Commit 2703086d authored by Laurent Heirendt's avatar Laurent Heirendt
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Merge branch 'develop' into 'master'

[release] Regular merge of develop

See merge request !305
parents 703e2132 0fe8cc11
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......@@ -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
......
......@@ -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
......
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- /cards/integrity:sanitisation
- /external/cards/integrity:sanitisation
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# 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/).
......@@ -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.
......
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# 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).
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# 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-->
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# 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!**
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