generator @ 53a922a1

-Subproject commit 642095d5a54a8b54b313784eb4eef66e0623e208
+Subproject commit 53a922a13c4e8916c97599b5242493a47ea0a2e2

.gitlab-ci.yml

@@ -109,7 +109,7 @@ build:pages:
     - |
       echo "Configuration: " && cat ".ci/_config_$CI_COMMIT_REF_NAME.yml"
     # Run Jekyll with custom configuration
-    - LOGFILE=/dev/stdout ./add-timestamp-to-howtocard.sh external
+    - LOGFILE=/dev/stdout .ci/add-timestamp-to-howtocard.sh external
     - bundle exec jekyll build -d build --config "_config.yml,.ci/_config_$CI_COMMIT_REF_NAME.yml"
 
 # check
@@ -176,7 +176,7 @@ deploy:vm:
     - echo "$KNOWNHOSTS" > ~/.ssh/known_hosts
     - chmod 644 ~/.ssh/known_hosts
   rules:
-    - if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "develop" && $CI_PROJECT_PATH == "R3/howto-cards"'
+    #- if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "develop" && $CI_PROJECT_PATH == "R3/howto-cards"'
     - if: '$CI_PIPELINE_SOURCE != "merge_request_event" && $CI_COMMIT_REF_NAME == "master" && $CI_PROJECT_PATH == "R3/howto-cards"'
   script:
     - ssh -p $SSHPORT $SSHCONNECT "mkdir -p ~/$CI_COMMIT_REF_NAME/sources/public/$CI_JOB_ID ~/$CI_COMMIT_REF_NAME/public"

cards.md

@@ -37,7 +37,8 @@ order: -1
 			<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/vpn-access' | relative_url }}">VPN connection</a></li>
+			<li><a href="{{ 'external/access/vpn-cerbere-access' | relative_url }}">Connect to Cerbere via VPN</a></li>
 			<li><a href="{{ 'external/access/vpn-mobile' | relative_url }}">VPN connection on your mobile phone</a></li>
 			<li><a href="{{ 'external/access/wifiNetworkAccessGuests' | relative_url }}">WiFi network access for guests</a></li>
 		</ul>
@@ -56,6 +57,8 @@ order: -1
 			<li><a href="{{ 'external/contribute/markdown' | relative_url }}">Markdown</a></li>
 			<li><a href="{{ 'external/contribute/mirror-fork' | relative_url }}">Mirror fork automatically</a></li>
 			<li><a href="{{ 'external/contribute/review' | relative_url }}">Reviewing in Git</a></li>
+			<li><a href="{{ 'external/contribute/ssh-key-generation' | relative_url }}">Key-based Authentication on GitLab</a></li>
+			<li><a href="{{ 'external/contribute/supersede' | relative_url }}">Take over a stale merge request</a></li>
 			<li><a href="{{ 'external/contribute/vscode' | relative_url }}">Contribute using Visual Studio Code</a></li>
 			<li><a href="{{ 'external/contribute/web-ide' | relative_url }}">Contribute using Gitlab Web IDE</a></li>
 
@@ -64,10 +67,13 @@ order: -1
 	<div class="index-box noborderbox" id="exchange-channels-card">
 		<h3>Exchange channels</h3>
 		<ul>
-			<li><a href="{{ 'external/exchange-channels/lft' | relative_url }}">LCSB file transfer (LFT) Quick Guide</a></li>
-			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
 			<li><a href="{{ 'external/exchange-channels/asperaweb' | relative_url }}">AsperaWEB Quick Guide</a></li>
+			<li><a href="{{ 'external/exchange-channels/atlas-hpc' | relative_url }}">Data transfer between Atlas and UL HPC Clusters</a></li>
+			<li><a href="{{ 'external/exchange-channels/calendar' | relative_url }}">Sharing calendar in Microsoft Exchange</a></li>
+			<li><a href="{{ 'external/exchange-channels/cryptomator' | relative_url }}">Cryptomator</a></li>
+			<li><a href="{{ 'external/exchange-channels/lft' | relative_url }}">LCSB file transfer (LFT) Quick Guide</a></li>
 			<li><a href="{{ 'external/exchange-channels/owncloud' | relative_url }}">Owncloud</a></li>
+
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="general-card">
@@ -87,52 +93,66 @@ order: -1
 		<ul>
 			<li><a href="{{ 'external/integrity/checksum' | relative_url }}">Ensuring Integrity of Data Files with Checksums</a></li>
 			<li><a href="{{ 'external/integrity/dmp' | relative_url }}">Data Management Plan</a></li>
-			<li><a href="{{ 'external/integrity/encryption/cloud' | relative_url }}">Data upload to cloud</a></li>
 			<li><a href="{{ 'external/integrity/encryption/disk' | relative_url }}">Encrypting the Startup Disk for Your Laptop/Desktop</a></li>
 			<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>
+			<li><a href="{{ 'external/integrity/transfer/owncloud-privatebin' | relative_url }}">Transfer of Human Data with OwnCloud</a></li>
 
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="lab-equipment-card">
 		<h3>Lab: Equipment</h3>
 		<ul>
-			<li><a href="{{ 'external/lab-equipment/cryostorage' | relative_url }}">Utilization of the cryostorage</a></li>
-			<li><a href="{{ 'external/lab-equipment/dishwasher-utilization-and-maintenance' | relative_url }}">Dishwasher utilization and maintenance</a></li>
-			<li><a href="{{ 'external/lab-equipment/hoods' | relative_url }}">Laminar Flow - Fume Hood - Biosafety Cabinet: what are the differences and when to use them?</a></li>
-			<li><a href="{{ 'external/lab-equipment/lightcycler' | relative_url }}">How to leave virtual instrument mode on the LightCycler</a></li>
-			<li><a href="{{ 'external/lab-equipment/maintenance-of-fridges' | relative_url }}">Maintenance of fridges and freezers</a></li>
-			<li><a href="{{ 'external/lab-equipment/maintenance_of_cold_traps' | relative_url }}">Maintenance of cold traps  </a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-autoclaves' | relative_url }}">Utilization of autoclaves</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-balances' | relative_url }}">Utilization of balances</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-bsc' | relative_url }}">Biosafety Cabinets: good practices</a></li>
-			<li><a href="{{ 'external/lab-equipment/utilization-of-pH-meter' | relative_url }}">Utilization of pH meter</a></li>
+			<li><a href="{{ 'external/lab-equipment/autoclaves' | relative_url }}">Autoclaves: utilization</a></li>
+			<li><a href="{{ 'external/lab-equipment/balances' | relative_url }}">Balances: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/biosafety-cabinets' | relative_url }}">Biosafety Cabinets: good practices</a></li>
+			<li><a href="{{ 'external/lab-equipment/cold-traps' | relative_url }}">Cold traps: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/cryostorage' | relative_url }}">Cryostorage: utilization</a></li>
+			<li><a href="{{ 'external/lab-equipment/dishwasher-utilization-and-maintenance' | relative_url }}">Dishwasher: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/electric-car' | relative_url }}">Electric Car</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers' | relative_url }}">-20°C Freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers-80' | relative_url }}">-80°C freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/freezers-150' | relative_url }}">-150°C freezers: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/fridges' | relative_url }}">Fridges: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/hoods' | relative_url }}">Hoods: Laminar Flow - Fume Hood - Biosafety Cabinet</a></li>
+			<li><a href="{{ 'external/lab-equipment/incubators' | relative_url }}">Incubators: maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/lightcycler' | relative_url }}">LightCycler: leave the virtual instrument mode</a></li>
+			<li><a href="{{ 'external/lab-equipment/pH-meter' | relative_url }}">pH meter: utilization and maintenance</a></li>
+			<li><a href="{{ 'external/lab-equipment/power-consumption' | relative_url }}">Power consumption of the equipment</a></li>
+
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="lab-good-practice-card">
+		<h3>Lab: Good Practice</h3>
+		<ul>
+			<li><a href="{{ 'external/lab-good-practice/mycoplasma' | relative_url }}">Mycoplasma contamination check</a></li>
 
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="lab-hsa-card">
 		<h3>Lab: Health & Safety, Access</h3>
 		<ul>
-			<li><a href="{{ 'external/lab-hsa/diphoterine' | relative_url }}">Usage of Diphoterine</a></li>
+			<li><a href="{{ 'external/lab-hsa/diphoterine' | relative_url }}">Diphoterine: utilization</a></li>
 			<li><a href="{{ 'external/lab-hsa/handwashing' | relative_url }}">Handwashing</a></li>
 			<li><a href="{{ 'external/lab-hsa/lab-coats' | relative_url }}">Lab coats</a></li>
 			<li><a href="{{ 'external/lab-hsa/personal-alert-safety-system' | relative_url }}">Personal alert safety system (PASS)</a></li>
 			<li><a href="{{ 'external/lab-hsa/pictograms' | relative_url }}">Pictograms</a></li>
+			<li><a href="{{ 'external/lab-hsa/ppe' | relative_url }}">Personal Protective Equipment (PPE)</a></li>
 			<li><a href="{{ 'external/lab-hsa/shipment' | relative_url }}">Shipment of biological or chemical samples with carrier</a></li>
 			<li><a href="{{ 'external/lab-hsa/spill' | relative_url }}">Spill in a laboratory</a></li>
-			<li><a href="{{ 'external/lab-hsa/spill-bsc' | relative_url }}">How to deal with a spill in a BSC</a></li>
-			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Chemical and Biological Waste Management</a></li>
+			<li><a href="{{ 'external/lab-hsa/spill-bsc' | relative_url }}">Spill in a Biosafety Cabinet</a></li>
+			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Waste Management: Chemical and Biological waste</a></li>
 
 		</ul>
 	</div>
 	<div class="index-box noborderbox" id="lab-quarks-card">
 		<h3>Lab: Quarks</h3>
 		<ul>
-			<li><a href="{{ 'external/lab-quarks/book-lab-equipment' | relative_url }}">How to book a Lab Equipment in Quarks</a></li>
-			<li><a href="{{ 'external/lab-quarks/quarks-general' | relative_url }}">Quarks - General information</a></li>
+			<li><a href="{{ 'external/lab-quarks/book-lab-equipment' | relative_url }}">Booking of a Lab Equipment</a></li>
+			<li><a href="{{ 'external/lab-quarks/general' | relative_url }}">General information on Quarks</a></li>
 
 		</ul>
 	</div>

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

@@ -32,7 +32,7 @@ This serves for internal authentication for resources provided by the LCSB, e.g.
 
 ## Requesting LUMS account as external collaborator, UL members or  UL student
 
-* In case you are not a member of LCSB/DLSM, please ask your collaborator at LSCB/DLSM to request the account for you. You will need to provide an institutional email address. 
+* In case you are not a member of LCSB/DLSM, please ask your collaborator at LCSB/DLSM to request the account for you. You will need to provide an institutional email address. 
 * Once the account is created, you will receive an email with your new LUMS account details and how to access services and VMS.
 
 ## Requesting LUMS account for externals collaborators, UL members or UL students 

external/access/vpn-access/vpn-access.md

+---
+card_order: 400
+layout: page
+permalink: /external/access/vpn-access/
+shortcut: access:vpn-access
+redirect_from:
+  - /cards/access:vpn-access
+  - /external/cards/access:vpn-access
+  - /access/vpn-access
+  - /external/external/access/vpn-access/
+---
+# VPN connection
+
+VPN is used to access the servers that are hosted at the LCSB, but are not reachable "externally" from the internet, such as the [pre-publication check page](https://publications.lcsb.uni.lu) and the internal version of the [How-To cards](https://howto.lcsb.uni.lu). VPN uses the same user login information as the university active directory account (i.e., the same as used for Fiori, ServiceNow and Outlook e-mail), and is available automatically for all employees.
+
+
+## Download and start the VPN
+
+Once you have reset your VPN Password, please download VPN client from [vpn.uni.lu](https://vpn.uni.lu/).
+
+**ENTER**
+
+1. Username - firstname.lastname
+2. Password - Password you have set for VPN
+
+**Note**- If firstname.lastname does not work, give a try with firstname.lastname@uni.lu
+<img src="img/vpn-download.png" height="300px"><br/>
+
+Then depending on your distribution of OS, it will suggest you a link to download.
+<img src="img/vpn-download-01.png" height="300px"><br/>
+
+
+## Troubleshooting
+
+Despite establishing the VPN connection, if you still cannot reach the internal websites and How-to cards, please make sure that you **do not use a custom DNS configuration**. The DNS configuration can be displayed under the **privacy and security options of your browser** or the **network settings of your operating system**.
+
+<img src="img/dns-settings.png" height="300px"><br/>

external/access/vpn-cerbere-access/vpn-cerbere-access.md

 ---
-card_order: 400
+card_order: 420
 layout: page
 permalink: /external/access/vpn-cerbere-access/
 shortcut: access:vpn-cerbere-access
@@ -9,48 +9,10 @@ redirect_from:
   - /access/vpn-cerbere-access
   - /external/external/access/vpn-cerbere-access/
 ---
-# VPN/CERBERE connection
 
-In addition to the LCSB account, external collaborators are provided with VPN account so that they can access the servers that are hosted at the LCSB.
+# Connect to Cerbere via VPN
 
-## VPN Temporary Password Reset
-
-1. To reset temporary VPN password please visit [PasswordReset](https://passwordreset.uni.lu)
-
-    <img src="img/password-reset-vpn.png" height="300px"><br/>
-
-2. Click on **Change password**
-
-3. Enter
-
-   * Username - firstname.lastname
-   * Password - Temporary password provided by Sysadmins for VPN
-
-   <img src="img/password-reset-vpn-01.png" height="300px"><br/>
-
-   * Click **Next**
-   * Enter the new password that you want to use.
-
-   <img src="img/password-reset-vpn-02.png" height="300px"><br/>
-
-## Download VPN
-
-Once you have reset your VPN Password, please download VPN client from [VPN](https://vpn.uni.lu/)
-
-**ENTER**
-
-1. Username - firstname.lastname
-2. Password - Password you have set for VPN
-
-**Note**- If firstname.lastname does not work, give a try with firstname.lastname@uni.lu
-<img src="img/vpn-download.png" height="300px"><br/>
-
-Then depending on your distribution of OS, it will suggest you a link to download.
-<img src="img/vpn-download-01.png" height="300px"><br/>
-
-## Connect to Cerbere via VPN
-
-1. Launch the VPN client and enter
+1. [Launch the VPN client]({{ '/?access:vpn-access' | relative_url }}) and enter
 
    <img src="img/vpn-connect-01.png" height="300px"><br/>
 

external/backup/computer/computer.md

@@ -51,10 +51,3 @@ The steps to switch **File History** on your computer is as follows:
 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://uniluxembourg.sharepoint.com/sites/siu/Documents%20partages/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/markdown/markdown.md

@@ -10,7 +10,7 @@ redirect_from:
 ---
 # Markdown
 
-Markdown is a lightweight markup language with plain text formatting syntax which became very popular in past decade and which nowadays serves as a standard in various digital communication channels.
+[Markdown](https://daringfireball.net/projects/markdown/) is a lightweight markup language with plain text formatting syntax which became very popular in past decade and which nowadays serves as a standard in various digital communication channels.
 
 ## Main features of Markdown
 
@@ -22,15 +22,16 @@ Markdown is a lightweight markup language with plain text formatting syntax whic
 * It is portable - since it is actually plain text, it can be opened by literally all text editors.
 * It is machine readable - as simple text, markdown documents can be tracked and version using a versioning system (Git, SVN)
 * It has small file size.
-* It is easy to convert to other formats - existing editors and command line tools (e.g. [pandoc](https://pandoc.org/) allows for easy conversion between Markdown and other widely used formats like HTML, PDF, docx, LaTeX, etc.
+* It is easy to convert to other formats - existing editors and command line tools (e.g. [Pandoc](https://pandoc.org/) allows for easy conversion between Markdown and other widely used formats like HTML, PDF, docx, LaTeX, etc.
 
 ## Quick reference
 
 * The following symbol <img src="img/visual-code_img_9.png" height="20"> behind the file name means that your changes/writing is not saved. Press CTRL+S to save your procedure
 * To preview your writing click on:
+
   <img src="img/visual-code_img_10.png">
 
-## Tips to write in markdown:
+## Tips to write in Markdown:
 
 | Markdown                           | Rendered Output           |
 |:-----------------------------------|---------------------------|
@@ -61,7 +62,7 @@ Markdown is a lightweight markup language with plain text formatting syntax whic
 |:-----------------------------------|---------------------------|
 |: Include links referring to a web `[page](https://www.markdownguide.org/)`. Avoid links in format `<link>` as it is not always parsed correctly. | Include links referring to a web [page](https://www.markdownguide.org/). Avoid links in format <link> as it is not always parsed correctly (like in this case).
 |:-----------------------------------|---------------------------|
-|: Include local pictures using markdown |
+|: Include local pictures using Markdown |
 |: ^^<pre>![My awesome picture](img/r3_logo.png)</pre> | ^^ ![My awesome picture](img/r3_logo.png)
 |: Or use HTML tag allowing you to alter the image properties (e.g. size) |
 |: ^^<pre>&lt; img src="img/r3_logo.png" width="40" &gt;</pre> | ^^<img src="img/r3_logo.png" width="40">
@@ -83,10 +84,10 @@ Plain syntax is usually enough. But special requirements lead to development of
 
 Another big advantage of Markdown is that it can contain HTML tags, which makes formatting very flexible.
 
-## When to use markdown?
+## When to use Markdown?
 
 * **Documentation** - Markdown is a perfect solution for description of a data package, project folder, workflow or code repository. Using Markdown ensures that the description will be accessible to everyone even after decades while still nicely structured. Guide for writing a good README is not covered by this HowTo page but you can find plenty of resources online, e.g.:
-  * [guide](https://data.research.cornell.edu/content/readme) from Cornell University, UK
+  * [Guide](https://data.research.cornell.edu/content/readme) from Cornell University, UK
   * [GitHub page](https://github.com/mhucka/readmine) for READMEs in a software repository
 * **Blogging and tutorials** - structured document with chunks of code, pictures and results of the analyses can be easily converted to HTML format and posted on personal/team websites.
 * **Notes and meeting minutes** - you can use following template for simple and nicely structured meeting notes:

external/contribute/mirror-fork/mirror-fork.md

@@ -17,7 +17,7 @@ you should follow the follow simple steps.
 2. Expand the section on `Mirroring repositories`
 3. In the field `Git repository URL`, enter the SSH clone address from the main repository. 
 
- <img src="img/img1.png">
+    <img src="img/img1.png">
 
 4. Select `Mirror Direction` as `Pull`
 5. Click on `Detect Host Keys`
@@ -30,9 +30,10 @@ You will see an entry in the table below the blue button. Often, there is an err
 
     <img src="img/copy-ssh-key.png" height="80">
 
-2. Then, browse to your profile picture (top right) and click on `Preferences`
-3. On the left of the page, click on `SSH keys`
-4. Paste the key (using CTRL+V or CMD+V) into the SSH field
-5. Click on `Add key`
+2. Then, browse to your profile picture (top left corner) and click on `Preferences`
+3. On the left of the page, click on `SSH Keys`
+4. Click on the 'Add new key' button on the SSH keys table
+5. Paste the key (using CTRL+V on Windows or CMD+V on macOS) into the SSH key field
+6. Click on `Add key`
 
 Now, the synchronization of the fork should perform successfully. You can click on the sync button or wait a few minutes. :white_check_mark:

external/contribute/review/review.md

@@ -64,12 +64,14 @@ To have a more readable view, with the pictures integrated, click on the 3 dots
 
 - Make your comment on the comment section and click on **Start a review** or on **Add comment now**. Clicking on *"Start a review"* will allow you to compile several comments before an email is sent to the assignee when you will click on **Finish review**. Clicking on *"Add comment now"* will send an email to the assignee for every comment.
 
+Clicking on the first icon will allows you to directly suggest a change that the assignee will be able to accept or not.
+
 <div align="center">
-<img src="img/img7.png">
+<img src="img/img9.png">
 </div>
 
 <div align="center">
 <img src="img/img8.png">
 </div>
 
-When all the threads are resolved, you will be able to **Approve** the merge request and the repository maintenair can proceed with the merge.
+When all the threads are resolved, you will be able to **Approve** the merge request and the repository maintainer will be able to proceed with the merge.
\ No newline at end of file