Merge branch 'develop' into 'master'

[release] Regular merge of develop

See merge request R3/howto-cards!250

.gitattributes

 *.png filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text
+*.mp4 filter=lfs diff=lfs merge=lfs -text

Gemfile

@@ -45,4 +45,4 @@ gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
 # Performance-booster for watching directories on Windows
 gem "wdm", "~> 0.1.1" if Gem.win_platform?
 
-gem 'jekyll-spaceship', "0.6.0"
+gem 'jekyll-spaceship', "0.9.9"

cards.md

@@ -79,6 +79,20 @@ order: -1
 			<li><a href="external/integrity/encryption/file">Encrypting Files and Folders</a></li>
 			<li><a href="external/integrity/naming">Naming files</a></li>
 			<li><a href="external/integrity/organization">Organization</a></li>
+			<li><a href="external/integrity/spreadsheets">Working with spreadsheets</a></li>
+
+		</ul>
+	</div>
+	<div class="index-box noborderbox" id="lab">
+		<h3>Lab</h3>
+		<ul>
+			<li><a href="external/lab/book-lab-equipment">How to book a Lab Equipment in Quarks</a></li>
+			<li><a href="external/lab/dishwasher-utilization-and-maintenance">Dishwasher utilization and maintenance</a></li>
+			<li><a href="external/lab/handwashing">Handwashing</a></li>
+			<li><a href="external/lab/maintenance_of_cold_traps">Maintenance of cold traps  </a></li>
+			<li><a href="external/lab/personal-alert-safety-system">Personal alert safety system (PASS)</a></li>
+			<li><a href="external/lab/utilization-of-balances">Utilization of balances</a></li>
+			<li><a href="external/lab/utilization-of-pH-meter">Utilization of pH meter</a></li>
 
 		</ul>
 	</div>

external/integrity/encryption/cloud/cloud.md

@@ -9,6 +9,52 @@ redirect_from:
 
 # Data upload to cloud
 
-Data encryption and hash-check for uploading to UL-LCSB onedrive or owncloud
+Data encryption and hash-check for uploading to UL-LCSB onedrive or owncloud from Windows.
 
-[Windows](https://git-r3lab.uni.lu/transmed/support/data-upload-to-cloud/-/wikis/Upload-data-from-Windows)
+| Requirements | Restrictions |
+| ------ | ------ |
+| Windows 8 or newer (recommended Windows 10) | Recommended for data size less than 100 GB |
+| RAM 2GB (recommended 4GB) | If transfer through Aspera is not possible |
+| Enough free disc space (data will be duplicated for encryption) | Larger data will take more time to encrypt |
+| Administrative rights to install software |  |
+| Web browser (Firefox, Edge or Chrome) |  |
+
+## Install `7zip` for encryption
+
+Download and install `7zip` from [here](https://www.7-zip.org/)
+
+## Install tool for MD5 checksum calculation
+
+1. Search Microsoft Store for `Simple Checksum Calculator` or go to this [link](https://www.microsoft.com/en-us/p/simple-checksum-calculator/9nblggh5l6t9?activetab=pivot:overviewtab)
+2. Install `Simple Checksum Calculator`
+
+
+## Encrypt your data with `7zip`
+
+1. Right click on the folder to encrypt > 7zip > Add to archive
+2. Select following values:
+   - Archive format: `zip`
+   - Compression: `store`
+   - Check `Show Password` box
+   - Encryption: `AES256`
+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)
+
+## Calculate the MD5 checksum with `Simple Checksum Calculator`
+
+1. Open `Simple Checksum Calculator` from the start-menu
+2. Select `File` tab from the top menu
+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)
+
+## Data upload
+
+1. Open the `OneDrive` or `ownCloud` URL link that you have received from UL-LCSB contact
+2. Upload the encrypted zip file
+3. After the upload completion, open [UNILU privatebin](https://hpc.uni.lu/privatebin/)
+4. Paste the **encryption password :key:** and **MD5 checksum :label:** in the Editor box and press send
+5. Copy the privatebin URL and send it your UL-LCSB contact through email
\ No newline at end of file

external/integrity/spreadsheets/spreadsheets.md

+---
+layout: page
+permalink: /external/integrity/spreadsheets/
+shortcut: integrity:spreadsheets
+redirect_from:
+  - /cards/integrity:spreadsheets
+  - /external/cards/integrity:spreadsheets
+---
+
+# Working with spreadsheets
+
+Spreadsheets are widely used tools for tabular data manipulation facilitating data input and allowing simple formatting, validation and visualization.
+
+This card describes tabular data format, common mistakes made in spreadsheets and how to use your spreadsheet application effectively while increasing re-usability, quality and accuracy of your data.
+
+## What is a table (tabular data format)?
+
+Data in tabular format follow 3 key conditions:
+
+ 1. table contains a one-line header containing unique machine readable column names
+ 2. table has rows representing individual observations
+ 3. table has columns representing attributes/features of the observations and contain values of one data type
+
+| Table                           | Not a table           |
+|:-----------------------------------|---------------------------|
+|<img src="./img/excel_data-sheet.png" height=200> | <img src="./img/excel_analyses-sheet.jpeg" height=200>|
+
+## Tips and Tricks
+
+### Keep the original
+
+Changes in spreadsheets are not tracked. Any update or change should produce a new file labeled by version with changes described in change log.
+
+### Export data after collection
+
+For reproducibility purposes, the collected data should be always exported from proprietary (.xlsx, .xls, ...) format into non-proprietary format (.csv, .tsv, etc.) with minimal metadata in README file.
+
+### Cell
+
+- Use field validation - validation rules on columns ensure you have data checked automatically already on input.
+- Avoid non-exportable proprietary content - visual formatting (cell coloring / outlining), embedded comments and charts, merged cells, ...
+
+### 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 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.
+- Keep data in long format (sometimes referred to as narrow, gathered or melted format). All columns should be meaningful for all observations. If a new observation requires a new column to be created or if the observation's data ends up in just one cell instead of the whole row, your table is most probably **not** in long format.
+
+#### MS Excel Table tool
+
+MS Excel feature called **Table** (found in Insert->Table) allows to create real table object instead of just cell range. Its main advantages are:
+
+- Table formatting and column validation is expanded automatically with a new observation/record.
+- Each table object can be referenced by its name - no more (named) cell ranges and hard-to-read formulas.
+- Automatically adds filter buttons and subtotals.
+
+### Sheet
+
+- Keep one table per sheet or workbook.
+- Start your table in the first column (and preferably on the first row).
+- Do not insert any values next or below your table - add the content to a new column, new table, analyses sheet or file with metadata.
+- Keep metadata about the table in separate sheet in tabular format or separate file. If you must, keep metadata **above** the table itself.
+
+### Analyses
+
+- Keep data separate from the analyses - create a link to the data from sheets or workbooks containing the analyses.
+- Use pivot tables - if your data is in long format (it should be), it is very easy to create dynamic summary tables.
+- Use pivot charts - you can produce your desired auto-refreshing charts while having data still in long format.
+- Script more advanced analyses and data manipulation using standard tools for data processing (R, Python, Bash, ...).
+
+## Further reading
+
+Data Curation Network - [Microsoft Excel Data Curation Primer](https://github.com/DataCurationNetwork/data-primers/blob/master/Excel%20Data%20Curation%20Primer/Excel%20Data%20Curation%20Primer.md)
+
+Data Carpentry - [Spreadsheet ecology lesson](https://datacarpentry.org/spreadsheet-ecology-lesson/)
+
+Wikipedia - [Wide and narrow data](https://en.wikipedia.org/wiki/Wide_and_narrow_data)

external/lab/book-lab-equipment/book-lab-equipment.md

+---
+layout: page
+permalink: /external/lab/book-lab-equipment/
+shortcut: lab:book-lab-equipment
+redirect_from:
+  - /cards/lab:book-lab-equipment
+  - /external/cards/lab:book-lab-equipment
+---
+
+# How to book a Lab Equipment in Quarks
+
+To help the lab users to plan their work and to ensure that a lab equipment will be free to use, the Quarks software provides a booking tool. This booking tool is also used by the support team to indicate the maintenance periods, or if an equipment is not available due to a failure or a breakdown.
+
+ - [1. How to look for an instrument](#1-how-to-look-for-an-instrument)
+ - [2. How to know if an instrument is bookable](#2-how-to-know-if-an-instrument-is-bookable)
+ - [3. How to add an equipment to your Favorites list](#3-how-to-add-an-equipment-to-your-favorites-list)
+ - [4. How to book an instrument](#4-how-to-book-an-instrument)
+ - [5. How to edit or cancel a booking](#5-how-to-edit-or-cancel-a-booking)
+ - [6. How to book a lab (location)](#6-how-to-book-a-lab-(location))
+ - [7. How to access the booking history](#7-how-to-access-the-booking-history)
+ - [8. How to request booking configuration change or report an issue with Quarks?](#8-how-to-request-booking-configuration-change-or-report-an-issue-with-Quarks?)
+
+## 1. How to look for an instrument
+
+In your Quarks account, go on the _Equipment_ platform. In the _Equipment_ section, you have a search tool to help you find an equipment among all the LCSB equipment. You can search by internal reference number (e.g. LCSB01685), model, manufacturer or serial number in the “quick search” field.
+If you want to add more search criteria, you can do so in the drop down list “Add a filter”.
+
+![1](img/1.png)
+
+## 2. How to know if an instrument is bookable
+
+You can easily know if the instrument you are looking for is bookable or not thanks to the calendar symbol in the “Actions” column.
+
+![2](img/2.png)
+
+You can also see if the instrument is bookable or not on the side panel that will appear by clicking on the instrument itself, in the reservation section. Instrument that might be used for long experiment, possibly overnight, have the “24h bookable” option.
+
+![3](img/3.png)
+
+A bookable instrument will have a calendar icon available. Typically, only specific equipment or equipment that is usually used for long experiments is bookable.
+
+## 3. How to add an equipment to your Favorites list
+
+In the “Actions” tools, you have the option to add an instrument in your favorite list by clicking on the heart.
+
+![4](img/4.png)
+
+To have a direct access to your favorite equipment, go in “Equipment” – “My favorites”.
+
+![5](img/5.png)
+
+For your favorite equipment, you have the option to receive notifications by email. You will receive a notification if someone has edited or cancelled a booking just before yours, like in the example below. You can decide to activate this function for equipment heavily booked.
+
+![6](img/6.png)
+
+To receive the notifications, click on the edit icon and select Yes for the Notifications.
+
+![7](img/7.png)
+
+![8](img/8.png)
+
+You can directly see for which instrument you have the notifications activated by looking in the Notifications column.
+
+![9](img/9.png)
+
+## 4. How to book an instrument
+
+You have three ways to create a new booking.
+1.	You can book your instrument by clicking on its name, you will have in the right window a reservation section.
+
+    ![10](img/10.png)
+
+    ![11](img/11.png)
+
+    You can select the date and time of your booking and also create a recurrent booking in the Periodicity section.
+
+2.	You can also directly access the reservation window by clicking on the “Calendar” icon.
+    ![12](img/12.png)
+
+3.	The other way of making a new reservation is in the “Reservation” – “Agenda” section.
+
+    ![13](img/13.png)
+
+    In the “Type” field, select Equipment. You can filter the equipment either by your Favorites and/or by using the different Conditional criteria.
+
+    ![14](img/14.png)
+
+    In “Bookable item”, you can write the name of the equipment and you will have drop down list of corresponding equipment.
+
+    ![15](img/15.png)
+
+    After you select the date of the booking (steps 1 to 3), click on the raw of your equipment. The “New reservation” side panel will open on the right. You can now create your booking and set up a Periodicity if needed.
+
+    **Step 1**
+
+    ![16](img/16.png)
+
+    **Step 2**
+
+    ![17](img/17.png)
+
+    **Step 3**
+
+    ![18](img/18.png)
+
+    **Step 4**
+
+    ![19](img/19.png)
+    ![20](img/20.png)
+    ![21](img/21.png)
+
+    By Clicking on the name of the equipment, you can have a weekly overview of the bookings for this equipment. You can also create a booking from here, by clicking on the calendar.
+
+    ![22](img/22.png)
+
+## 5. How to edit or cancel a booking
+
+You can edit a booking by clicking on the time period. The right window will be displayed.
+
+![23](img/23.png)
+
+![24](img/24.png)
+
+Click on “Edit” and you will be able to change the date and time. If you click on “Cancel”, the entire booking will be cancelled.
+
+![25](img/25.png)
+
+You can also edit or cancel your booking in the “Reservations” – “ Reservation” section. Click on the equipment name and the right window with your booking information will be displayed.
+
+![26](img/26.png)
+
+![27](img/27.png)
+
+## 6. How to access the booking a lab (location)
+
+In some cases the equipment reservation is organized via lab booking. If you want to reserve a lab please select under Reservations “Locations” instead of “Equipment” as Type. The further way of proceeding is similar to described above for Equipment reservations.
+
+![29](img/29.png)
+
+
+## 7. How to access the booking history
+
+You can have an overview of all the bookings in the “Reservations” – “Reservations” section. You can filter them by date, type (Location or Equipment), name (Bookable item) and person who have made the booking (Reserved by).
+
+![28](img/28.png)
+
+
+## 8. How to request booking configuration change or report an issue with Quarks?
+
+If you wish to make one equipment bookable or make it 24 hours bookable [please send a ticket](https://service.uni.lu/sp?id=sc_cat_item_lsmc&sys_id=1dac368d54be72000a5374545c1c6a62&business_service_id=014ebe3ddb6a14148bcbf9b41d96195e&action_id=ec38cb7ddbaa14148bcbf9b41d9619a3). 
+
+For all issues related to Quarks [please send a ticket](https://service.uni.lu/sp?id=bs_dep_catalog_entry&sys_id=0840cf71dbaa14148bcbf9b41d9619cb).
+