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# Sensitive Data (SD) services user guide - Table of contents

!!! Note
    To select the correct user guide, begin by identifying the type of data you are processing:
    
    1. **Research data** (e.g. consented data collected for research purposes): follow the relevant guides for storing and analysing or publishing and reusing research data.
    
    2. **Secondary use of health and social data, register data** provided by the Findata authority or a public register: follow the guide designed for analyzing register data and comply with the Finnish legal requirements. 
    
    Not sure which guide fits your case or new to CSC's SD services? Email us at servicedesk@csc.fi with the subject line "SD Services"

## 1. Research data

### 1.1 Store and analyse research data

* [Start here: Creating a CSC project academic type](sd-store-and-analyze-research-data.md)
    * [Access as a project manager](sd-use-case-new-user-project-manager.md)
    * [Access as a project member](sd-use-case-new-user-project-member.md)
    * [Resource planning for your CSC Project](sd-billing-units.md)

#### 1.1.1 Store and share with SD Connect

* [Store and share with SD Connect](sd_connect.md)
    * [Login to SD Connect](sd-connect-login.md)
    * [Upload](sd-connect-upload.md)
    * [Share](sd-connect-share.md)
        * [Transfer data to another project](sd-connect-share-tranfer-data.md)
        * [Use folder as your shared workspace](sd-connect-share-workspace.md)
        * [Give access to folder content only in SD Desktop](sd-connect-share-read-to-sd-desktop.md)
    * [Download](sd-connect-download.md)
    * [Delete](sd-connect-delete.md)
    * [Command line interface](sd-connect-command-line-interface.md)
    * [Troubleshooting](sd-connect-troubleshooting.md)

#### 1.1.2 Analyze and compute with SD Desktop

* [Analyze and compute with Sensitive Data Desktop](sd_desktop.md)
    * [Login to SD Desktop](sd-desktop-login.md)
    * [Create virtual desktop](sd-desktop-create.md)
    * [Manage virtual desktop](sd-desktop-manage.md)
    * [Access virtual desktop](sd-desktop-access-vm.md)
    * [Working with your virtual desktop](sd-desktop-working.md)
    * [Customisation - software & tools](sd-desktop-software.md)
    * [Import data](sd-desktop-access.md)  
    * [Export data via user interface](sd-desktop-export.md)  
    * [Export data programmatically](sd-desktop-export-commandline.md)
    * [Troubleshooting](sd-desktop-troubleshooting.md)

### 1.2 Publish and reuse research data

#### 1.2.1 Publish with Fedarated EGA

* [Publish with Fedarated EGA](federatedega.md)
    * [Publish data](fega-submission.md)

#### 1.2.2 Reuse with SD Apply

* [Reuse with SD Apply](sd-apply.md)
    * [Apply access to FEGA data](sd-apply-access.md)
    * [Approve access to FEGA data](sd-apply-approval.md)
    * [Enable reuse of FEGA data](sd-apply-dac.md)

## 2 Secondary use of health and social data (register data)

### 2.1 Start here: Accessing secondary use health or social data via Sensitive Data services and a CSC project Findata type

* [Start here: Accessing secondary use health or social data via Sensitive Data services](secondarydata-access.md)
    * [Access with Findata permit](findata-permit.md)
    * [Access with register permit](single-register-permit.md)

### 2.2 Analyze with SD Desktop for secondary use

* [Analyze with SD Desktop for secondary use ](sd-desktop-audited.md)
    * [Login to SD Desktop](sd-desktop-secondary-login.md)
    * [Create virtual desktop](sd-desktop-secondary-create.md)
    * [Manage virtual desktop](sd-desktop-secondary-manage.md)
    * [Access virtual desktop](sd-desktop-secondary-access-vm.md)
    * [Work with your desktop and software](sd-desktop-secondary-working.md)
    * [Import data](sd-desktop-secondary-access.md)  
    * [Export data](sd-desktop-secondary-export.md)  
    * [Troubleshooting](sd-desktop-secondary-troubleshooting.md)
 
### 3. Additional Resources

* [What's new with Sensitive Data services :material-arrow-right:](../../support/wn/data-new.md)
* [Frequently Asked Questions (FAQ) :material-arrow-right:](../../support/faq/index.md)
* [Useful terminology :material-arrow-right:](sd-terminology.md)
* [SD Services homepage on _research.csc.fi_ website :material-open-in-new:](https://research.csc.fi/sensitive-data-services-for-research/){ target=_blank }

## 4. Tutorials (advanced)

Please note: some of this tutorials require prior knowledge of SD services or advanced coding skills.

* [Adding missing Python libraries to Pythion in SD Desktop](./tutorials/sd-pythonlibs.md)
* [Adding RStudio and R libraries to SD Desktop](./tutorials/rstudio.md)
* [Auto-apptainer](./tutorials/auto-apptainer.md)
* [Backup for SD Desktop](./tutorials/backup_sd_desktop.md)
* [Decrypting all files in a directory](./tutorials/decrypt-directory.md)
* [Extending SD Desktop software environment with your own Apptainer containers](./creating_containers.md)
* [Install VS Code in SD Desktop](./tutorials/vscode.md)
* [Install Whisper in SD Desktop](./tutorials/whisper.md)
* [Whisper step by step tutorial](./tutorials/whisper-course.md)
* [Podman in SD Desktop](./tutorials/podman-in-sd-desktop.md)
* [Running temporary PostgreSQL database in SD Desktop](./tutorials/postgresql.md)
* [Using Allas storage service to receive sensitive research data](./sequencing_center_tutorial.md)

## 4. Misc
* [Useful terminology: services and technical aspects](sd-terminology.md)
* [SD Desktop: Cent0S7 migration to Ubuntu](./migration-to-ubuntu.md)
