu) - a website in both English and French providing you an overview of life, habits and processes in Luxemburgs, also supported with facts and figures.
+
+- [Contrat d’accueil et d’intégration - CIA](https://forum-cai.lu/) - a program from the government designed for new inhabitants of Luxemburg. Information is avaliable in English, French and German.
+
+- [AngloInfo](https://www.angloinfo.com/luxembourg) - a site for expats living in Luxemburg promoting events and activities
+
+- [EURAXESS](https://www.euraxess.lu) - An initiative launched to promote research careers and facilitate the mobility of researchers across Europe
\ No newline at end of file

external/integrity/encryption/cloud/cloud.md

@@ -40,7 +40,7 @@ Download and install `7zip` from [here](https://www.7-zip.org/)
 3. Enter a password and make a copy of the encryption password :key:
 4. Click save to save the encrypted zip file
 
-![](./media/7zip-encryption-windows.mp4?width=400)
+![](media/7zip-encryption-windows.mp4?width=400)
 
 ## Calculate the MD5 checksum with `Simple Checksum Calculator`
 
@@ -49,7 +49,7 @@ Download and install `7zip` from [here](https://www.7-zip.org/)
 3. Click on the file icon box in the left panel and load the encrypted zip file
 4. Make a copy of the MD5 checksum key :label:
 
-![](./media/Get_MD5_checksum_windows.mp4)
+![](media/Get_MD5_checksum_windows.mp4)
 
 ## Data upload
 

external/integrity/encryption/disk/encryption_disk.md

@@ -9,7 +9,7 @@ redirect_from:
 # Encrypting the Startup Disk for Your Laptop/Desktop
 Encrypting an entire hard disk is an effective protective measure against computer theft and loss. In this lab card we provide instructions for switching on disk encryption on macOS and Windows platforms.
 
-**IMPORTANT NOTICE:** One important requirement of using Encryption is that you must  manage your Encryption Passwords/Keys. Failing to do so will mean **loosing your data indefinitely**. In this [link](https://howto.lcsb.uni.lu/?access:passwords) we list  tools that can be used for password management. **Please make sure you have arrangements for password management before starting the encryption of data**.
+**IMPORTANT NOTICE:** One important requirement of using Encryption is that you must  manage your Encryption Passwords/Keys. Failing to do so will mean **loosing your data indefinitely**. In this [link]({{ '/?access:passwords' | relative_url }}) we list  tools that can be used for password management. **Please make sure you have arrangements for password management before starting the encryption of data**.
 
 
 ## macOS

external/integrity/encryption/file/encryption_file.md

@@ -9,7 +9,7 @@ redirect_from:
 # Encrypting Files and Folders
 Encryption is an effective measure to protect sensitive data. In this lab card we provide instructions for file/folder encryption on platforms commonly used by LCSB staff.
 
-**IMPORTANT NOTICE:** One important requirement of using Encryption is that you must  manage your Encryption Passwords/Keys. Failing to do so will mean **loosing your data indefinitely**. In this [link](https://howto.lcsb.uni.lu/?access:passwords) we list  tools that can be used for password management. **Please make sure you have arrangements for password management before starting the encryption of data**.
+**IMPORTANT NOTICE:** One important requirement of using Encryption is that you must  manage your Encryption Passwords/Keys. Failing to do so will mean **loosing your data indefinitely**. In this [link]({{ '/?access:passwords' | relative_url }}) we list  tools that can be used for password management. **Please make sure you have arrangements for password management before starting the encryption of data**.
 
 ## macOS
 The built-in mechanism for file-level encryption on a Mac is  Encrypted Disk Images (*.dmg* files). In order to create a disk image:

external/integrity/naming/file_naming.md

@@ -16,7 +16,7 @@ Good file name follows three basic principles:
 * human readable
 * plays well with default ordering
 
-If you are looking for information on how to organize and structure your folders, you may find this [dedicated card](https://howto.lcsb.uni.lu/?integrity:organization) helpful.
+If you are looking for information on how to organize and structure your folders, you may find this [dedicated card]({{ '/?integrity:organization' | relative_url }}) helpful.
 
 ## Machine readable
 
@@ -56,7 +56,7 @@ Beware of typos and avoid using multiple names varying in small ways unless it h
 ## Exploiting machine readable names
 
 You may already have a lot of files collected for your project or you have received big dataset from one of your collaborators. Then you might think about organizing and renaming them to be compliant with your new or existing naming policy.
-If the names are consistent and you don't want to loose time renaming them by hand, you may try to use dedicated tools (e.g. [PSRenamer](https://www.powersurgepub.com/products/psrenamer/index.html)) or simple commands in your command line (**rename** for Mac and Linux, **ren** for Windows).
+If the names are consistent and you don't want to loose time renaming them by hand, you may try to use dedicated tools (e.g. [PSRenamer](https://github.com/hbowie/psrenamer) or simple commands in your command line (**rename** for Mac and Linux, **ren** for Windows).
 
 Once your skills develop, you will be able to use machines and machine readable file names to perform advanced operations on them, e.g. search using regular expression.
 Imagine folder with thousands of files. Running simple R command

external/integrity/organization/organization.md

@@ -21,7 +21,7 @@ able to find back the files easily.
 A key rule is to name the folders with straightforward but explicit names, and to include the decision tree of where to put a given file inside the folder structure. In fact, the directory tree should in some sense
 reflect the decision tree.
 
-More details on naming files and folders are provided in the dedicated [file naming card](https://howto.lcsb.uni.lu/?integrity:naming).
+More details on naming files and folders are provided in the dedicated [file naming card]({{ '/?integrity:naming' | relative_url }}).
 
 ## Suggestions
 

external/integrity/sanitisation/sanitisation.md

+---
+layout: page
+permalink: /external/integrity/sanitisation/
+shortcut: integrity:sanitisation
+redirect_from:
+  - /cards/integrity:sanitisation
+  - /external/cards/integrity:sanitisation
+---
+
+# Sanitising Data Files
+
+In this lab card we list software  that can be used to permanently delete **individual files** from storage. If you need to sanitise an entire storage device (e.g. laptop, external hard drive), this will be done for you by University IT Services, please create a ticket on [ServiceNow](https://service.uni.lu/) (using item **Catalogue/IT/Information Security Services** ).
+
+Table 2 lists software that can be used on different platforms for permanent file removal.
+
+|Platform|Instructions|
+|-----|------------------------|
+| macOS |For OSX versions prior to 10.11 (El Capitan) you may use the **Secure Empty Trash**  option, which appears when right clicking on the Trash icon.|
+| |OSX version 10.11 (El Capitan) onwards, Apple has deprecated the  **Secure Empty Trash**, as it is not effective on Solid State Drives (SSDs). The approach to be adopted on Macs is to [turn on disk encryption]({{ 'external/integrity/encryption/disk' | relative_url }}) for your entire disk, or to keep sensitive data files in [encrypted disk images]({{ 'external/integrity/encryption/file' | relative_url }}).|
+| Linux | Use the **shred** command, instructions can be found [here](https://www.lifewire.com/shred-linux-command-4094148).|
+| Windows | Use the **SDelete** command line utility, instructions can be found [here](https://docs.microsoft.com/en-us/sysinternals/downloads/sdelete).|
+
+Please note if your files reside on server-side storage then permanent file removal may not take full effect. This is due to (1) the storage redundancy features on some server platforms, or (2) automatic server backups. To get more information, and to request removal of backups, you may contact University or LCSB IT Support by creating a ticket on [ServiceNow](https://service.uni.lu/).
+

external/integrity/spreadsheets/spreadsheets.md

@@ -42,7 +42,7 @@ For reproducibility purposes, the collected data should be always exported from
 
 ### Table
 
-- Keep header column names machine readable. You can follow the same best practices as for file naming (see our [Card on file naming](../naming/file_naming.md)).
+- Keep header column names machine readable. You can follow the same best practices as for file naming (see our [Card on file naming]({{ '/?integrity:naming' | relative_url }})).
 - Keep values in columns atomic.
 - Use primary keys - values in one particular column should be unique for the whole table. This will allow you to create unique references pointing to one and only one observation/record.
 - Do not insert empty rows or columns which would split the table in two.

external/lab/quarks-general/quarks-general.md

+---
+layout: page
+permalink: /external/lab/quarks-general/
+shortcut: lab:quarks-general
+redirect_from:
+  - /cards/lab:quarks-general
+  - /external/cards/lab:quarks-general
+---
+
+# Quarks - General information
+
+## How to access Quarks?
+
+https://quarks.lcsb.uni.lu
+
+### What does mean SSO connection?
+
+SSO connection means connection with Uni credentials. name.lastname@uni.lu and associated password
+
+(VPN connection is required if not connected to the local network)
+Use the Quarks website with the computer to enter the new batch number and final location of the product
+Use the Quarks application to enter the batch number and final location of the chemical products received (by scanning)
+## How is organized the Quarks flow at LCSB?
+1. Ordering an article via the purchase platform in Quarks
+
+2. If it is a chemical, the product is automatically created in the chemical product inventory of Quarks. Biological reagents and medication are also automatically created in the chemical product inventory.
+3. Reception of the article by support team. If it is a chemical, the label is printed and placed in the dedicated box.
+4. The buyer come to pick up the deliveries and the labels
+5. The buyer
+
+     - Use the Quarks website with the computer to enter the new batch number and final location of the product
+
+     - Use the Quarks application to enter the batch number and final location of the chemical products received (by scanning)
+
+
+## How are organized the Quarks devices?
+
+- Computers of the lab or personal computers allow to access the website
+
+- Scanners also called the TC20 allow to use the Quarks application in order to move, discard or get information about a product by scanning its Quarks label. To connect to the application, you have to use your uni credentials.
+
+<div align="center">
+<img src="img/40.png">
+</div>
+
+- In the laboratories, you can also acces the website or the application using the tablets.
+
+- Scanners and tablets have charging support to ensure it is always charged.
+
+<div align="center">
+<img src="img/41.png">
+<img src="img/42.png">
+</div>
+
+
+- The printers available in the laboratories are linked via USB to the adjacent computer. Those printers are also linked to the network of the University.
+
+## How to print labels?
+**From your personal compute**
+
+Please find here the instruction to install the printer for windows users:
+https://www.zebra.com/us/en/support-downloads/printer-software/printer-setup-utilities.html
+
+Zebra Printer Setup Utility Support &  Downloads | Zebra
+www.zebra.com
+
+Download Zebra's Printer Setup Utility, an easy way to quickly and easily configure select Zebra industrial, mobile and desktop printers.
+Download the app : Zebra Setup Utilities for Windows (1-Oct-2019)
+
+ Once it is done, you need to install the printer:
+
+1. Install New Printer
+2. Next
+3. Install Printer
+4. Look for the printer ZDesigner GK420t
+5. Next
+6. Add Port
+7. Next
+8. IP Address : 10.213.18.13
+9. Next
+10. Select the 2 sub-programs Launch
+11. Finish
+
+
+2 softwares will be installed on your computer. The first one is for the printer, the second one is for the bar codes.
+
+IP addresses:
+- BT2-Support 10.213.17.166
+- BT2-1   10.213.17.167
+- BT2-2   10.213.17.207
+- BT2-3   10.213.18.13
+- BT1-Support
+- BT1-4   10.213.19.164
+- BT1-5   10.213.19.138
+
+When you will print the label in Quarks, choose the **ZebraGK420t printer** and the following parameters.
+
+In **preferences** you will be able to choose:
+<div align="center">
+<img src=" img/43.png">
+ </div>
+And
+<div align="center">
+<img src=" img/44.png">
+</div>
+Go in **printers and scanners** and right click on your printer (zebra). You will have printer preferences and should fix it for your session. Click on **apply**.
+
+**From the laboratory – USB link**
+
+The printers are in the open laboratories, generally in the center of the open lab. Please if you canno’t find it, check with your technicians. There is one printer for each floor. We have additional printer on first floor BT1 and second floor BT2 for support team. Support team is providing the labels.
+
+
+## In which cases will I need to print labels?
+
+You have to print a label for chemicals, kits, biological reagents, homemade solutions, reconditioning labels
+
+## What are the roles in Quarks?
+
+Quarks gives us the possibility to have different roles profiles, with different rights.
+
+**Viewer**: only view orders from own group
+
+**Researcher**: place article in a cart and view orders from/for own group, create new article
+
+**Technician**: place article in a cart and view orders from/for own group, create new articles, receiving notifications on status of all orders
+
+**Budget responsible**: validate carts of own group, choose budget codes for orders, have an overview of the spending
+
+## How is a newcomer assigned to a group?
+
+After first log in in Quarks, the Support team will attribute a role and a group to the newcomer.
+
+# Help needed?
+In case of any question, request or issue, [please send a ticket](https://service.uni.lu/sp?id=bs_dep_catalog_entry&sys_id=0840cf71dbaa14148bcbf9b41d9619cb).
+

external/on-offboarding/checklistArrival/checklistArrival.md

+---
+layout: page
+permalink: /external/on-offboarding/checklistArrival/
+shortcut: on-offboarding:checklistArrival
+redirect_from:
+  - /cards/on-offboarding:checklistArrival
+  - /external/cards/on-offboarding:checklistArrival
+---
+# Checklist upon arrival in Luxemburg
+
+This checklist for newcomers will provide you with some practical advice what to take care of before arriving in Luxembourg. The pdf document for download can be found [here](https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20upon%20Arrival%20in%20Luxembourg.pdf).
+
+### Welcome to Luxembourg!
+Arriving in a new country means also dealing with bureaucracy. Here we would like to give you a first overview of the things that you need to do upon arrival.
+
+### Living in Luxembourg
+- Register at your [local commune](https://www.syvicol.lu/fr) ("Hotel de Ville") within
+    - 3 days of arrival for all non-EU citizens
+    - 8 days for EU citizens staying longer than 3 months
+Take with you your passport, renting contract of accommodation, certified
+birth certificate and work contract. After registration you will receive a
+paper card that states on which address you have been registered. At the
+same time you can also register your drivers license (only for EU citizens)
+##### Within 3 months:
+- Register your vehicle. For more information [check here](https://www.euraxess.lu/).
+- Apply for your residence permit (only for non-EU citizens)
+##### Within 1 year:
+- Apply for a [Luxembourg driving license](https://www.euraxess.lu/) (only for non-EU citizens)
+
+### Children
+- Register children at their school
+
+### Money
+- Open a bank account and order credit/debit cards. Be aware that it can
+take up to 3 weeks until you receive those bank cards.
+- Take with you your passport, work contract and the paper card you got from the commune when registering.
+
+<!--Process owner: Comm'department-->
+

external/on-offboarding/checklistBeforeArriving/checklistBeforeArriving.md

+---
+layout: page
+permalink: /external/on-offboarding/checklistBeforeArriving/
+shortcut: on-offboarding:checklistBeforeArriving
+redirect_from:
+  - /cards/on-offboarding:checklistBeforeArriving
+  - /external/cards/on-offboarding:checklistBeforeArriving
+---
+# Newcomer Checklist before Arriving in Luxembourg
+
+This checklist for newcomers will provide you with some practical advice what to take care of before arriving in Luxembourg. The pdf document for download can be found [here](https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Newcomer%20Checklist%20Before%20Arriving%20in%20Luxembourg.pdf).
+
+### Entering Luxembourg
+- Check the validity of your passport!
+- Check your entry and residence conditions! Depending on your nationality you will need a **visa and/or residence permit**. Detailed information on who needs such permits and which documents are required can be found [on the euraxess](https://www.euraxess.lu/) homepage.
+- Depending on your nationality you will need a **work permit**. HR will take care of this procedure. They will send you the necessary documents that you need to fill in.
+
+
+### Getting to Luxembourg
+- To avoid extra expenses, only book your flight once you know the first working day of your employment and that you got a visa.
+- Luxembourg itself has a small **airport** called Findel in Luxembourg City. Alternatively, one could fly to airport Frankfurt Hahn or Charleroi where low budget airlines are travelling to. There is a direct cheap [bus connection](https://www.flibco.com/en) between those airports and Luxembourg.
+- Please check the Luxembourgish [railway website](https://www.cfl.lu) for national and international train connections. To get to the LCSB get off at station Belval Université. Detailed information on how to find the LCSB building can be found [on the university website](https://wwwen.uni.lu/lcsb/contact%20).
+
+### Health
+- All LCSB employees will be covered by CNS health insurance that covers up to 2/3 of your health expenses. To cover the rest of the expenses every employees is free to arrange private insurance at own expense. For details on health insurance and social security check the [Daily Life section of euraxess](https://www.euraxess.lu/node/174962/).
+
+
+### Looking for accommodation
+- In Luxembourg most apartments are rented out by estate agencies. It’s quite common to pay 1 month rent as agency fee and up to 3 months rent as deposit to the landlord. Euraxess provides [further information and compiled a list of useful websites](https://www.euraxess.lu/luxembourg/information-researchers/accommodation) for this.
+- Alternatively, it is also possible to apply for university housing: PhD students can rent student accommodation for their entire stay at the UL. More information can be found [on the university website](https://wwwen.uni.lu/students/accommodation). Researchers can apply for a short- term stay (1 to 3 months) in university housing. [This file](http://wwwen.uni.lu/content/download/56478/668845/file/Housing%2520procedure%2520and%2520online%2520application.pdf%20) provides further information on this.
+
+
+### Tax
+- You will receive your tax card automatically per post after the University of Luxembourg has registered you at the social security system. Hand this tax card to HR. They will take care of the rest.
+- General information on taxation can be found [on the euraxess website](https://www.euraxess.lu/).
+
+
+### Children
+- The LCSB has partnered with a nursery in Esch-sur-Alzette. For more information, please contact: mike.hansen@uni.lu
+- If you are accompanied by children bring their school reports. Ceck [the euraxess website](https://www.euraxess.lu/) for more information about the Luxembourgish school system.
+
+
+
+### Money
+- Please be aware that it can take up to 3 weeks after opening a new bank account until you receive your new banking cards. So make sure you prepare other means to bridge this period.
+
+If you have any questions, don’t hesitate to contact us. We are looking forward to welcoming you in person.
+**See you soon at the LCSB!**

external/on-offboarding/checklistGetStarted/checklistGetStarted.md

+---
+layout: page
+permalink: /external/on-offboarding/checklistGetStarted/
+shortcut: on-offboarding:checklistGetStarted
+redirect_from:
+  - /cards/on-offboarding:checklistGetStarted
+  - /external/cards/on-offboarding:checklistGetStarted
+---
+# Newcomer's checklist
+
+### Welcome to the LCSB!
+Below you can find a to-do-checklist and some practical information aiming to guide your through the first days at the LCSB together with the (corresponding people in charge) in brackets.
+
+### To Do's
+* Sign your contract (HR department)
+* Attend the University Welcome Meeting: Have your picture taken for our website and get a library card for online access of publications
+* Attend the LCSB Welcome Meeting: Administrative welcome presentation (communication team) & Biosafety introduction (safety team)
+* Fill in the newcomer's profile for your introduction on the intranet and in the newsletter (communication team)
+* Get introduced to your team members, especially to the administrative team (your godparent)
+* Have your E-Mail adress added to the relevant LCSB mailing lists (your godparent)
+* Read the biweekly LCSB newsletter and explore the [LCSB Intranet](https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx)
+* Hand in you tax card to the HR once you received it by post (HR department)
+* Get your entrance badge (your team's secretary)
+
+
+### Services and Websites
+You will need two accounts to make use of services and tools:
+* **UNI-LU account:** To use the IT services, also known as SIU, will give you your account at your first working day
+* **LUMS account:** This account is used for particular services (see below) and will be created after you have your UNI-LU account. Your godparent can assist you in that.
+
+
+#### The **UNI-LU account** is used to access the following services:
+
+* Mail services, including web mail accessible from the browser via: [https://owa.uni.lu](https://owa.uni.lu)
+* Microsoft Office & Teams: [https://portal.office.com](https://portal.office.com)
+* University’s Service Portal to create tickets for IT, office setup, and other issues: [https://service.uni.lu](https://service.uni.lu)
+* SAP, to make leave requests, see and print payslips and other HR-related services: [https://fiori.uni.lu/fiori](https://fiori.uni.lu/fiori)
+* Webex which is used for all virtual work meetings (implemented due to the COVID-19 pandemic), unless the other party requires the use of other software. You can login with UNI-LU account at: [https://unilu.webex.com/](https://unilu.webex.com/)
+* University Intranet: [https://intranet.uni.lux](https://intranet.uni.lux)
+* LCSB Intranet: [https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx](https://intranet.uni.lux/the_university/lcsb/lscb_internal/Pages/default.aspx)
+* specific communication channels, such as Slack, Basecamp an others, depending on your team. Your godparent will provide you with further information.
+
+
+#### The LUMS account is used to access the following services:
+
+* Owncloud, a file cloud deployment at LCSB: [http://owncloud.lcsb.uni.lu](http://owncloud.lcsb.uni.lu)
+* Gitlab, where the bioinformatics core team we manages its work products, source code and websites: [https://gitlab.lcsb.uni.lu/](https://gitlab.lcsb.uni.lu/)
+* other specific and licence-dependent software that is relevant for your work
+
+
+#### Enjoy your time at the LCSB!
+If you have any questions, do not hesitate to ask!
+

external/on-offboarding/checklistGodparent/checklistGodparent.md

+---
+layout: page
+permalink: /external/on-offboarding/checklistGodparent/
+shortcut: on-offboarding:checklistGodparent
+redirect_from:
+  - /cards/on-offboarding:checklistGodparent
+  - /external/cards/on-offboarding:checklistGodparent
+---
+# Checklist for godparents
+
+Thank you for accepting thegodparent role and taking the time to help him/her get started at the LCSB!
+Below you can find a checklist for the first steps with this task together with the (corresponding people in charge) in brackets.
+The overview checklist in .pdf-format ist avaliable [here](https://intranet.uni.lux/the_university/lcsb/lscb_internal/LCSB%20Handbook/Appendix%20files/Godparent%20Checklist%20-%20newcomers.pdf).
+
+### Tasks for the godparent
+
+- Welcome the new employee
+- Introduce the new employee to the administrative staff in order to provide him/her with:
+    * an entrance badge (your team's secrretary)
+    * office supplies (communications team)
+    * a computer (your team's secrretary)
+ 
+- Show the new employee around and introduce him/her to your group and to the LCSB team
+- Make sure that the new colleague receives and signs the Biosafety Information Pack before starting lab work, as all LCSB employees (also administartive staff) must be aware of the guidelines and risks of the labs.
+- Explain and show:
+    * LCSB intranet and newsletter and UL intranet
+    * Uni/LCSB policies and culture: how to find details about them on the intranet
+    * ATLAS server structure
+    * Meetings at LCSB: team meeting (mandatory!), group meetings, TGIF, CETs etc.
+    * Infrastructure: transport, lunch, chèques repas etc.
+    * email signature and confidentiality disclaimer
+    * business cards (to order them contact your group’s team secretary)
+ 
+- Make sure the new employee is added to the relevant email lists. For this please [open a ticket at ServiceNow](https://service.uni.lu/sp), mentioning the name and **email address of the new employee** and the **email addresses of the required email lists** that he should be added to.
+- For details, see the LCSB Handbook on the intranet.
+
+### Thanks for your help!

external/on-offboarding/godparent/godparent.md

+---
+layout: page
+permalink: /external/on-offboarding/godparent/
+shortcut: on-offboarding:godparent
+redirect_from:
+  - /cards/on-offboarding:godparent
+  - /external/cards/on-offboarding:godparent
+---
+# Godparents for Newcomers
+Please also consult the [checklist for godparents](https://howto.lcsb.uni.lu/?hr:newcomers:checklistGodparent).
+
+### Summary
+In order to help new employees to easily integrate in their new workplace and senior members to better know and understand the new colleague, each new employee will be assigned a "godparent".
+
+### What is a godparent?
+Being a godparent is a voluntary function within the LCSB.
+A godparent is as a person who, through its experience at the centre and in Luxembourg has gained an extensive knowledge about procedures, rules, corporate culture etc. and who desires to help others, advice new colleagues when they arrive in Luxembourg and who desires to build new relationships.
+### What should a godparent do?
+A godparent is free to organise and build the relationship with a new employee. However, the following task should be covered.
+* Welcome the new employee
+* Show the new employee around and introduce him/her to the team and to other LCSB/ Uni.lu members: most importantly to the administrative in order to provide a badge, office supplies…
+* Make sure that the new colleague receives and signs the Biosafety Information Pack, as all LCSB employees must be aware of the regulations and risks of the labs
+* Explain Uni/ LCSB policies and culture
+* Make sure the new employee is added to the relevant email lists. For this please [open a ticket at ServiceNow](https://service.uni.lu/sp), mentioning the name and **email address of the new employee** and the **email addresses of the required email lists** that he should be added to.
+* Make sure the newcomer gets access to ATLAS as appropriate.
+Duration of godparenting: Minimum 2 months and no longer than 6 months.
+### How to become a godparent?
+All LCSB members are eligible to become godparents. There are no minimal qualifications required, mentors must only work for at least 6 month at the Uni.
+However, in general HR in collaboration with the LCSB’s administration team will shortlist few potential candidates. Potential candidates shall be contacted and asked if they accept the function. In a case of refusal the next candidate on the list will be contacted.
+Preferred candidates for this assignment are members of the same unit or project, a relevant research field, or the same hierarchical level. To avoid conflicts of interest, in principle PI or superiors are to be avoided as godparents.
+

external/on-offboarding/onboarding/onboarding.md

+---
+layout: page
+permalink: /external/on-offboarding/onboarding/
+shortcut: on-offboarding:onboarding
+redirect_from:
+  - /cards/on-offboarding:onboarding
+  - /external/cards/on-offboarding:onboarding
+---
+# Onboarding new members at the LCSB
+
+## Purpose
+The LCSB regularly welcomes newcomers who have just joined one of the research groups or the support teams.
+The on-boarding process aims to ensure their smooth insertion within their group and within the LCSB.
+It completes the introduction at the Welcome Day of the university by providing information specific to the LCSB.
+On top of practical information, this process should convey the LCSB values and the way we all work together.
+
+
+## 1. Godparents
+When a new member joins the LCSB, his team should assign him a godparent who will guide him during the on-boarding process.
+The group PI are asked to nominate a senior member of the group as “god-parent”.
+The godparent should show the newcomer around the LCSB premises, introduce them to all the relevant LCSB staff (help for networking during social events), and take care of some of the early procedures such as:
+- prepare a desk
+- get a computer
+- get phone
+- show how to get office supplies
+- register for mail lists
+- explain Uni/LCSB intranet, services and [important links](https://howto.lcsb.uni.lu/?general:links)
+- introduce to the team
+- explain the lunch voucher system and where to get food
+
+
+## 2. Welcome meetings
+- **University Welcome Day**: The newcomers have to attend the University Welcome Day to get a general overview of the university and have their official picture taken for the website.
+- **LCSB Welcome meeting**: Once a month a two hours meeting is organised at the LCSB for the members who arrived recently. During the first part, a round table allow participants to introduce themselves and to place their “location sticker” on the LCSB map in BT2 staircase. Then, a member of the communication team presents the LCSB, its goals and values, and provides some practical information (who’s who, basic procedures, where to find answers, etc.). The second part is dedicated to security and safety (building evacuation, emergency exits, lab safety…).
+The participants also get a copy of the LCSB annual and research reports and the slides used during the meeting are shared. The newcomers receive a calendar invitation for this meeting, sent by the communication team.
+
+In order to introduce the newcomers to the whole LCSB team, the new members are mentioned in the LCSB newsletter (Photo, name, position and email address in the “Newcomers” section). They can also introduce themselves during the weekly team meeting at the LCSB.
+
+## 3. Checklist for administrative tasks
+
+- Get entrance badge at the Maison du Savoir (Security office on 2nd floor). Check with your team secretary what kind of access you have (rooms and hours) and how to update it if needed.
+- Get acquainted with your colleagues, especially your group, the group secretary and the administrative team. The godparent should show the new employee around and introduce them to the LCSB team.
+- Get access to the relevant mail lists (LCSB-Team + group list). The godparent should open a ticket in ServiceNow mentioning the name and the email address of the new employee and the required email lists that they should be added to.
+- Familiarise with different LCSB tools: ATLAS server (to get access, [open a ticket in service now](https://service.uni.lu/sp)), the regular meetings (team meetings, TGIaF, CETs), the lunch vouchers distribution, etc. The godparent should explain how things work at the Uni/LCSB (policies and culture).
+- Fill in the profile on [LCSB intranet](https://intranet.uni.lux/the_university/lcsb/lscb_internal/). Check that the information on the personal webpage on university website is accurate and that the newcomer is mentioned in LCSB people list and in the group member list on the website.
+- Set up the proper email signature and confidentiality disclaimer for your university mailbox: [Guidelines on the intranet](https://intranet.uni.lux/the_university/sc/Lists/Policies%20%20Procedures/DispForm.aspx?ID=9)
+- Order business cards through your group’s secretary if needed.
+- Read the biweekly LCSB newsletter and explore the intranet to stay up to date with what is happening at the LCSB. Send an email to the LCSB communication team if the newcomer hasn’t received it after a few weeks.
+- Complete your trainings to get further access to the labs. The godparent should make sure that the new colleague receives the Biosafety, Data Management and Data Protection Training before starting lab work, as all LCSB employees must be aware of the guidelines and risks.

external/ppc/add-gitignore/add-gitignore.md

+---
+layout: page
+permalink: /external/ppc/add-gitignore/
+shortcut: ppc:add-gitignore
+redirect_from:
+  - /cards/ppc:add-gitignore
+  - /external/cards/ppc:add-gitignore
+---
+
+# Add a .gitignore to your repository
+
+The version control system git tracks all files in a repository.
+
+Sometimes, you do not want certain files or directories to be tracked, but fully ignored by `git`. These files or directories
+can include binaries, images, dependencies, log files, or analysis results. Also, hidden system files are usually picked up by `git`.
+
+The idea is to create a file named `.gitignore` that lists all the files and directories that should be ignored by `git`.
+
+For instance, in order to ignore all log files with the suffix `.log`, the content of the `.gitignore` file should be:
+
+```
+*.log
+```
+
+A common example is to ignore system files as well, such as the `.DS_Store` file:
+
+```
+.DS_Store
+```
+
+*Note:* Sometimes, you might not see the hidden system files. You can do so by browsing to the directory in the terminal and typing:
+
+```bash
+$ ls -lash
+```
+
+Once the `.gitignore` file has been created, you can add and commit the file as any other file in the `git`-tracked repository. A relatively complete collection of `.gitignore` templates can be found [here](https://github.com/github/gitignore).
+
+More information on the `.gitignore` mechanism can be found [here](https://www.atlassian.com/git/tutorials/saving-changes/gitignore).

external/ppc/publish-repo/publish-repo.md

+---
+layout: page
+permalink: /external/ppc/publish-repo/
+shortcut: ppc:publish-repo
+redirect_from:
+  - /cards/ppc:publish-repo
+  - /external/cards/ppc:publish-repo
+---
+
+# Publish a repository
+
+By default, the repositories created on the LCSB Gitlab are private, i.e. they cannot be seen by anyone outside LCSB.
+
+In order to change the visibility of the repository, you can do so by browsing to `Settings` and then expanding the section on `Visibility, project features, permissions`.
+
+There, you can set the visibility to `Public`. It is important to note that the group must be public in order to change visibility of the repository.
+
+Remember to follow the [LCSB policy regarding code development](https://howto.lcsb.uni.lu/?policies:LCSB-POL-BIC-07). In case of questions, please do not hesitate to contact the [R3 team](mailto:lcsb-r3@uni.lu).
\ No newline at end of file

external/publication/10WaysImproveEnglish/10WaysImproveEnglish.md

+---
+layout: page
+permalink: /external/publication/10WaysImproveEnglish/
+shortcut: publication:10WaysImproveEnglish
+redirect_from:
+  - /cards/publication:10WaysImproveEnglish
+  - /external/cards/publication:10WaysImproveEnglish
+---
+# 10 ways to improve your English
+
+Francisco ARAGAON ARTACHO, former postdoc in the Systems Control group, has made a list of the ten most important points that helped to improve his English. In this article he shares them with you and explains what he means by each of them.
+
+**1. Believe improving your English is something very important**
+I think this is the most important point. If you don't believe a good written English is important, you will never improve it. So... why is it important? The way you write will give your reader a first impression about you. Even more, the reader will even get an impression about your personality (tidy / messy / arrogant / smart / knowledgeable / dumb). He / she probably doesn't know you, nor knows how good your ideas are. Don't give him / her a bad first impression: it will be hard to change his/her mind. While refereeing, I've directly rejected several papers because the English was terribly bad, or because it was full of typos. Nobody wants to read a text with many typos and which is clearly against the "golden rule" to never make a referee angry! Before submitting a paper / grant proposal, check it carefully. If one of your co-authors is a native English speaker, ask him / her to check the grammar of what you wrote. If not, ask a friend. If possible, wait for a week and read it again. You will probably discover that what you wrote is not as nice as you thought. You will find many typos and errors.
+
+**2. Read**
+Read as much texts in English as you can, especially novels. If you read good writers, perhaps (probably) something good will stick in your mind. Try to use their "fancy words and sentences" whenever it is possible.
+
+**3. Listen**
+I believe listening to music and watching movies / TV shows helped a lot to improve my English. Even during the most boring talk at a conference you may learn something good for your English.
+
+**4. Use synonyms**
+Synonyms are good. Avoid repeating words / structures whenever is possible. Use as many different sentence connectors as you can / know. Your text will look better and will be nicer to read. I normally use [Thesaurus](http://thesaurus.reference.com/).
+
+**5. Use a dictionary**
+While writing, I always have a dictionary open in my browser. I especially like [wordreference.com](http://www.wordreference.com/), which even has the British / American pronunciation for many words.
+
+**6. Check what Google says about your sentences**
+If you're not sure about a sentence you wrote, google it (or part of it), using quotation marks. If there are only a few hits, your sentence is probably wrong. If you doubt between two versions of the same sentence, the one with more results in Google is probably going to be the correct one.
+
+**7. Write short sentences**
+Long sentences make the reader feel exhausted, so do your best to avoid them. Try to punctuate correctly: use commas, colons, and semicolons.
+
+**8. Write short paragraphs**
+In a similar way to the previous point, long paragraphs are exhausting. I remember that when I was a kid I hated books without "white space" (breaks), and I guess I still have some similar feeling. A text with short paragraphs always looks easier to read at first glance. Additionally, while aiming to write short paragraphs, you will be forced to structure your ideas (next point).
+
+**9. Structure your thoughts through the text**
+Structure your ideas to explain yourself. It is very important to use sentence connectors, as for example: moreover, however, besides, although, nevertheless, in spite of, then, therefore, thus, hence, whence, on one hand / on the other hand, additionally, further, furthermore, otherwise...
+
+**10. Ask people to correct you**
+People (wrongly) believe that it is impolite to correct others when they're not speaking in their native language. I guess this happens because no one likes to be wrong, and even less to be pointed out for being wrong. At the beginning, when I started learning English, people used to correct me very often. Unfortunately, as soon as my English was "good enough", I noticed that I was getting less and less corrections, despite my English wasn't that good. For example, only last year my Aussie housemate told me that I was pronouncing "yellow" wrong (and, probably, every single word starting with "y" - pronouncing it like "j" in "jelly") because he wanted to piss me off. At that moment I guess he was disappointed to see that I liked to be corrected, but he started telling me my mistakes since then. Thus, if you want to be corrected you'll need to ask the others to do it, and remember to thank them with a not-very-fake-looking smile when they do it :).
+

external/publication/publishInBiotools/publishInBiotools.md

+---
+layout: page
+permalink: /external/publication/publishInBiotools/
+shortcut: publication:publishInBiotools
+redirect_from:
+  - /cards/publication:publishInBiotools
+  - /external/cards/publication:publishInBiotools
+---
+
+# Publishing a tool in *bio.tools*
+
+First, *bio.tools* serve two main purposes:
+
+- dissemination of your tools
+- collecting systematic and reasonable statistics about the available
+  software for many purposes, including data science and performance reports
+
+To get your contents in, you need to fill an application and get an account.
+Filling out the application is particularly straightforward.
+
+After you get the account, you can click "Add content" in the "Menu" on the top
+right, then go through around 10 tabs that allow you to fill lots of
+interesting information about your tool, and finally submit it, which makes the
+contents immediately visible.
+
+This card collects some reminders about what you should not forget while
+submitting the tool, perhaps useful as a checklist.
+
+## General tips
+
+### Use search and consult the curation guide to resolve ambiguities
+
+The guide is currently here:
+https://biotools.readthedocs.io/en/latest/curators_guide.html#summary-group
+
+It includes helpful and authoritative guidelines for almost all fields that you
+can fill, including examples.
+
+As the last resort when you do not know what to do with a field, you can try
+search suggestions in the structured search box above, and try to be at least
+consistent with the rest of the database. In the search box, type in a single
+letter, wait for a moment (or press arrow down), choose the annotation
+category, and see what others have used.
+
+### Add a "backup" maintainer
+
+This may remove a lot of unnecessary workload from you, and will help everyone
+at times when you are not available. (Or, at least, reduce the stress levels.)
+
+### Add _many_ links to all types of documentation
+
+This helps in two ways:
+- The search engines will be able to categorize and index your contents better,
+  possibly giving more helpful links to your tools.
+- Users of *bio.tools* will be able to explore the most relevant parts of your
+  documentation very quickly, helping them to make a faster decision about
+  using your tool. For example, it is often a relief to quickly see that a
+  bioinformatics tool has an explicit step-by-step tutorial, and that a web
+  visualization framework has a complete useful API reference.
+
+Include the (interesting) relations to other tools. This adds a bit more
+interesting data to both search engines and statisticians who process
+*bio.tools* content, and gives an documentation of possible "use-cases".
+
+## Proper labeling
+
+### Choose the bio.tools ID correctly
+
+As the name says, the "Persistent biotoolsID" cannot be changed. It will be
+permanently displayed as an identifier in almost all content that is
+autogenerated from *bio.tools*. For users, that concerns mainly the URLs, so
+you may want to apply similar formatting guidelines as for URLs (use hyphens
+`-` instead of underscores `_`, do not use capital letters, ...).
+
+### Add your tool to proper collections
+
+Collections group the results of various larger cooperated (or loosely
+organized) efforts, such as "Galaxy tools", "Parkinson disease research", and
+"3D BioInfo".
+
+If your tool is related to ELIXIR, you should fill in the correct ELIXIR node,
+platform, community _and_ collection. Remember to:
+
+- Add _all_ involved ELIXIR nodes.
+- **Add your tool to the node-specific ELIXIR collections.** For LCSB, that is
+  usually **ELIXIR-LU**. This is counter-intuitive and seems duplicate to the
+  categorization by ELIXIR nodes, but:
+  - at least 2 nodes use collections labels instead of node labels to scrape
+    data about their tools
+  - there is search support only for the collections; currently (March 2021) it
+    seems that you cannot easily search for tools by ELIXIR nodes
+
+### Fill in the tool "Function" very verbosely
+
+The main reason for categorizing tool functions is to provide a systematic way
+for listing the tools in topic-based catalogues that can be browsed by users.
+
+The categories and data formats available for describing your tool function
+rarely give a precise match. That is okay, you can choose a broader category.
+
+Use all categories that match even a small part of your tool; it will
+potentially help *bio.tools* users to find your tool even if they do not know
+what precisely they are searching for.
+
+Selecting a very specific category ("deeper" in the topic tree) also implies
+all "parent" categories, so you do not have to be afraid of over-specification.
+*Bio.tools* search box will automatically include your tool in searches for the
+broader categories.
+
+## References and publications
+
+### Be comprehensive about publications
+
+Add _all_ publications where you described, showcased, and benchmarked the
+tool. Also add preprints.
+
+There are several purposes for the precise publication tracking:
+- the users may (and often will) sort the tools by the citation count, likely
+  trying the most tested approach first
+- the publications provide an additional form of documentation (often more
+  colorful than the API docs)
+- the links and citation counts provide a nice, easily available statistic
+  about ELIXIR performance
+
+### Use the Credit tab
+
+The purpose of the "Credit" tab is not immediately obvious -- basically, you
+can credit anything that has helped you with creating the tool. This is
+currently used for at least 3 purposes:
+
+- systematic tracking of non-ELIXIR collaborators (add ORCIDs)
+- listing the **industry partners**
+- listing affiliations to particular research institutions
+  (**remember to add LCSB**)

index.md

@@ -5,7 +5,7 @@ order: 1
 ---
 
 {% comment %}
-The Bioinformatics Core and Lab Support teams assist researchers from the Luxembourg Centre for Systems Biomedicine ([LCSB](https://www.uni.lu/lcsb)) with the organization, management, and curation of research data through its R3 initiative.
+The Bioinformatics Core and Lab Support teams assist researchers from the Luxembourg Centre for Systems Biomedicine ([LCSB](https://wwwen.uni.lu/lcsb)) with the organization, management, and curation of research data through its R3 initiative.
 The How-to cards are intended to provide practical guidance in implementing Data Management, Data Protection, IT setup, lab support, and others.
 {% endcomment %}
 
@@ -17,6 +17,12 @@ The How-to cards are intended to provide practical guidance in implementing Data
             "icon": "<i class=\"large material-icons\">sticky_note_2</i>",
             "link": "{{ '/cards#general' | relative_url }}"
         },
+        {
+            "title": "On&Off boarding",
+            "caption": "A new colleague joined or my current colleague will leave. What do I have to do?",
+            "icon": "<i class=\"large material-icons\">compare_arrows</i>",
+            "link": "{{ '/cards#on-offboarding' | relative_url }}"
+        },
         {
             "title": "Access",
             "caption": "How can I get access to systems and infrastructure?",
@@ -29,6 +35,12 @@ The How-to cards are intended to provide practical guidance in implementing Data
             "icon": "<i class=\"large material-icons\">add_circle</i>",
             "link": "{{ '/cards#contribute' | relative_url }}"
         },
+        {
+            "title": "Backup",
+            "caption": "Guidelines regarding backing up your data",
+            "icon": "<i class=\"large material-icons\">backup</i>",
+            "link": "{{ '/cards#backup' | relative_url }}"
+        },
         {
             "title": "Exchange channels",
             "caption": "I am looking to share data or information",
@@ -47,6 +59,18 @@ The How-to cards are intended to provide practical guidance in implementing Data
             "icon": "<i class=\"large material-icons\">science</i>",
             "link": "{{ '/cards#lab' | relative_url }}"
         },
+        {
+            "title": "Publication",
+            "caption": "I want to publish my article",
+            "icon": "<i class=\"large material-icons\">menu_book</i>",
+            "link": "{{ '/cards#publication' | relative_url }}"
+        },
+        {
+            "title": "PPC",
+            "caption": "I need information on the pre-publication check (PPC)",
+            "icon": "<i class=\"large material-icons\">fact_check</i>",
+            "link": "{{ '/cards#ppc' | relative_url }}"
+        }
     ];
 
     document.addEventListener('DOMContentLoaded', function() {