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SD Desktop (Sensitive Data Desktop)

Before you start

  • Independently of the login method used, you need a CSC username and password to import data into your Desktop computing environment. If you don't remember it, check how to reset it at Account: How to change password

  • All the project members belonging to a specific CSC project can access the same computing environment in SD Desktop. Currently, it is possible to launch 3 Desktops (or workspaces) for each CSC project. Each CSC project has its own virtual private computing environment and each computing environment is isolated from other CSC projects or CSC accounts, unless you authorize it.

  • It is the project manager's or group leader's responsibility to review frequently the list of members belonging to a project in MyCSC and verify who can access the data present in the project using SD Desktop or SD Connect. Remove the project members that do not need to have access to the data when their contribution is no longer needed.

  • SD Connect and SD Desktop have not yet been security audited. Because of that, users may not process any personal data granted for the purposes of the Act on the Secondary Use of Health and Social Data (552/2019) by Findata.

Login

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To access SD Desktop go to MyCSC and:

Login to SD Desktop is possible with user identity federation systems (Haka, Virtu and Elixir ID or with a CSC account at

https://sd-desktop.csc.fi

using any modern web browser.

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Launching a private Desktop

After launch, you can login into your Desktop from any modern internet browser. Each Desktop will be accessible all along the duration of your CSC project.

Each Desktop is CSC project specific. Thus, if you add colleagues/collaborators as project members in the same CSC project, they will be able to access the same Desktop. To edit the same files or datasets, you need to save them in the same shared folder.

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To launch your Desktop, in Homepage, click on Go To Launching Page :

  • select your CSC project

  • choose the operating system (for beta versions, only possible operating system is Linux CentOS 7)

  • optionally, you can name the Desktop (update: 1 September 2021).

  • optionally, you can extend the disk space clicking on add an external disk. You can add up to 200 GB. The default disk space is 80 GB. Note: you can extend the disk space only before launching the Desktop (update: 1 September 2021).

  • select the preferred computing environment (based on your needs) and click on Launch Desktop

The system will create a secure connection to your private computing environment. The process is completely automated and might take up to 30 minutes.

In SD Desktop (Open Beta) you can choose between four different Desktops :

Desktop Core Memory
(GiB)
Root
disk
(GB)
Correspondent Flavour Example usage Billing
Units
/h
Light computation 3 4 80 standard.medium testing the service 1.3
Small computation 6 15 80 standard.xlarge office software 5.2
Medium computation 8 30 80 standard.xxlarge running statistical or genome analysis 10.4
Heavy computation 8 168 80 hpc4.40core non-interactive programmatic computation 78

If you are not sure what is the best option for your needs/research, contact us at servicedesk@csc.fi (email subject: SD Desktop). Do not choose the Heavy computation option for simple computing or analysis, as it consumes a large amount of resources.

All the Desktop are provided with the same software. The complete and updated list can be found in the following paragraph: Pre-installed list of software.

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Screenshot_SD_Desktop_0109_launchingpage

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If the launch is successful, when you return to SD Desktop Homepage, you will be able to access the computing environment from:

  • Recent connections, clicking on the image of your Desktop

  • All connections if you click on + you can see all the connections associated with each project (e.g. project_NNNNN_NNNN). If you click on the connection ID you will also be able to access your computing environment.

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In the Desktop you will be able to access different applications from the menu bar on the page top left corner (e.g. Open Office, Jupter Notebook ). If you need to work on files or datasets with your colleagues, save them in the Shared-directory. The file will be visible and accessible to all the members of the same CSC project.

As previously mentioned, you can logout from your computing environment at any moment (in the workspace view, top right corner of the browser, select your username and log out). Logging out will disconnect the work session. You will always be able to access your Desktop again after logging in. Never use the lock or reboot buttons in SD Desktop as after that you will not be able to connect to the Desktop again.

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Screeshoot_SDDesktop_0109_wrokspace

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Accessing encrypted sensitive data within SD Desktop

This workflow is available only on Desktops launched after November 4th, 2021.

SD Access Filesystem is an application that allows you to access encrypted data stored in SD Connect from your Desktop. The encrypted files will be visible in read-only mode (similarly to opening a pdf file or streaming a YouTube video). This solution allows you to process large amounts of data without the need of storing any copy on your Desktop. If the files have been encrypted with CSC public encryption key, they will be automatically decrypted by the application.

Once you are logged into your Desktop you can access encrypted data stored in SD Connect by following these steps:

  • Open SD Access Filesystem (you can find the link to the application on your Desktop)

  • Insert your CSC credentials (username and password. Note: we disabled the copy/paste options for security reasons; thus you need to type in your password)

  • Click on ok. The application will create a new folder called Projects accessible from your desktop or from the terminal. Do not close or log out from SD Access Filesystem.

SD Connect Filesystem

  • From the Projects folder you can access subfolders named with your CSC project ID, from which you can visualize all the encrypted files stored in a specific bucket.

FIlesystem 2

  • If the files are encrypted with the CSC public encryption key you will be able to access their content in read-only mode. The current streaming speed can be up to 50 MB/s.

  • The Projects folder is available only when the SD Access Filesystem application is open. If you log out from the application, you will not be able to access the data stored in SD Connect, unless you previously made a full copy of it.

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If you need to edit the files/data:

  • access the files of interest in the Project folder using SD Access Filesystem
  • make a copy and save it in your home directory (the files will be visible only from your browser) or in the shared folder (in this case, the files will be accessible also by all the colleagues belonging to your CSC project).

For security reasons, your private workspace in SD Desktop is completely isolated from the Internet. If you need to visualize or import specific scripts into your Desktop (for example from GitHub or other trusted repositories) you can use the same procedure described above.

Importing encrypted sensitive data to SD Desktop

The SD Connect Downloader application will be available only till December 2021.

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Once you are logged in into your SD Desktop you can import encrypted sensitive data stored in SD Connect.

Note

If you use the CSC Sensitive Data Service public encryption key to encrypt the data, the files are automatically decrypted. If you use your own key pair to encrypt the data, the application will make a copy and you need to manually decrypt them using Crypt4GH CLI.

To import the data:

  • Open SD Connect Downloader client (you can find the link to the application on your Desktop)

  • insert your CSC credentials (username and password. Note: we disabled the copy/paste options for security reasons, thus you need to type in your password)

  • select your CSC project

  • select the correct bucket

  • select the files you want to import

  • click on download objects (the application will make a copy of the encrypted files in SD Desktop).

  • click on open download location

The files are downloaded to a directory called SDCONNECTDATA which is in the user's home directory. The folder is automatically opened by Open Download Location.

Note: If you used CSC Sensitive Data Service public encryption key to encrypt the data, the files are automatically decrypted .

If you used your own key pair to encrypt the data, the application will make a copy and you need to manuallay decrypt them using Crypt4GH CLI.

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For security reasons, your private workspace in SD Desktop is completely isolated from the Internet. If you need to import specific scripts in SD Desktop (for example from GitHub or other trusted repositories) you need to use the same procedure described before:

  • download your scripts from GitHub and save them in a specific bucket in SD Connect

  • access SD Desktop and use the SD Connect Downloader to make a copy of the scripts

RStudio in SD Desktop

To access RStudio in SD Desktop open the terminal in your virtual Desktop 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

Also when using RStudio, you need to save your data in Shared-directory if your colleagues need to work on the same files.

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Deleting your computing environment

At the end of your research or your analysis, you can delete your Desktop and all the data in it.

In SD Desktop Homepage click on Go to the launching page. Here, in Available instances click on Delete Desktop.

Note

All the data present in the computing environment will be deleted and it will not be possible to retrieve them.

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Screeshot_SDDesktop_0109_deletingvm

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Data export from SD Desktop

For security reasons, your Desktop is isolated from the internet and it is not possible to export data from the virtual computing environment.

For more information write to servicedesk@csc.fi (email subject SD Desktop)

Troubleshooting

Problem Possible solution
Access Launched a new Desktop, but now the screen is balck/freezed. The creation of a new Desktop can take up to 30 minutes. Come back later.
Cannot login to SD Desktop Create a CSC account and a project in the MyCSC portal. Add service access for Allas (a CSC storage solution) and SD Desktop to your project.
Cannot turn off my Desktop. You can log out from Desktop at any moment (in the workspace view, top right corner of the browser, select your username and log out). You will always be able to access your Desktop again after logging in. Never use the lock or reboot buttons in SD Desktop as after that you will not be able to connect the desktop again
Collaborative project My collaborator added me to their CSC project, but I cannot access SD Desktop. Accept the terms of use and add service access for SD Desktop in the MyCSC portal.
Me and my colleague are members of the same CSC project. I cannot see the data they have analysed/edited in our private Desktop. Save the files in the Shared directory, if you need to work on/edit files or datasets with your colleagues.
Cannot add more project members to the same Desktop. Your Desktop has too many simultaneous connections. Max 10 users can use the same Desktop at the same time. Furthermore, each individual user can have only one active connection to one Desktop. Remember to log out of the Desktop to end the active session.
Copy- Paste Function I cannot copy and paste my password or commands from outside the Desktop. We disabled the copy/paste options for security reasons, thus you need to type in everything manually. Alternatively, you can import documents or scripts to SD Connect and do the copy-paste process inside SD Desktop.
Data export Cannot export results. Currently, a user can not export any data out from the SD Desktop for security reasons. We are implementing a feature to SD Desktop for data export later this year. Check our webpage for more information.
Data Import The SD Connect Downloader client doesn’t work when I add my credentials. Use the username and password of your CSC account. Check that your project has service access for Allas (a CSC storage solution). Check that you haven’t changed your environment variables. Do not use passwords that contain @
I imported data from SD Connect with the Downloader client but the data isn't decrypted. If you want the data to be automatically decrypted in SD Desktop, you need to encrypt the files with a CSC Sensitive Data Services public key.
Need to import more than 80 GB of data. I already have an extra volume. SD Connect Downloader client saves a copy of the data in SDCONNECTDATA folder (which has a disk space limit of 80 GB). You can make a link to the added volume from your terminal: ls -s /path_to_volume_mount_point ~/SDCONNECTDATA
Disk space/ Volume Cannot add disk space to my Desktop. It’s possible to add disk space only when you are launching a new Desktop.
Cannot make a copy of a big dataset. Check that you have enough disk space on your Desktop. The maximum disk space of each Desktop is 280 GB.
Mac OS Mac keyboard is not recognized e.g. command+C is not translated to CTRL+C. You need to change the keyboard settings.
Software Cannot open RStudio on my Desktop. To access RStudio in SD Desktop, you need to open the terminal in your virtual Desktop and launch RStudio with start-rstudio-server.Check for more instructions above inthe user guide.
Need a software not provided in Desktop Contact us at servicedesk@csc.fi (subject SD Desktop)

Last edited Wed Jan 19 2022