Skip to content

Getting Started

What is LabKey

LabKey is a research data management platform designed to enhance research efficiency for scientists. It enables effective data integration, collaboration, and workflow management, allowing teams to store, organize, and share research data securely. The LabKey service at University of Basel is the professional version and includes a sample and freezer management module.

Who is it for

LabKey is designed for researchers looking to structure and centralize their data. It serves as an effective alternative to Excel, providing a reliable single source of truth for reference data, especially in collaborative research environments.

How to access LabKey

Access LabKey

Once a UniBas account is acquired, LabKey is accessible from the University of Basel network, including via VPN. sciCORE provides three LabKey instances:

2-Factor Authentication

To ensure the security of research data, sciCORE LabKey enforces mandatory Two-Factor Authentication (2FA) for all users. This security layer requires a time-based code from an authenticator app in addition to your standard login credentials.

First-Time Login & Setup

You do not need to enable 2FA manually; the system will automatically prompt you to enroll during your first login.

  1. Prepare your device: Ensure you have an authenticator app installed on your smartphone (e.g., Microsoft Authenticator, or Google Authenticator.)
  2. Initial Setup: Upon your first login, LabKey will display a QR Code and a “Secret Key”.
  3. Link your account: Scan this QR code using your authenticator app to generate a 6-digit security code. Please also consider copying and saving the Secret Key for future reference
  4. Complete Enrollment: Enter the 6-digit code into the LabKey prompt to finalize your access.

For visual examples of the setup screen and the login process, please refer to the official documentation:

Important: API & Remote Access

Because 2FA is mandatory, standard password authentication will not work for remote data access (e.g., connecting via R, Python, or HTTP).

  • API Keys: You must generate and use an API Key for all script-based access.
  • Instructions: Follow the guide on Generating and Using API Keys to maintain access to your data through external tools.

Support & Recovery

  • Device Issues: If you lose your mobile device or need to reset your 2FA registration (e.g., when switching to a new phone), please contact sciCORE Administration.
  • Lab Access (Desktop 2FA): If you cannot use a mobile phone while in the lab and need to set up 2FA on a desktop computer instead, please refer to our FAQs for instructions on using desktop-based authenticator tools.

https://docs.scicore.unibas.ch/LabKey/faqs/#general

Understanding LabKey Folder Structure

LabKey organizes data in a hierarchy of folders, which helps you structure your research projects clearly:

  • Site (Home Folder): The top-level container of the LabKey environment.
  • Projects: A Project corresponds to a team or an area of work and can contain any number of “folders and subfolders” underneath to present each collaborating team with precisely the subset of LabKey modules needed.
  • Subfolders: Nested folders within projects to further organize tools, data, and workflows.

Additional information

Detailed information can be found in the LabKey documentation Projects and Folders

Data Management

Data Storage Guidelines

LabKey is not intended for storing large raw data files. Users should avoid uploading files larger than a few megabytes (MB).

Info

sciCORE performs regular backups of the entire LabKey system, retaining them for three months for disaster recovery purposes.

Tip

It is recommended for the users to make periodic safety copies of the data contained in the LabKey environment. sciCORE can provide advice on the implementation of such a backup strategy.

Handling Sensitive Data

Sensitive data can be stored in LabKey; however, it is strongly recommended to anonymize or pseudonymize sensitive information before uploading. This ensures compliance with data protection regulations and minimizes the risk of unintended data exposure. Please note that the responsibility for assessing and accepting this risk lies with the Principal Investigator (PI) of the group.

Additional information

For comprehensive guidelines on handling personal and sensitive data, please refer to the University of Basel Data Protection Guidelines