generator @ 53a922a1

-Subproject commit d73c076d4d529517a1457fc4a7a09d8906b6a13c
+Subproject commit 53a922a13c4e8916c97599b5242493a47ea0a2e2

.gitlab-ci.yml

@@ -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

@@ -57,6 +57,7 @@ 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>
@@ -66,10 +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">
@@ -89,52 +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

@@ -16,7 +16,7 @@ VPN is used to access the servers that are hosted at the LCSB, but are not reach
 
 ## Download and start the VPN
 
-Once you have reset your VPN Password, please download VPN client from [VPN](https://vpn.uni.lu/)
+Once you have reset your VPN Password, please download VPN client from [vpn.uni.lu](https://vpn.uni.lu/).
 
 **ENTER**
 
@@ -30,3 +30,8 @@ Then depending on your distribution of OS, it will suggest you a link to downloa
 <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/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

external/contribute/ssh-key-generation/ssh-key-generation.md

+---
+layout: page
+permalink: /external/contribute/ssh-key-generation/
+shortcut: contribute:ssh-key-generation
+redirect_from:
+  - /cards/contribute:ssh-key-generation
+  - /external/cards/contribute:ssh-key-generation
+  - /contribute/ssh-key-generation
+  - /external/external/contribute/ssh-key-generation/
+---
+
+# Key-based Authentication on GitLab
+
+Key-based authentication allows GitLab users to identify their device once on their account and avoid having to log in via their credentials every time. GitLab uses SSH protocol to communicate with Git.
+
+SSH uses a public and a private key:
+- The public key must be registered in GitLab, where it "identifies" your device.
+- The private key must stay secret and preferably you should only keep it on a single device. The private key is the only key that can be used to authenticate your identity against the public key uploaded to GitLab -- if it becomes public, anyone can impersonate your identity and thus use your GitLab account. **Make sure you do NOT upload the private key anywhere by accident, not even to GitLab.**
+
+# Prerequisites
+
+To use SSH, one of the following must be installed on your device:
+
+- The OpenSSH client, which comes pre-installed on GNU/Linux, macOS, and [Windows 10 via Powershell or WSL](https://docs.gitlab.com/ee/user/ssh.html#use-ssh-on-microsoft-windows).
+- SSH version 6.5 or later. Earlier versions used an MD5 signature, which is not secure.
+
+To view the version of SSH installed on your system, run the following command in your terminal (on Linux or macOS) or Git Bash (on Windows):
+
+```
+ssh -V
+```
+
+# Key Generation
+
+> :warning: Please note that the steps below describe SSH key generation. If you already have one, **your existing key may be overwritten.**
+
+1. Start a terminal
+
+2. Type the following command at the command prompt and run it after replacing your firstname and lastname:
+  ```
+  ssh-keygen -t ed25519 -C firstname.lastname@uni.lu
+  ```
+3. Accept the suggested filename and directory
+
+4. Press `Enter` to continue. Defining a password is not necessary and can be skipped. 
+
+5. To copy the contents of your public key file into the clipboard, run the following command:
+
+    - For macOS:
+    ```
+    tr -d '\n' < ~/.ssh/id_ed25519.pub | pbcopy
+    ```
+    - For Windows:
+    ```
+    cat ~/.ssh/id_ed25519.pub | clip
+    ```
+
+# Saving the SSH Key on GitLab
+
+Once the content of the public key is copied in the clipboard, you need to register it with your GitLab account.
+
+To save your key to your account:
+
+1. Log in to GitLab using your LUMS account
+
+2. Navigate to the `Preferences` menu
+
+    ![preferences](img/preferences.png)
+3. User settings will be displayed on the left-hand side menu. Click on the `SSH Keys` option
+
+    ![ssh-menu](img/ssh-menu.png)
+
+4. On the `SSH Keys` page, click on `Add new key` button to add your public key
+
+    ![new-key](img/new-key.png)
+
+5. Paste your new key into the `Key` box, name the key and save it by clicking the `Add key` button
+
+    ![key-details](img/key-details.png)
+
+# Troubleshooting
+
+Please refer to the [GitLab Docs](https://docs.gitlab.com/ee/user/ssh.html#troubleshooting) or [create a ticket](https://service.uni.lu/sp?id=sc_cat_item&table=sc_cat_item&sys_id=c1d98bacdb9cf810ca53454039961917) for further assistance regarding the key-based authentication.