FAQs

In 2017, the Swiss Confederation launched the BioMedIT network project, as integral part of SPHN. A project of SIB Swiss Institute of Bioinformatics, the secure and cutting-edge IT environment BioMedIT is established nationally to support computational, biomedical research and clinical bioinformatics, ensuring data privacy. Given the sensitive nature of health-related information, research using patient data imposes high demands on IT infrastructures and processes to fulfil the stringent legal and ethical requirements. The goal of SIB’s BioMedIT project is to build and maintain a secure and protected IT environment, providing researchers with access to a cutting edge research IT infrastructure for analysis of sensitive data, without compromising data privacy. BioMedIT is a national infrastructure resource that can jointly be used by all Swiss Universities, research institutions, hospitals and other interested partners.

You may find more information at https://biomedit.ch

The BioMedIT Network builds on three legally independent scientific IT competence platforms:

• sciCORE in Basel, operated by the University of Basel,
• Unil / SIB in Lausanne, operated in collaboration by SIB and Unil, and
• SIS in Zurich, operated by ETHZ.

Under the umbrella of the BioMedIT Network Project, all three engaged institutions committed to build a high performance computing infrastructure (in addition to their already existing scientific compute clusters) especially designed for sensitive (confidential) data for Personalized Health and data-driven research: sciCOREmed in Basel, SENSA (Secure sENSitive data processing plAtform) in Lausanne, and Leonhard Med in Zurich – the BioMedIT nodes.

Central infrastructure components (such as tools, platforms, etc.) and procedural solutions are under the responsibility of SIB’s PHI Group. PHI operates a central service layer and is responsible for the coordination of the BioMedIT Network Project.

A BioMedIT node is a local or regional node that provides a secure compute and storage infrastructure for handling (securely storing, managing and processing) sensitive research data, whether clear text, pseudonymized or coded personal data. They are the entry and exit points for data transfers between data providers and recipients. Each data provider is associated with a single node and all data from that provider passes through the node.

The node may be a destination node for projects hosted on the node or it may be a transfer node for projects hosted on another node.

More information about the Nodes including contact details may be found on https://biomedit.ch.

Access for almost all operations on the BioMedIT network is through the BioMedIT portal https://portal.dcc.sib.swiss. The BioMedIT website https://biomedit.ch provides additional details of all resources supported on BioMedIT.

The access to the BioMedIT Portal requires a SWITCH edu-ID protected by two factor authentication (2FA) with a validated email address from a Swiss university, hospital or other similar institution. Sending data from a Data Provider into the BioMedIT Network is covered in the FAQ sections Data Providers and Data Transfers.

Confidential data should stay confidential. Sending it to another person by attaching a file to an email or putting it on a USB stick is very risky. Data which is confidential should be encrypted and sent by secure means. BioMedIT has been set up to do just that. A Data Provider connects securely to a single contact point in the BioMedIT network (irrespective of the intended final destination of the data). From this contact point data can be securely routed anywhere inside the BioMedIT network to Universities, University Hospitals and other institutions in Switzerland. Encryption of data, secure transfer protocols, monitoring and logging of the transfer process, management of the keys used for encryption and decryption, and strict control of user access and rights on the network significantly enhance the security of the transfer of sensitive data.

A secure encryption and transfer tool, sett, has been developed to make the transfer process as easy as possible for all users of the BioMedIT network.

A pre-requisite for any data sent from a data provider into the BioMedIT network is that appropriate ethical and legal approvals exist for the data proposed to be sent. The question of compliance with the GDPR requirements must be settled at this stage if the data set will contain records from EU nationals. Similarly HIPAA requirements might need to be met if the data set will contain records from US nationals. If these ethical, legal and privacy considerations are met the remaining questions are mainly technical and administrative. The project staff should discuss with the DCC and relevant BioMedIT node how the data transfer and management process can best be handled.

Based on the Funding Principles and Funding Regulations, the Swiss Government allocated around CHF 18 million to BioMedIT for the first period 2017-2020. Funding continues for the second phase of the project which runs from 2021 until the end of 2024.

The project is under the responsibility of SIB Swiss Institute of Bioinformatics. The matching funds’ principle applies to all financial contributions, i.e. the participating institutions must provide their own contributions (in cash and/or in-kind) to match the funds provided by BioMedIT.

The BioMedIT website at https://biomedit.ch and the SPHN website contain detailed information about BioMedIT and its resources. The documentation contained here and in our DCC GIT WIKI provide more detail on specific aspects of BioMedIT.

You may visit the BioMedIT website at https://biomedit.ch or the SPHN website at https://sphn.ch.

For additional information write to dcc@sib.swiss.

For day to day operational issues or something specifically related to BioMedIT write a mail to biomedit@sib.swiss. A ticket will be opened with your request and you will be contacted by one of the BioMedIT support personnel.

A number of work instructions, user guides and the like are publicly available in this site and at https://biomedit.ch/.

The procedure for becoming a Data Provider to the BioMedIT network is described in detail in the document Onboarding of Data Providers. In summary there are two parts - administrative and technical. A prospective Data Provider will contact a BioMedIT node, DCC or a project and submit a request to DCC to be added as a new Data Provider. Technical (and possibly administrative) contact details will be provided. The technical contact will provide details about the data transfer system of the Data Provider and receive information from the associated BioMedIT node about the server to be used for connection to the BioMedIT network. More information can be found in the document Data Transfer for Data Providers. Before any patient data can be transferred from a Data Provider to the BioMedIT network the legal basis must be confirmed. This will normally involve the parties providing and receiving data agreeing to and signing a Data Transfer and Use Agreement (DTUA). A DTUA is project specific and describes the data to be transferred (including the format of the data and meta-data) and the purpose for which it will be used. A DTUA will be signed by the authorised representatives of the provider and recipient as well as the project leaders.

Assuming that you have agreed with the BioMedIT node to which you wish to connect that they will serve as your entry point into the BioMedIT network, you will need to provide them:

1. List of IP addresses used as exit points to send data to the BioMedIT network (required for whitelisting in the BioMedIT nodes).
2. Expected data volume and frequency of transfers
3. The Data Provider’s public SSH key
4. Contact details of the persons nominated as administrative and technical contacts (name, email address and role)

Please refer to Onboarding of Data Providers for more information.

Once a Data Transfer Request is approved the Data Provider assembles the agreed data set (selects records, carries out necessary de-identification and any other preparation work required). The sett tool is then used to compress the data (optional), encrypt it with the public key of the recipient and the private key of the Data Provider, sign the data package and finally to transfer it using SFTP to the BioMedIT node to which the Data Provider is connected. If this node is not the node where the B-Space is located the package is routed onwards to the Landing Zone of the Data Provider at the destination node. Once there the package is sent to the project work space in the secure environment of the BioMedIT node and (again using sett) decrypted, unpacked and copied into the appropriate directory of the project.The transfer takes place using what is often called end-to-end encryption (encrypted before leaving the Data Provider and only decrypted after arriving in the B-space). The transfer of the encrypted data package takes place over a secure, encrypted path which further enhances security.

This is a great question and one which is often asked! The answer is not immediately obvious. If a hospital is taking part in a project hosted on Node X then the easiest thing is to just connect directly to this Node. The problem with the approach is scalability. With one project per data provider things are simple. At present there are 3 BioMedIT nodes in Switzerland but this could very well increase in future. Now the hospital (Data Provider) has to keep track of multiple projects on multiple BioMedIT nodes and each Node has to separately onboard each hospital. Each hospital would have a Landing Zone for data transfer set up on each Node. Some projects are already being hosted on more than one BioMedIT node so a hospital as a Data Provider would need to work out where individual data sets should be sent - to one node, another node, both nodes.. Keeping track of all of these things, particularly in the future when other hospitals, potentially also ones from outside Switzerland, are transferring data to projects in the BioMedIT network would be a real problem. Logging and monitoring of data transfers, necessary if a proper audit trail is to be kept, would be quite complicated and become difficult to maintain an oversight. Tracking down which package went where and from whom would be more complex than necessary. The solution adopted on BioMedIT is to associate each Data Provider with one BioMedIT node and to onboard the hospital with just that node.All data transfers from a Data Provider are then sent to only that one Node, always the same one, and hopefully the problem is solved.On BioMedIT this method of connecting a data provider with a project has become known as the Snowflake architecture - a data package “falls” into one node and is routed automatically to the node or nodes where the project is hosted. It is the case that in the past some SPHN driver projects have established data transfer paths directly to nodes other than the ‘main’ BioMedIT node. Requests from future projects or Data Provider to be connected to a specific node will be assessed on a case by case basis.

There are three ways to set up and transfer data which are currently in use on the BioMedIT network.

Most Data Providers are using the secure encryption and transfer tool, sett, to manage the transfer.

While most use the GUI version there is also a command line version with slightly reduced functionality (mainly in key management) but some additional features such as facilitating automated transfers.Both versions provide some degree of checking for valid Data Transfer Request IDs and that the recipient is actually a Data Manager of the project.The third alternative, not to use sett but a variety of individual tools, is not as popular. If this last option is chosen careful attention must be paid to the correct construction of the data package and metadata file as well as verifying DTR ID and recipient.

There are a number of reasons why a data transfer might not work.

• As a Data Provider you need to be onboarded to a BioMedIT node. Done? See above for more information on onboarding.
• Do you have the most up to date version of sett? Occasionally an update of the portal system might require the use of the latest version of sett.
• If the encryption of a data package using sett fails:
  • Try the Test function of the encryption section of sett. Does this work? Are there error messages?
  • If Test worked then try Package & Encrypt. Does this work? Are there error messages?
• Possible problems: Do you (Data Provider) have valid GPG keys with the public key signed by the DCC and uploaded to the BioMedIT keyserver?
• There needs to be a valid DTUA (and possibly other agreements) in place between the Data Provider and the Project/Institution. Done?
• The sending of data into the BioMedIT network requires that an authorised Data Transfer Request (DTR) exists.
• The Data Manager of a Project creates the DTR and approval to send data requires confirmation of readiness (legal and technical).
• Is the DTR ID correct?
• Is the DTR authorised (there is a flag in the BioMedIT Portal which must be set to AUTHORIZED)?
• Did the Verify DTR ID work (box in Encrypt section of sett is checked by default, requires that the user’s computer can access the internet)?
• To encrypt data a Data Provider requires the public key of the Data Manager which has been signed by the DCC. Is this public key valid and signed?
• The public key being used to encrypt the data must belong to a person who has been assigned the role of Data Manager of the project in the BioMedIT Portal/User Register. Is there an error message about the role of the recipient?
• Is the DTR for the project of which the person whose public key is being used is a Data Manager?
• If the encryption works but the transfer does not: Try the Test function of the transfer section of sett. Does this work? Are there error messages?
• If Test worked then try Transfer selected files. Does this work? Are there error messages?
• Did you have the IP addresses used by the Data Provider whitelisted by the BioMedIT node? (This is normally done as part of the on boarding process)
• Did you generate SSH keys and send the public key to the BioMedIT node? (Authentication to the SFTP server used for transfer is via keys and not with a password).
• Did you receive information about connecting to the SFTP server of the BioMedIT node to which you are onboarded? This information would normally consist of the User name, Host URL of the SFTP server and the Destination directory and is required information for the use of sett to transfer data. Note that the destination directory on some servers might be upload while on others it is uploads. Check that the information you input to sett matches what you have received.

If you have tried all of the above check with your IT section if communication to a SFTP server is permitted on your network.

If none of the above seems to be a problem then please send a ticket to the BioMedIT help-desk at biomedit@sib.swiss stating the nature of the problem including error messages received (copy and paste the message into the email or take a screenshot/photo).

The information in the other answers in this section provide the background on how to become an approved and onboarded data provider for projects on BioMedIT. Provided your hospital can meet these requirements there is no reason why you cannot send data into the BioMedIT network.

In principle any research project dealing with sensitive or confidential data and needing to leverage a secure computing environment can use BioMedIT. Typically the BioMedIT node which is hosting the project will act as a service provider but there is no reason it cannot be a project partner as well. Projects can, if desired, take advantage of the HPC facilities offered by the BioMedIT nodes. Projects to be hosted on a BioMedIT node need to be onboarded. When this is done and the project is listed on the BioMedIT Portal users who are authorised to use the BioMedIT Network can be assigned a role on the project. Where a project receives data from a provider which is already linked to and onboarded at a BioMedIT node requests to transfer data can be made by the project Data Manager. Where a new data provider is being used the data provider must be onboarded to one of the BioMedIT nodes. To initiate the setup of the project the Project Leader should contact the head of the nearest BioMedIT node (SENSA in the Romandie, sciCORE in central Switzerland or SIS in the east/south of Switzerland).

More information about the Nodes including contact details may be found on https://biomedit.ch.

In all cases there are standard operating procedures (SOPs) and work instructions (WIs) which deal with the requirements for a project and/or a data provider to become part of the BioMedIT Network.

Requirements

A project goes through a process of administrative and technical onboarding during the set-up phase. The main requirements for a successful onboarding are: deciding where the project should be hosted (which BioMedIT node) agreeing on the project requirements for: computing facilities storage remote access archival of project data at completion of project establishing and agreeing a Data Transfer and Use Agreement between the Data Providers, BioMedIT node(s) and the project agreeing a Service Level Agreement agreeing the costing of the hosting, technical support, user management and any other scientific support. The project may at this time also discuss with the proposed hosting node what will happen to the project data at the completion of the project, whether the project work space is to be archived and stored for a certain length of time, and access to this data/workspace after the project is formally complete. Removal or maintenance of long term user access rights might also be discussed. The associated costs to be met for providing these services should also be agreed between the project and the BioMedIT hosting node.In the BioMedIT Portal a portal administrator will create the project record and include details about the Project Leader (PL), hosting node, resources to be made available, and (if the PL opts out of accessing the portal/project work space) will assign to a user (upon the request of the PL) the role of Permissions Manager for the project.

There are four roles which relate to persons associated with a project in the BioMedIT Network:

• Project Leader: Overall responsibility for project - technical and administrative aspects of project hosting on one or more BioMedIT nodes, user management, data management.
• Permissions Manager: Carries out user management in the BioMedIT Portal
• Data Manager: Creates Data Transfer requests in the BioMedIT Portal and ensures that the necessary documentation and technical requirements are met for each data transfer from a data provider to the project.
• User: Accesses data in the project work space on BioMedIT.

The Permissions Manager (PM), accountable to the Project Leader, carries out all the user management on the project. Each project must have at least one project member with the user role of PM. The PM is responsible for assigning, modifying and revoking the user roles of “(default) User” and “Data Manager” to authorised BioMedIT users. A PM acts as contact for the new project members to support them with registration and authorisation as users of BioMedIT.

Only the Project Leader (PL) or the designated Permissions Manager(s) (PM) may assign users to a project and specify the role(s) they can be allocated.While a PL can assign a user as a PM, Data Manager (DM) or ordinary User the PM can only assign a user as DM or User. A DM may not assign user roles. The assigning/removing of users/roles to a project is carried out on the BioMedIT Portal at any time. (Instructions can be found in the BioMedIT Portal User Guide)

Note: Assigning or changing the role of User will automatically trigger an email to the BioMedIT node where the B-space is hosted. If the User role is assigned the Node will create a local user account in the B-space. If the role is removed the Node will remove access to the B-space for that user.

Before you (Permissions Manager) can assign a team member as a user of your Project, each user, including the Permission Manager, needs to go through the following steps:

• Create a SWITCH edu-ID account and enable the two factor authentication (2FA) (SWITCH homepage)
• Sign the AUP of the BioMedIT node where the project is being hosted (please get in contact with the BioMedIT node)
• Complete the BioMedIT Security Awareness Training course
• Register at the BioMedIT Portal by logging in with your SWITCH edu-ID (and second factor authentication)

All additions or alterations will trigger automatic emails to the PL and DCC as well as being logged in the BioMedIT Register system to provide an audit trail.

The Data Manager (DM), accountable to the PL, manages all data transfers from one or more data providers to the project.

Each project must have at least one project member with the user role of DM.

The DM is responsible for the management of the PGP cryptographic key pair used for encrypting, decrypting and signing data packages.

The DM also generates the Data Transfer Requests in the BioMedIT Portal to ensure that all administrative and technical matters relating to the transfer of data have been positively addressed.

The DM unpacks and decrypts the data packages transferred from a data provider (there may be multiple data providers for a single project) in the B-space on the BioMedIT node where the project is hosted.

Both the project and the relevant data providers must have been previously on-boarded to a BioMedIT node before any data may be transferred.

With the express authorisation from the PL the DM is responsible for the packaging, encrypting and signing of data packages which are to be transferred out of the B-space in the secure BioMedIT environment.

Before you can access the workspace there are a number of things that need to be done:

• You must become an authorised BioMedIT user.
• Create an SWITCH eduID (using the email address from your institution) if you do not already have one and enable two factor authentication (2FA)
• Login to the BioMedIT Portal with this eduID and set a user name
• Complete the Security Awareness training
• Send a request to the project Permissions Manager to be assigned a role on the project

When you are assigned a role on the project and you log into the BioMedIT Portal you should see the project listed under Projects.

There will be one or more ways (referred to as Resources) in which you can access the B-space (Graphical remote desktop or Command line in a terminal).

Note: access to a Gitlab instance for the project may also be shown as an available resource.

> LeonhardMed at SIS (Zürich)

When you open a Remote Desktop session you should see files and folders in your home folder (your username will be the name of the folder, (LeoMed at SIS example) /cluster/home/dduck). There should also be a folder visible in the File Manager with the same name as the project. This folder, accessible by all users on the project, is where the project data is stored.This folder will be located at (example for IMAGINE project hosted on LeoMed at SIS) /cluster/dataset/imagine.There may also be a folder called (example for IMAGINE project) /cluster/dataset/imagine but this is the same folder as /cluster/dataset/imagine. If you see a folder (example for IMAGINE project) like /cluster/dataset/imagine_lz this is the landing zone folder used by the Data Manager when transferring data via the BioMedIT secure data transfer process. You can find some more information here.

> sciCOREMed at sciCORE (Basel)

When data is transferred with sett, the landing zone is mounted from GPFS NFS to /transfer. The data is then visible in the /transfer folder until it is decrypted into the /project/data folder (on NetApp over NFS). Additionally the user has access to the /project/home folder, which is on Ceph filesystem.

> SENSA / SIB (Lausanne)

When you open a Remote Desktop session you should see files and folders in your home folder. The project folder is auto-mounted from the WEKA FS and should be visible at login.

To become an authorised BioMedIT user:

1. Create a SWITCH eduID (using the email address from your institution) if you do not already have one, and enable two factor authentication (2FA).
2. Login to the BioMedIT Portal with this eduID and set a user name. At this stage you cannot yet be assigned to a project.
3. Complete the mandatory BioMedIT Security Awareness Training
4. Sign your BioMedIT node’s Acceptable Use Policy (AUP) and any other relevant documents from the project.

Log into the BioMedIT Portal and follow the instructions detailed in the BioMedIT Portal User Guide

After one successful production data transfer from data provider to the project work space, a DTR which is marked as AUTHORIZED and with maximum number of packages set as unlimited may be re-used for future data transfers. A new request will only be needed if either the legal basis or the technical setup changes.

The main piece of information a DP needs is the verified and approved public PGP key of the Data Manager of the project. In addition the DP needs to know the Data Transfer Request ID (this information is available in the BioMedIT Portal). The BioMedIT node will have already passed on the necessary information for sending data (URL, username, directory) from the Data Provider to the BioMedIT Network.

Public-key cryptography is a method for secure communication between two or more users. In this system, each user has a pair of unique keys consisting of a private key and a public key. Public and private keys are linked in the sense that, whatever has been encrypted with the a given public key can only be decrypted with the matching private key, and whatever has been signed with a given private key will only be recognized by the matching public key.

You can read more about key management, and how sett does most of the hard work for you, in the documentation of sett on the sett User Guide

To get your public PGP key authorized, it must be registered in the BioMedIT Portal. Instructions are available in this section of the sett User Guide.

No! A private key is just that - private. If you have lost the password to the key it is gone forever.

You will need to revoke the previous key and generate new public and private PGP keys. See here for details.

If you generated the keys within sett a revocation certificate was generated automatically for you. See here for details.

If you think that the private key is no longer private you should revoke the key and generate new keys.

Once a Data Transfer Request is approved the Data Provider assembles the agreed data set (selects records, carries out necessary de-identification and any other preparation work required). The sett tool is then used to compress the data (optional), encrypt it with the public key of the recipient and the private key of the Data Provider, sign the data package and finally transfer it using SFTP to the BioMedIT node to which the Data Provider is connected. If this node is not the node where the B-space is located the package is routed onwards to the Landing Zone of the Data Provider at the destination node. Once there the package is sent to the B-space in the secure environment of the BioMedIT node and (again using sett) decrypted, unpacked and copied into the appropriate directory of the project. The transfer takes place using what is often called end-to-end encryption (encrypted before leaving the Data Provider and only decrypted after arriving in the B-space). The transfer of the encrypted data package takes place over a secure, encrypted path which further enhances security.

When data is transferred the current status will be shown in the portal (number of packages transferred and the path the packages take from the Data Provider to the B-space). See Data Transfer - LOGS

The ticket system in use on BioMedIT uses the email address biomedit@sib.swiss

If you are receiving mails from this address it means that either you raised a ticket for support or are part of a data transfer process between a Data Provider and a Project.

Should you not wish to receive further emails from biomedit@sib.swiss in relation to data transfers just reply to one of the mails requesting that you be deleted from the list of correspondents.

sett stands for “Secure Encryption and Transfer Tool” and is essentially a python-based wrapper around GnuPG and sftp that automates the packaging, encryption, and transfer of data.

It is available both as a GUI program sett-gui, and a command line version sett. Most functionalities of sett are available both in the GUI and the command line.

Developed as part of the BioMedIT project, it is licensed under the LGPL (GNU Lesser General Public License) and the source code is available at https://gitlab.com/biomedit/sett/.

Fore more information, visit the sett User Guide

Full documentation for sett (including information on key management) may be found at sett User Guide.

Issues concerning sett are created on the gitlab page at https://gitlab.com/biomedit/sett/-/issues. This link is also accessed from within the sett GUI by clicking Help → Report an issue.

The developers monitor the issues on gitlab for any bugs, problems or feature requests.

sett was developed at the request of a number of the data providers to the BioMedIT network. The packaging, encryption, signing, transfer and subsequent decryption can all be done outside of sett using available software (GUI and command line). The only constraint is that the data package must conform to the format required by sett as the metadata associated with the encrypted package contains information used in routing and error checking.

More information about this format can be found here.

The process of encrypting and sending data using sett incorporates a number of checks (Valid DTR ID, project and Data Manager match) which reduces the risk of transfer failure. These checks are not available outside of the sett tool.

Installation of standard programs and application stacks can be requested by a BioMedIT project user by contacting their Data Manager and/or BioMedIT node contact.

BioMedIT project spaces support automated installation of various standard bioinformatics application stacks On-Demand. 

Should the requested application/program not be in the list of supported application stacks for automated On-Demand installations, an application stack can be made available to your project space after its careful evaluation by designated BioMedIT node.

At the time of writing there is no possibility to include programs from operating systems other than Linux.

Long term storage and archiving of data is currently handled by the BioMedIT node where the project is hosted. Please contact the BioMedIT node to discuss this matter.

A SWITCH edu-ID is an identity provider service offered by SWITCH, a Swiss organization dedicated to providing internet services for the Swiss academic community. It’s designed to offer a single user identity for accessing various online services within the academic and research spheres in Switzerland.

SWITCH edu-ID serves as a digital identity for students, researchers, and staff, allowing them to access multiple online resources using a single set of credentials. It simplifies the process of accessing various educational services, such as libraries, research databases, learning management systems, and more, by providing a unified login system.

It enhances security, streamlines access to educational resources, and facilitates collaboration among individuals and institutions within the Swiss academic community.

Links to creating a SWITCH edu-ID and other frequent operations can be found here.

Two-step login enhances security by prompting users to specify a second authentication factor when logging in. The second factor (your password is the first factor), is either a code generated on your phone using an authenticator app or sent to your mobile phone by SMS.

You may also know this feature as two-factor authentication (2FA), two-step verification or secure login. Services that demand a higher level of authentication security, e.g. those that enable account management or financial transactions often require two-step login. Note: If neither of the above methods work it is possible to use (a previously generated) one-time recovery code.

A guide to enabling 2FA can be found at How can I enable/disable two-step login? on the SWITCH website.

You should generate and safely store a set of recovery codes in case they are ever needed.

You can access the landing page at https://biomedit.ch and the BioMedIT Portal at https://portal.dcc.sib.swiss (the portal only with a SWITCH edu-ID).

It is possible to set up a SWITCH edu-ID without an AAI - when creating the account ensure that you select Create without SWITCHaai -, but to gain access to a B-space, you must provide be an institutional (non-personal) email address. Members of a data provider organisation (not a university, university hospital or similar) may be permitted to transfer data into the BioMedIT Network provided that the organisation has been formally ‘onboarded’ to a BioMedIT node and the user has a valid, signed public GPG key and valid SSH keys. There are work instructions available to show you how to create SSH keys under Windows or Linux.

In these courses, the users are introduced to data privacy regulations, respective laws and practical concepts of information security, all important subjects when dealing with confidential human data. After working through the courses the user will have a better idea and an increased awareness of the need for security when handling sensitive data.

You may find the links and instructions to enroll here.

There are three main working groups on BioMedIT:

• BioMedIT Interoperability Working Group

Launched early 2018, the BioMedIT Interoperability Working Group aims to streamline the computational process for researchers. The activities of the working group are to develop and deploy solutions which abstract the underlying IT infrastructure and enable researchers to focus on the development of novel analyses.

• BioMedIT IT Security Working Group

A project oriented BioMedIT IT Security WG has been set up to address security issues specifically relevant to the BioMedIT project. The SIB Data Protection and Security Board is an overarching body responsible for establishing and reviewing overall policy.

• BioMedIT Data Management/Research support RDF Working Group

The working group provides support to researchers in data management aspects using the SPHN Semantic Framework and Semantic Web technologies. It is responsible for building and implementing a support network for data management with Semantic Web technology on BioMedIT that includes tools and services for RDF, terminology service, documentation and user guide, and training on FAIR health-related data for research.

For more information, visit the BioMedIT website.

An initiative of the Swiss Government, the Swiss Personalized Health Network is a national initiative under the leadership of the Swiss Academy of Medical Sciences (SAMS). In collaboration with the SIB Swiss Institute of Bioinformatics it contributes to the development, implementation and validation of coordinated data infrastructures in order to make health-relevant data interoperable and shareable for research in Switzerland. 
SPHN has adopted a federative approach by building upon – and supporting – existing data sources and infrastructures across the country. To make health data interoperable and accessible for research, SPHN rallies all decision-makers from key clinical, research-, research support institutions and patient organizations around the same table.

Read the SPHN Fact-Sheet.

Under the umbrella of the SPHN initiative a secure and cutting-edge IT environment (BioMedIT network, a project of SIB) is being established to support computational, biomedical research and clinical bioinformatics, ensuring data privacy. In the same way as SPHN the BioMedIT network builds on existing infrastructure and expertise in each of the three BioMedIT nodes.