Kapseli user guide

On this page you’ll find simple instructions for ordering Kapseli, using it and verifying the anonymity of the results.

How to order Kapseli

1. Log in to our e-service (asiointi.findata.fi).
2. From the top menu select “Submit application”
3. Scroll down and select “Order or update of the Kapseli operating environment or the data storage service” from under Select a new application form from below and click “Fill in the application”.
4. Complete the application form
   • Enter your own name in the applicant field
   • After this, using the “Invite a member” button add all the persons and email addresses that need user rights to Kapseli
   • The invited persons will join using multi factor authentication
   • Complete the rest of the form
   • Please note, that R-Tools is not automatically installed in Kapseli. If you need R-Tools, indicate this in the additional information section of the form.
5. Finally, select Send application from the “Actions” section.

Instructions for using Kapseli

Kapseli’s user interface is very much in line with the desktop of your own computer, but Kapseli’s desktop is at the end of a remote connection. Due to security regulations, there are a few differences in use of Kapseli compared to the use of an ordinary desktop.

• There is no internet access from Kapseli. Although the browser is installed, you can only use it locally for example to open documents in the HTML format.
• Copying data between the remote desktop and your own computer is blocked.
• It’s not allowed to take any photo of Kapseli.
• You can not transfer data, images or other material independently to Kapseli. All data is transferred through Findata’s audits.

The IP address you use with Kapseli must be static, i.e. most often your organization’s IP address. In general, when working remotely, the IP address of your own organization can be accessed via a remote connection, such as a VPN connection.

If there is change in the organization’s connections, ask your organization’s IT support about the entire address space of IP addresses, so that the change does not hinder the use of Kapseli. Kapseli cannot be used via private IP addresses.

Logging in Kapseli

Before logging in make sure your account has been registered and is ready to use. If you’re not sure whether your account is ready to use get in touch with Findata’s contact person.

1. Install Duo Mobile app (duo.com) to your phone and activate it. The developer is Duo Security Inc. If you’ve already installed and activated the app go to point 2.
   • Installing: find Duo Mobile from your phones app store and install it.
   • Activating: the phone numbers reported when ordering Kapseli will get an automatic activating message for Duo Mobile. The app is activated by clicking the link in the activating message.
2. Log in Kapseli at kapseli.findata.fi using your computers browser.
   • Choose the identification method from the list that you chose while registering.
3. Choose the operating environment you’re going to use. If you have just one operating environment in use go to the next section.
   • After choosing the environment the system goes to the second phase of identification.
4. The second phase of identification.
   • Log in the operating environment.
   • You’ll get a notification about logging in to Duo Mobile. To approve the log in choose ‘Approve’ in Duo Mobile.

Data transfer and folder structure of Kapseli

All software installations and data transfers in Kapseli take place through orders and audits. No data can be independently exported to or imported out of Kapseli.

The data permit specifies the data for which a processing permit has been granted. We collect, link, pre-process and if necessary, pseudonymise or anonymise the data. Additional information needed for use of the data, such as publicly available statistical data, also requires an audit by Findata and a transfer of data to the Kapseli.

We request the materials from the controllers primarily in CSV format and deliver them to Kapseli in CSV format (semicolon as separator, UTF-8 encoding).

Folder structure:

• Data (D:)
• Backup (E:)
• CRAN (N:)
• Output (O:)
• Work (W:)

You can find the files specified in the data permit in the Data (D:) folder. The Data folder is write-protected. Other information supplied to Kapseli, such as any program codes, will also be moved to the Data folder after an audit.

Use the Work (W:) folder when you process and analyse the data. Copy the files you want to use from the Data folder to the Work folder.

The Output (O:) folder is intended for data transfer. The data from this folder is transferred to Findata’s system to be audited. Note that the data to be transferred must be in anonymous format. This also concerns the program codes.

Export the data that you want to back up to the Backup (E:) folder.

The CRAN (N:) folder contains the software packages required for using the R software.

Exiting the system

There are two ways you can exit Kapseli:

• Sign out is located behind the human figure at the bottom left. Use this option when you have finished processing the data. When you exit from Sign out, you release the resources on the remote workstation.
• Disconnect is located behind the Power button. Use this option if you need to leave analyses running when you leave the workstation. The resources will then remain reserved.

After both options, you will see the options Reconnect and Logout. Select Logout when stopping the use of the system. Close your browser unless you want to log back in.

Software in Kapseli

All new Kapseli packages include the software according to the table below as standard. We will expand the software selection as needed.

For previously ordered Kapseli environments, software versions will be updated upon the subscriber’s request. If you are using an older version and wish to update to the one listed below, please arrange a scheduled update by sending an email to kapseli@findata.fi. Include the Kapseli ID (e.g., A01) and the software to be updated in your message.

Linux CentOS 7

Software	Version	Further information
Emacs		
Golang		
LibreOffice		Base, Calc, Draw, Impress, Math, Writer
Nextflow		
Pigz		
Python	3.7.9.	Includes the following packages: tensorflow nltk spacy scikit-learn seaborn plotly bokeh pydot xgboost lightgbm catboost eli5 torch keras dist-keras elephas gensim scrapy beautifulsoup4 numpy scipy pandas statsmodels matplotlib pyfuse3 crypt4gh trio httpx qrcode
R + R studio	4.2.1	Includes CRAN library packages. Please note that R-Tools is not automatically installed in Kapseli. If you need R-Tools, indicate this in the additional information of the subscription form.
VS Code

Windows Server 2016 Standard

Software	Version	Further information
7-Zip	23	
Adobe Acrobat Reader DC	Up to date	
Anaconda 3	2023.07	Uses Python Wheel 3.11
GeoDa	1.22	
Git	2.43.0	
Google Chrome	Up to date	
IBM SPSS Statistics	29	If the software license requires an update, notify kapseli@findata.fi.
LibreOffice	7.6	Base, Calc, Draw, Impress, Math, Writer
LyX	2.3	
MiKTeX	23.1	
Notepad++	8	
QGIS	3.32	
R	4.3	Includes CRAN library packages. Please note that R-Tools is not automatically installed in Kapseli. If you need R-Tools, indicate this in the additional information of the subscription form.
RStudio	2023.06.2+561	
SAS	9.4	If the software license requires an update, notify kapseli@findata.fi.
Stata	16	If the software license requires an update, notify kapseli@findata.fi.
WinPython	3.11	

If you need other software in addition to the standard software, it is possible to use them by additional order. Orders for additional software are made in connection with the Kapseli order or while using the Kapseli by updating the Kapseli order in the transaction service.

Orders for additional software

If you need additional software other than those available as standard, these can be provided by additional order.

You can order additional software when you fill the Kapseli order application. If you have a valid Kapseli subscription, you can order software by updating your Kapseli order in our e-service.

The additional software can be either access or licence based. If software requires a licence, you will be responsible for acquiring a licence for yourself. We will charge a fee of 86.00 euros/hour (+VAT 24%) for the installation of the user’s own tools/software to the Kapseli machine package.

Transferring own files to Kapseli

Kapseli functions as your project’s desktop throughout the processing of the data. In principle, the data is processed in Kapseli and only the final analysis results are brought outside the system. This applies also to the code needed for analysis, meaning that the code should be produced within the system.

In practice, however, an earlier program code is often used as an analysis framework. Earlier program code and other own files such as study protocol or descriptions of variables, can be imported into Kapseli through an audit by Findata.

See the instructions for further details from Data transfers to Findata -page.

Using the R program’s CRAN mirror repository

Enabling CRAN mirror repository on RStudio

Cran mirror repository can be found at cran.findata.local.

1. Remove .Renviron -file under your Documents -folder or Project folders (WORK). You
   may also edit file and remove following lines:
   RSTUDIO_DISABLE_PACKAGES=TRUE
   R_LIBS_USER=N:/
2. Create .Rprofile -file under your Documents -folder with lines below
   local({
   r <- getOption(“repos”)
   r[“CRAN”] <- “https://cran.findata.local/”
   options(repos = r)
   })
   • .Rprofile -file can also copied from D:\ -network drive (DATA).
3. Restart RStudio.
   • You can install R packages with install.packages(“PACKAGE”) -command.
   • If you prefer a graphical user interface to install packages, in RStudio you will find it at Tools -> Install Package. After a package is installed, use the library() function to load package.

Verifying of the anonymity of results

All those who process personal data must provide the results of their analyses in an anonymous form that cannot be used to reveal any data or aspects concerning individual participants following the instructions given by Findata. According to the Act on the Secondary Use of Health and Social Data, Findata must ensure anonymity. This applies to all materials that have been authorised under said Act.

Anonymisation refers to a process in which the material is processed in a way that

• it cannot be used to identify any individual persons either directly or indirectly
• it cannot be used to make any conclusions concerning a specific individual person
• any information concerning a specific person cannot be linked to any other material

See also