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Central Services
- 1: DCC GIT
- 2: Harbor
- 3: Federated Query System
1 - DCC GIT
The BioMedIT Code Repository Service (based on Git), is accessible to registered BioMedIT users to create, collaborate and share their application codes with other BioMedIT users.
1. Login to GitLab
1.1 GitLab is available via federated login from BioMedIT portal’s Quick Access link:
1.2 The following page will be displayed.
Click on Federated Login
2. Resources
2 - Harbor
Harbor is an open source registry that secures artifacts with policies and role-based access control, ensures images are scanned and free from vulnerabilities, and signs images as trusted. Harbor, a CNCF Graduated project, delivers compliance, performance, and interoperability to help you consistently and securely manage artifacts across cloud native compute platforms like Kubernetes and Docker.
1. How to request access
1.1 Registry is available via federated login from the BioMedIT portal’s Quick Access links:
1.2 Click on the button: Login via OIDC provider
2. Resources
3 - Federated Query System
The Federated Query System (FQS) allows queries on anonymized and nationally harmonized data coded in national or international terminologies. Researchers can assess whether and where patients or patient data potentially suitable for a specific research question exist at one or several of the Swiss University Hospitals (UHs).
The system enables researchers to verify the feasibility of their project by running simple queries against a subset of clinical data of all UHs. Additionally, it allows designing and optimizing inclusion and exclusion criteria for study protocols without transferring any patient data. These queries may include demographic information (age and gender), diagnosis (ICD-10), procedures (CHOP), medication (ATC) and lab test (LOINC) and lab results with units (according to UCUM). Overall, the system includes 70 Mio data points from 450 000 patients, which signed the general consent.
1. Access requirements
In order to gain access to the FQS, users must meet the following requirements:
- The user’s institution must have signed an agreement with the SIB. Currently, all five Swiss university hospitals are part of this network, additional institutions will have the possibility to join at a later time point.
- Users have a SWITCH edu-ID account with their employing institution linked in their profile (though SWITCHaai).
- Each user has individually agreed to abide by the FQS Acceptable Use Policy.
2. Registration to the FQS
2.1 From the BioMedIT Portal’s Home, at the Quick Access tiles, click on the Federated Query System icon:
2.2 If it is the first time you access the Federated Query System, the system will display the Registration Form below, with your name and current affiliations in your SWITCH edu-ID.
If you do not have any linked affiliations in your SWITCH edu-ID, the system will give you the option to update your account.
a. Click on add your organizational identity on edu-ID. Update your account.
b. Return to this screen and click on I ADDED MY AFFILIATION when ready.
2.3 In the Registration Form,
a. Enter your institution
b. Enter your institutional email
c. Click on NEXT
2.4 The Acceptable Use Policy will be displayed.
a. Read carefully all sections
b. Click on I have read & agree when all the terms are read, understood, and agreed.
2.5 You will get confirmation that your request was sent.
2.6 Within 24 hours, you will receive an email with your account details and the option to set your credentials.
a. Open the email
b. Click on Set Password.
2.7 The Privacy Policy will be displayed:
a. Read carefully all sections
b. Click on I accept when you read, agreed and understood all the terms.
2.8 The Change Password screen will be displayed.
a. Enter a password that meets the security requirements
b. Click on Save changes
2.9 You will received confirmation that your password was changed successfully.
a. Click on the Log out button
3. Login to the FQS
3.1 From Quick Access tiles in the BioMedIT Portal’s Home, click on Federated Query System icon:
3.2 The Login page will be displayed.
a. Read the Acceptable Use Policy
b. Select I confirm when the you read and understood the Acceptable Use Policy
c. Click on Continue to Login
3.3 The Login to the SPHN Federated Query System page will be displayed.
a. Enter your username or email. You can find your username in the confirmation email you received from the DCC.
b. Click on the → icon
3.4 The Email verification required page will be displayed asking you to enter a code.
a. Check your inbox. You should have received an email with the code:
3.5 In the Email verification required page:
a. Enter the code your received by email
b. Click on Apply code
3.6 You will be prompted to enter your password.
a. Enter your password
3.7 If your credentials are correct, you must have logged in to the FQS successfully.