Working with your desktop: tips and essentials

Once a virtual desktop has been created, each CSC project member can access it through their browser. When you log in, you will enter a virtual computer running on a Linux operating system. If you are new to Linux, it might feel a little different from other systems like Windows or macOS. No technical experience is required to work with it, but while Windows is designed to be user-friendly from the start, Linux can have a learning curve, especially if you need to use the command line.

The guide below provides instructions to help you get comfortable with both Linux and the SD Desktop’s security setup:

Introduction to Linux

Linux is an open-source operating system, meaning it’s free to use, and its code is openly available for people to view and modify. It's commonly used in many research applications due to its stability, security, and flexibility.

Look and feel: Linux may look slightly different from Windows, depending on the “desktop environment” used. But don’t worry – it still has familiar elements like windows folders and menus. You will find the main menu at the top left corner, where you can access all available software.
File structure: Instead of “My Documents” or drives labeled C: or D:, Linux has a different way of organizing files. The main directory starts with /, and you’ll see folders like /home for your personal files.
Benefits: Linux is very stable and less likely to crash, making it ideal for long or intensive computing tasks.

SD Desktop is a secure environment designed specifically for analysing sensitive data and the services has certain features that may work differently than a regular computer. For each of these features, a specific step-by-step guide is available below. If you are using the service for the first time, reviewing these guides will help you become familiar with how everything works.

Isolated from the internet: your virtual desktop is completely isolated from the internet. This means that although you can open a web browser like Firefox, you will not be able to access websites or online repositories directly. This feature helps keep your data safe by reducing the risk of online threats.
Encrypted file only: Only encrypted files are accessible from your virtual desktop. All files exported from the virtual desktop also need to be encrypted. This adds an extra layer of protection for your data.
Controlled file access with Data Gateway: The import of data and software is restricted in SD Desktop. You cannot import any data or software yourself for security reasons. If you are working with a dataset for which you have received a permit from a data controller, the only way to access the data for analysis is by utilizing a specific application called Data Gateway and imported only via SD Apply.
Data export from SD Desktop is restricted. Only non-sensitive results can be exported from the workspace, and those can only be exported by the CSC specialists. Instructions for exporting your results are provided in the next section.
Limited storage space: The virtual desktop is designed primarily for data analysis and has limited storage space. To expand storage, you can add an external volume (such as an external hard drive) during the desktop setup. This external volume is accessible to all project members and also serves as a backup for imported data.
Open source software only: Only open-source software can be installed in the virtual desktop, as it does not currently support licensed or proprietary software. Installing additional software to the virtual desktop is limited. Always contact servicedesk@csc.fi about software needs before starting to work with the data.
Copy-paste restrictions: For security reasons, copy-pasting from your own computer to SD Desktop is limited. You can still transfer text with a few extra steps, as explained in the Instructions how to copy-paste. These restrictions ensure that no unauthorised data is copied or exported from the secure environment.
Shared file access for team members: Any files saved in the shared-directory or on the external volume can be accessed by other project members working in the virtual desktop, allowing safe collaboration.

Accessing the secure environment

1. Connecting to your desktop

After login, you will see all your virtual desktops listed at the front page, under All connections.
Select project (e.g. project_NNNNN) and click the plus-sign.
Now you can see all desktops that belongs to this project (desktopname-NNNNNNNNNN). Access virtual desktop by clicking the name.

When you open the connection, a virtual computing environment will open in your browser. If you are accessing the virtual desktop for the first time, you will see the panel getting started, from which you can, for example, adjust the screen resolution.

2. Disconnecting from the virtual desktop

In the workspace view, top right corner of the browser, select your username and log out.
In the new window, click on Home.
- This will close all applications and disconnect the work session. You can access the same desktop anytime after logging in to the services.
Reconnecting to an analysis session:

You can reconnect to a previous session only if the browser window is exactly the same size as when the original session was in use. This is typically only possible if you're using the SD Desktop in full-screen mode on the same machine. If the window size has changed, you will most likely be unable to reconnect to the old session.

    ![check the paragraph below](../sensitive-data/images/desktop/SD-Desktop-Frontpage.png)

Copy-paste from your laptop to virtual desktop

The copy-paste function from your computer/laptop to your virtual desktop is limited for security reasons. However it is possible to copy-paste text with Clipboard. Copy-paste works only in one direction: from your computer to virtual desktop.

Step by step

Go to virtual desktop and open the Clipboard with a key combination Ctrl+Alt+Shift and click Paste.
Activate the copy-paste function by selecting input method Text input (the Clipboard panel will close automatically after the selection).
Now you can copy text normally from your computer (Ctrl+C or mouse right click).
Paste the text inside your virtual desktop (Ctrl+V).

Note: Don't close Clipboard panel with Cntrl+Alt+Shift, this might disable the copy-paste function. Please note you have to activate the copy-paste function again every time you use your virtual desktop.

Appearance of the Clipboard (Guacamole tools) may vary a bit depending on browser and local operating system.

Default software available in SD Desktop

You can work with your virtual desktop like with a standard computer, accessing several pre-installed programs from the applications menu bar (top left corner). Examples include Open Office, image-viewing applications, video and audio players, Jupyter Notebooks etc. You can also open a terminal and use Linux from the command line.
For more information on accessing R-Studio, please check the paragraph below.
Below we list some of the most commonly used tools that are by default installed in the virtual desktop or available via request. The list is not complete and there are small differences between different desktop options. Installing additional software to the virtual desktop is limited. Always contact servicedesk@csc.fi about software needs before starting to work with the data.

Note

The virtual Desktop is isolated from the internet and importing of software is restricted, as required by the data permit authority. Thus, users cannot directly import software/scripts or other files on to their virtual Desktop when working with secondary use data. If you need a specific program that is not pre-installed, it is recommended to contact CSC Service Desk before applying for the data permit. This way, we can figure out if it is possible to customise your virtual desktop.

Category	Software
Office Tools	LibreOffice
Programming	Go Python 3 including 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 & RStudio	R / RStudio Server - Matching the r-env-singularity/4.0.5 module on Puhti (R 4.0.5 + RStudio Server 1.4.1106, Bioconductor 3.12) - 1000+ pre-installed R packages (versions available on Apr 20, 2021) - Intel® oneAPI Math Kernel Library (oneMKL) - GIS software (PROJ, GDAL, SAGA) - CUDA drivers - TensorFlow (used with R TensorFlow back-end) - R + RStudio Server versions matched with Puhti r-env-singularity module (R 4.0.5 + RStudio Server 1.4.1106, MRAN, Bioconductor 3.12)
Workflow Engines	- Nextflow - Snakemake
Software Containers	- Apptainer - Podman (Only in Ubuntu machines)
Scientific Software	- Plink 1.9 - Samtools 1.8 - Minimap2 2.26
Terminals & Interfaces	- Byobu (Only in Ubuntu machines.) - Jupyter

Software available via request

Available via request to servicedes@csc.fi (subject:sensitive data), only if no data has been yet imported to the virtual desktop.

Category	Tool
Statistics	RStudio 4.2.2 - R statistics tool with a graphical user interface and help tools for adding libraries. After installation, right-click the RStudio desktop icon and select: Allow launching.
	PSPP - Open Source alternative for SPSS statistics tool. After installation, right-click the PSPP desktop icon and select: Allow launching.
Imaging and Videos	Audacity - Sound editor. After installation, right-click the Audacity desktop icon and select: Allow launching.
	ELAN 6.7 - Annotation tool for audio and video recordings. After installation, right-click the ELAN desktop icon and select: Allow launching.
	OpenShot 3.1.1 - Video editor. This tool works only in Ubuntu 22-based virtual desktops. After installation, right-click the OpenShot desktop icon and select: Run as a program.
	Praat - Toolkit for speech and sound analysis.
	QuPath 0.4.2 - Software for bioimage analysis.
	Whisper - Automatic speech recognition.
Geosciences	QGIS 3.1.1 - A Free and Open Source Geographic Information System. QGIS at CSC servers
Biosciences	GATK - A genomic analysis toolkit focused on variant discovery.
	GCTA 1.94.1 - A tool for Genome-wide Complex Trait Analysis.
	GCTB 2.05b - Genome-wide Complex Trait Bayesian analysis.
	IGV 2.16.2 - Integrated Genomics Viewer. After installation, right-click the IGV desktop icon and select: Allow launching.
	MultiQC 1.10 - NGS Read quality checking tool.
	PRSice 2.0 - Polygenic Risk Score software for calculating, applying, evaluating, and plotting the results of polygenic risk scores (PRS) analyses.
	Regenie 3.3 - Program for whole genome regression modelling of large genome-wide association studies.
	Salmon 1.9.0 - Program to produce transcript-level quantification estimates from RNA-seq data. Salmon 1.9.0 at CSC servers
Miscellaneous	auto-apptainer - Tool to add command line applications using the Apptainer container library provided by CSC.
	add-python-lib - Help tool to add Python libraries.
	Backup tool - Help tool to automate backup and export in SD Desktop.
	OpenRefine - Data pre-prosessing and conversion tool for various data formats.
	VS Code 1.90.2 - Code editor. After installation, right-click the VS Code desktop icon and select: Allow launching.
	WEKA 3-8-6 - Data mining software.

Accessing RStudio

The computing environment i.e. virtual desktop (visible from your browser) is isolated from the internet. For example, you can open a Firefox web browser in your virtual desktop but not access any site online. At this moment, you will also not be able to access any repositories directly. To open R Studio for data analysis the following steps are required:

Open the terminal and launch RStudio with:
```
start-rstudio-server
```

This will return a URL and a service-specific password:

RStudio Server - Sensitive Data Desktop Edition
---------------------------------------------------------------------------------------
Copy/Paste this URL into Firefox:

http://localhost:8787/

-----------------------------------------------------------------------------------------
Enter these at the RStudio Server sign-in screen
----------------------------------------------------------------------------------------
Username: accountname  Password: Example23241232
----------------------------------------------------------------------------------------
To stop RStudio Server: Ctrl+C

Next:
- paste the URL in Firefox
- after a few seconds, you can input the username and password (service-specific) and access the server.

Note

Only files saved in the external volume are accessible to other project members using RStudio.