Commit 2703086d authored by Laurent Heirendt's avatar Laurent Heirendt
Browse files

Merge branch 'develop' into 'master'

[release] Regular merge of develop

See merge request !305
parents 703e2132 0fe8cc11
Pipeline #46444 passed with stages
in 3 minutes and 22 seconds
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---
# 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
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# 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.
\ No newline at end of file
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
......@@ -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)
......@@ -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
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......@@ -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`).
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......@@ -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**
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......@@ -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) -
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# Belval Campus Map
![](img/BelvalCampusMap.png)
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# 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)
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# 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|
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# 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).|
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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
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# 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
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......@@ -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
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# 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
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# 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:
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