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Best Practices for Client Side Encryption


The intended audience of this document is end users who want to store sensitive data in to CSC's data services for research.

Scientific research data may contain also sensitive data. There is no single simple definition of sensitive data but rather it is derived from national and EU legislations.1 The data controller – this means the customer, i.e. usually the research project or a researcher – is responsible for knowing if the data is sensitive or not and handling it appropriately. In case of using CSC's data services for research the question about sensitivity of the data must be resolved by the customer already before transferring the data to CSC's services, which acts as data processor that perovides storage and computing resources for the data controller.

Generic examples of use cases where CSC's services might be used with encrypted sensitive data are:

  • Using CSC sensitive data services for analysing data
  • Distributing sensitive research data to customer's partner organisations
  • Disaster recovery copy of customer's local sensitive research data
  • Sharing sensitive research data within a research group

Some use cases may not be applicable to all CSC's data services, please see the Terms and Conditions and Service Description of each service itself.

CSC provides a set of services that are intended to support management of sensitive data.  Currently these servises include:

  • SD Connect : A service for storing and sharing sensitive data
  • SD Desktop : A service for prosessing sensitive data

These services provide secure and easy to use tools and protocols that CSC recommends to be used for sensitive data. However, the you can store sensitive data to CSC also by using other tools too, as long as the processes follow the general guidelines described below.


Protecting data with encryption has been around for a long time and the basics of secure encryption are well understood. This document gives some best practises on how to encrypt the data once the customer has decided that encryption is an appropriate means to protect the data content.

There are two main encryption methods, symmetric and asymmetric encryption. In symmetric encryption, same key is used for encrypting and decrypting the data. In basic asymmetric encryption, there are two keys, a private key and a public key. Data encrypted with public key can be decrypted only with private key. For verifying the origin of data, the data (normally a hash of the data) signed with private key can be verified with public key.

In general use case to store data, straightforward symmetric encryption usually is good choice. In that general case, all who need access to the data content – for instance a research group – are equal, they all know the same symmetric key.

When the use case is more targeted to data distribution and has specific recipient(s) for the data, asymmetric encryption has advantages in key management. The data uploader could use recipient's asymmetric public key to encrypt, or actually encrypt the recipient specific symmetric key with it. The key management is more flexible with asymmetric encryption but the drawback is that there is a copy of the data for each recipient.


This document gives some best practises on how to encrypt data if storing it in to CSC's data services for research. The decision whether encryption is appropriate means to protect the data content against unwanted exposure is at the responsibility of the customer.

Customer's own environment is out of the scope of this document. As the sensitive data exists at the customer's own environment already before it will be stored (transferred) to CSC's data service, this document assumes that all the necessary safeguards at the customer side – policies, procedures, practises, etc. – are already in place.

Classified data, which requires separation by the service other than access control is out of the scope of this document.7

Computational processing of data is out of the scope of this document, as this document simply describes the best practises for storing sensitive data. You can access CSC's data services for research directly from your own environment just like from CSC's supercomputing environment, from the point of view of service there is no difference from where the data is transferred to it.

Risks of encryption

Using encryption to protect data reduces the risk to expose the data content to unwanted parties, but it also introduces some new risks which need to be considered. This chapter highlights the main two risks.

1. Losing your encryption keys – or to be more precise, key to decrypt the data – is equivalent to losing your data. If you still have your data files but don't have the decryption key anymore, you can't restore the actual data content. You need to plan how to manage your keys before you start to use data encryption, more details on this can be found in Key management.

2. Using poor encryption tools. Picking just some nice or reliable looking software to take care of encryption may well introduce a risk of exposing the data content. It may be unintentional like poor software engineering or weak algorithms in the software. It may also be intentional, a deliberate attack targeted to data which is considered important enough to be encrypted. See Standards and algorithms and Notes on specific software.

The SD Connect service mitigates these risks by applying automatically strong asymmetric encryption for the stored data. The service also adds a CSC hosted encryption key to the data. This can be used in cases where the users own encryption key is lost.

Best practises

Copying sensitive data from customer's own protected environment to CSC's data service requires protecting the data both in transit and at rest on CSC's data service.

Access to these services is protected in transit by encrypted traffic based on HTTPS/TLS.

From the customer's perspective, protecting data at rest on a remote service is best done by protecting it with client-side encryption and not exposing the encryption related keys to the storage service. Client-side encryption is a method where customer encrypts the data at customer's own environment before transferring it to the service. When using client-side encryption and not exposing the keys, the customer is the only party who controls exposing the content of the data.4 6 Even with this, it is good to remember that encryption should not be the only protection; storing securely at remote location should always be a layered approach with more than one measure, i.e. clear user roles and access control definitions, least privileges principle, etc.5

The data which is stored at CSC's data service should not be the only existing copy of the data.

Make sure you don't leak sensitive information in file or directory names. Either anonymise or randomise such names or create a package – for instance zip or tar – of the files/directories and then encrypt the whole package.

Standards and Algorithms

Symmetric encryption algorithm to use is AES (either in CBC or CTR mode, but never in ECB) with minimum key length of 256 bits, thus an AES-256 encryption.

AES-128 and AES-192 are also currently considered to be strong enough, but as performance penalty is rather small between those and AES-256, and with the fact that switching later to a stronger version of AES would mean re-encrypting all the data, it is better to start straight with AES-256.2 3

Asymmetric encryption algorithm to use is RSA and the minimum key length is 4096 bits.2 3

Symmetric encryption software usually gives an option to use a passphrase as a "user friendly key". The actual encryption key is then derived from this passphrase using a key derivation algorithm. The key derivation algorithm must also be strong enough, preferred ones are scrypt, bcrypt, or PBKDF2 (with high iteration count, for instance 100 000).2 8

Key management

Symmetric encryption software usually gives an option to use a password, or a passphrase as a "user friendly key". In those cases, the protection of your data is only as good as the encryption password is; encryption does not help if you use a weak or an easy to guess password. Guidance on how to create strong passwords can be found for instance in references.9

Leaking a symmetric or asymmetric decryption passphrase/key means you must encrypt the original content with a new passphrase/key, and replace all stored old passphrase/key encrypted data with the new encrypted data. This holds true also for asymmetric keys in data at rest, unlike other use cases where key revocation could be used.

Losing your symmetric data encryption passphrase/keys is equivalent to data loss. You, or your research project should have either a copy of data content locally available (in plain format or encrypted with some other key), or a method to recover the encryption keys to access the data content even if the original data encrypting party loses the passphrase/keys. Consult your local organisation where and how to save your encryption passphrase/keys securely for recovery purposes.

Data decryption passphrase/key information must be transferred securely between the encrypting party and the decrypting party. This is often referred to as Key Transport.

Asymmetric encryption is the easiest way to manage data encryption key transport with a large number of key holders, as public keys can be – as the name suggests – public and exchanged openly. There are also existing Public Key Infrastructures or "web of trusts" that can certify the origin of the public key. Being sure that a public key is the desired recipient's public key is essential as whoever holds the corresponding private key can decrypt data which is encrypted with the public key. In this kind of hybrid encryption systems, the symmetric data encryption key is encrypted with an asymmetric public key and then transported together with the encrypted data.

For a small group of parties also a face-to-face data decryption key transport can be an option.

Storing and retrieving encrypted data from the CSC's service can also be arranged at the customer's local environment so that the trusted local environment has a service that takes care of accessing the CSC's storage service on behalf of the end user. So, only that local trusted service needs to know the keys instead of the local end users.

There is unfortunately a bit too much flexibility in the ways different applications behave when encrypting files — not in the actual encryption per se, but for instance in how they store the metadata about selected encryption choices into the encrypted file or how to derive the key from a passphrase.

The easiest way to deal with this lack of interoperability is to decide and document what encryption software to use and how to use it in your project before you start storing encrypted data in to CSC's data services for research.

Notes on specific software


GnuPG version 2 is likely the most widely used good free of charge and open source suite of software for encrypted messaging. GnuPG 2.2 is compliant with the OpenPGP RFC4880 and can utilise asymmetric encryption with public keys for easier key exchange and transport. Selecting option --rfc4880 for maximum portability would select symmetric encryption algorithm to be 3DES which is not considered good enough anymore.

On command line the algorithm defaults can be seen with option --verbose. Starting with version 2.1 the default for symmetric encryption is AES128, for older versions it is CAST5. On command line AES256 encryption is selected with options --symmetric --cipher-algo AES256 which should be the symmetric algorithm to be used.

Example symmetric encryption run where file data.dat is encrypted:

gpg --symmetric --cipher-algo AES256 data.dat

That example command creates encrypted file data.dat.gpg.


openssl is more a toolkit for encryption related needs than a standalone application. It is anyway easy to use tool for symmetric encryption.

AES256 encryption is selected with options enc -aes-256-cbc. If you use password to generate the actual encryption key, then use only version 1.1.1 or later and with options -pbkdf2 -iter 100000. These same options must also be used when decrypting the data.

Example run with openssl 1.1.1 where file data.dat is encrypted to data.enc:

openssl enc -aes-256-cbc -pbkdf2 -iter 100000 -in data.dat -out data.enc
enter aes-256-cbc encryption password:
Verifying - enter aes-256-cbc encryption password:

If you choose to generate the actual random binary key and initialisation vector yourself then you can also use older versions than 1.1.1 of openssl.


Crypt4gt is an asymmetric encryption tool that is designed for encrypring large datasets. This tool is recommended by Global Alliance for Genomics and Health, and it is used as the encryption tool of CSC sensitive data services. More detailed description of this encryption tool can be found from the SD Connect instuctions.

Cyberduck (cryptomator)

Cyberduck includes an open source tool called cryptomator for client-side encryption. Cyberduck's strong point is its multiplatform GUI interface, drawback is so far short history as cryptography tool, compared to GnuPG or openssl.

To make managing encryption easy for the end user, the Cryptomator treats a remote directory as if it were a single encrypted structure (a vault), but it actually encrypts each file for its own. In addition to the content of files, file and directory names are encrypted.

  1. CSC Services for Research. Sensitive data 

  2. Kryptografiset vahvuusvaatimukset luottamuksellisuuden suojaamiseen – kansalliset suojaustasot[...]/ohje-kryptografiset-vahvuusvaatimukset-kansalliset-suojaustasot.pdf 

  3. NIST Special Publication 800-57 Part 1 Revision 4. Recommendation for Key Management. Part 1: General 

  4. Best practices for securing PaaS web and mobile applications using Azure Storage 

  5. Security Best Practices for Amazon S3 

  6. Security Guidance for Critical Areas of Focus in Cloud Computing v4.0 

  7. Katakri 2015 – Tietoturvallisuuden auditointityökalu viranomaisille 

  8. NIST Recommendation for Password-Based Key Derivation. Part 1: Storage Applications 

  9. 6 Techniques For Creating Strong Passwords 

Last update: March 16, 2023