Merge branch howto-cards:master into jt-data-transfer-owncloud-privatebin

generator @ 53a922a1

-Subproject commit d73c076d4d529517a1457fc4a7a09d8906b6a13c
+Subproject commit 53a922a13c4e8916c97599b5242493a47ea0a2e2

cards.md

@@ -67,11 +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/owncloud' | relative_url }}">Owncloud</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">
@@ -122,6 +124,13 @@ order: -1
 
 		</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>
@@ -134,7 +143,7 @@ order: -1
 			<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 }}">Spill in a Biosafety Cabinet</a></li>
-			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Chemical and Biological Waste Management</a></li>
+			<li><a href="{{ 'external/lab-hsa/waste' | relative_url }}">Waste Management: Chemical and Biological waste</a></li>
 
 		</ul>
 	</div>

external/exchange-channels/atlas-hpc/atlas-hpc.md

+---
+layout: page
+permalink: /external/integrity/transfer/atlas-hpc/
+shortcut: integrity:transfer:atlas-hpc
+redirect_from:
+  - /cards/integrity/transfer:atlas-hpc
+  - /external/integrity/transfer:atlas-hpc
+  - /integrity/transfer/atlas-hpc
+  - /external/external/integrity/transfer/atlas-hpc/
+---
+
+# Data transfer between Atlas and UL HPC Clusters
+A recommended storage pattern is to have the master copy of data on Atlas (project folder) and only store data on the UL HPC Clusters temporarily for the required practical duration of computational analysis. The derived data and results should hereafter be transferred back to Atlas. This How-to Card describes the different methods to transfer data between Atlas and the UL HPC Clusters. The three recommended methods to transfer data are:
+
+1. [Via laptop with ```scp``` or ```rsync```](#1. Via laptop using scp or rsync)
+2. [Via dedicated Virtual Machine (VM)](#2. Via dedicated Virtual Machine (VM) using rsync)
+3. [Via Large File Transfer (LFT)](#3. Via Large File Transfer (LFT)) 
+
+Please refer to the dedicated knowledge bases to see how to [connect to UL HPC Clusters](https://hpc-docs.uni.lu/connect/access/) and to [mount Atlas](https://service.uni.lu/sp?id=kb_article_view&sysparm_article=KB0010233). 
+
+<img src="img/data-transfer-flow.png">
+
+## 1. Via laptop using `scp` or `rsync`
+When using the UL laptop to transfer data between UL HPC Clusters and Atlas, you must [mount Atlas via smb on laptop](https://service.uni.lu/sp?id=kb_article_view&sysparm_article=KB0010233) before using `scp` and `rsync` for the transfer. While both commands ensure a secure transfer of data between the UL HPC Clusters and Atlas, `rsync` may be much faster for handling large amounts of small files (which are transferred very quickly in batches), and for selective incremental updates of large datasets (it is capable to automatically transferring only the changed files, thus saving time).
+* `scp`: transfers all files and directories.
+* `rsync`: transfers only the files which differ between the source and the destination.
+
+Please visit the [UL HPC documentation](https://hpc-docs.uni.lu/data/transfer/#data-transfer-tofromwithin-ul-hpc-clusters) to see how to use `rsync` and `scp`.
+
+## 2. Via dedicated Virtual Machine (VM) using rsync
+Data can be transferred via a dedicated VM, which can be requested via [ServiceNow](https://service.uni.lu/sp?id=sc_cat_item&table=sc_cat_item&sys_id=49956812db3fa010ca53454039961978). 
+Instead of transferring data between Atlas and UL HPC Clusters through the laptop as described above, the transfer will go through the dedicated VM. Once connected to the VM and mounted to Atlas, the ```rsync``` command can be used in the same way as described in the [UL HPC documentation](https://hpc-docs.uni.lu/data/transfer/#data-transfer-tofromwithin-ul-hpc-clusters). This method is recommended for **recurring transfers of very large datasets** that benefit from high-speed network connection between the VM and the HPC.
+
+
+**Note**: For larger transfers between Atlas and UL HPC Clusters, you may want to run the operations in background using `screen` or `tmux`. These prevent interruption of data transfer in cases when your `ssh` connection gets interrupted.
+
+## 3. Via Large File Transfer (LFT)
+An alternative solution is to use LFT for transferring data between Atlas and UL HPC Clusters. This method can reliably transfer large data volumes (typically several terabytes). However, LFT can only be used if the data is already on LFT (e.g., received from external collaborators). In this case, you can make a copy of the data and directly download it to the UL HPC Clusters for computational analysis. Note that a **master copy of the data must still be manually uploaded to Atlas** for internal archival.
+
+Please refer to the [dedicated How-to Card on LFT]({{'/?exchange-channels:lft' | relative_url }}) for detailed information.
+
+**Note**: In cases when the analysis data are not already received via LFT, we strongly recommend to use one of the other (simpler) methods instead.

external/integrity/encryption/file/encryption_file.md

@@ -83,20 +83,15 @@ In order to use turn on EFS for a folder:
 
 ## Cloud Platforms
 
-As per LCSB Policy, you should not store sensitive human data on commercial cloud services (e.g. Google Drive, Dropbox). However, there may be situations where commercial clouds are used:
+As per LCSB Policy, you should NOT store sensitive human data on commercial cloud services (e.g. Google Drive, Dropbox). However, there may be situations where commercial clouds are used:
 
-- There is a project/consortium level agreement to use external cloud storage,
-- You're working with sensitive data, and need to temporarily co-access it with research collaborators,
+- There is a project/consortium level agreement to use external cloud storage.
+- You're working with sensitive data, and need to temporarily co-access it with research collaborators.
 - You're working with non-sensitive data and using the cloud as a backup target.
 
 In such cases, you may use the following desktop tools to encrypt cloud folders.
 
-- [boxcryptor](https://www.boxcryptor.com/en/) (Paid). If you're holding sensitive LCSB research data  on commercial cloud (case 2 above), you must use Boxcryptor. Contact the LCSB IT  team to request a license.
-    - [Installation/Mac](http://bit.ly/BXC-MAC_INSTALLATION)
-    - [Installation/Windows](http://bit.ly/BXC-WINDOWS_INSTALLATION)
-    - [Sharing Folders](http://bit.ly/BXC-FILE_SHARING)
-    - [Encrypt Folder](http://bit.ly/BXC-FILE_ENCRYPTION)
-    - [Decrypt Folder](http://bit.ly/BXC-FILE_DECRYPTION)
+- [Cryptomator](https://cryptomator.org/). If you're holding sensitive LCSB research data on commercial cloud (case 2 above), you must use Cryptomator. Request a license via ServiceNow and visit the dedicated [How-to card on Cryptomator]({{ '?exchange-channels:cryptomator' | relative_url }}) for further information.
 
 - [Cyberduck](https://cyberduck.io/cryptomator/) (Free).
 

external/lab-equipment/biosafety-cabinets/biosafety-cabinets.md

@@ -41,10 +41,10 @@ If you are not sure a BSC is the right hood to use for your experiment, please c
 
 <div align="center">
 <img src="img/image1.jpeg">
-<img src="img/image2.jpg" width="161" high="190">
+<img src="img/image2.jpeg" width="161" high="190">
 </div>
 
--   Be aware that **UV-lights act only on surfaces exposed to them**, the surfaces in the shadow are not disinfected and a chemical disinfection is still necessary after a UV decontamination.
+-   Be aware that **UV-lights act only on surfaces exposed to them**, the surfaces in the shadow are not disinfected and a chemical disinfection is still necessary after a UV decontamination. UV lights are damaging plastic material and gives a false feeling of disinfection while not being 100% efficient. Because of this, we do not recommend the usage of UV lights and advise to prefer the usage of disinfectant.
 
 -   The BSC must be **decontaminated before and after each use**. The interior surfaces should be wiped with an appropriate disinfectant that would kill any microorganisms that could be found in the cabinet. 70% ethanol is not effective against yeast and fungi, you should **use Bacillol 30 foam or tissues**.
 
@@ -73,7 +73,7 @@ Corrosive chemicals such as bleach should be avoided, but if used, should be fol
 
 -   Control the cells in the **microscope** before starting to work to **detect contamination** in your cell culture (change in the medium color, cloudiness of the medium, cross-contamination with other cell lines, ...).
 
--   Set up workspace in a direction **from clean to dirty**.
+-  Plan your work : set up workspace in a direction **from clean to dirty**.
 
 <div align="center">
 <img src="img/image7.png">
@@ -82,8 +82,9 @@ Corrosive chemicals such as bleach should be avoided, but if used, should be fol
 -   **Never cover the front or rear grids** with any material, even temporarily.
 
 -   **Avoid movement of materials or excessive movement of hands and arms** through the front access opening during use. After entering, allow the cabinet to stabilize before resuming work.
+- Work inside the BSC at a minimum distance of 15cm from the sash opening.
 
--   Take care **not pass** with your hands **over open bottles, flasks or tip boxes**.
+-   Take care **not pass** with your hands **over open bottles, lids, flasks or tip boxes**.
 
 -   When you open a flask or a medium, you can place the **lid with the opening up or down** on the bench, but make sure you put it **outside your working area**, at the back of the BSC so you do not pass over it with your hands or arms.
 
@@ -93,6 +94,12 @@ Corrosive chemicals such as bleach should be avoided, but if used, should be fol
 
 -   When work is completed, clear the workspace and clean the space with Ethanol 70% or with Bacillol 30. Please refer to the [Chemical and Biological Waste Management]({{ '/?lab:waste' | relative_url }}).
 
+- **Switch OFf the BioSafety Cabinet**
+Lower the glass and turn off the main Key-Switch.
+
+<div align="center">
+<img src="img/image8.jpeg">
+</div>
 
 ## UV lights
 

external/lab-equipment/cold-traps/cold-traps.md

 ---
 layout: page
-permalink: /external/lab-equipment/cold-traps
+permalink: /external/lab-equipment/cold-traps/
 shortcut: lab:cold-traps
 redirect_from:
   - /cards/lab-equipment:maintenance_of_cold_traps
@@ -89,4 +89,4 @@ When necessary, the acid cartridge (LIMS ID: 10608) should be exchanged
 * Remove the cartridge and replace it with the new one  
 * Close back the container  
 * Place the old cartridge in the chemical hood for evaporation in a retention container  
-* 24 hours later, trash it in a blue bin UN3291  
\ No newline at end of file
+* 24 hours later, trash it in a blue bin UN3291

external/lab-good-practice/mycoplasma/mycoplasma.md

@@ -11,8 +11,7 @@ redirect_from:
   - /external/cards/lab:mycoplasma
 ---
 
-# Cell culture good practices: mycoplasma contamination check
-
+# Mycoplasma contamination check
 
 Mycoplasma is a genus of bacteria that belongs to the class Mollicutes. What sets mycoplasmas apart from many other bacteria is their lack of a cell wall. The absence of a rigid cell wall makes them resistant to certain antibiotics that target cell wall synthesis. Meaning that even if you have antibiotics in your cell culture media, you can have a mycoplasma contamination.
 

external/lab-hsa/spill/spill.md

@@ -19,7 +19,7 @@ During the emergency phase (first phase) you have to ensure your and your collea
 Prevent aggravation if possible (recap flasks, shut down power or heat source).
 
 In case somebody has been exposed to chemicals (skin or mucosa) rinse with **Diphoterine** as soon as possible.
-To know more about the usage of Diphoterine, consult the dedicated card <a href="{{ '/lab-hsa/diphoterine/' | relative_url }}">here</a>.
+To know more about the usage of Diphoterine, consult [the dedicated how-to card]({{ '/?lab:diphoterine' | relative_url }}).
 
 In case of contact with biological reagents, rinse with water for 15min. You can use the eye shower of the lab/corridor.
 

external/lab-hsa/waste/waste.md

@@ -11,7 +11,7 @@ redirect_from:
   - /external/cards/lab:waste
 ---
 
-# Chemical and Biological Waste Management
+# Waste Management: Chemical and Biological waste
 
 To ensure a clean and safe lab environment, it is essential to know how to discard the waste in a proper way. 
 Please follow the [Docebo Training](https://cdn5.dcbstatic.com/dcd/scormapi_v60/launcher_full.html?host=unisupport.docebosaas.com&id_user=13109&id_reference=297&scorm_version=1.2&id_resource=145&id_item=145&idscorm_organization=145&id_package=145&launch_type=fullscreen&id_course=42&player=hydra&autoplay_enabled=0&name=waste-management-concept&return_url=unisupport.docebosaas.com&as_json=1&auth_code=11a2729cf9428533597f378018d08c615064b379&use_sw=1&context=lms&rtl=false) and refer to the **Chemical and Biological Waste Management concept of the University**: