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GFB Metadata Repository in LabKey

This page provides guidance for researchers and users of the Genomics Facility Basel (GFB) on how to access and benefit from the LabKey -based metadata repository.

Why LabKey for GFB users?

  • No need to manually download files: Metadata and data are transferred automatically.
  • Accessible hours after sequencing: Reduces waiting time.
  • Structured data storage: Located in a secure userstore with backup.
  • Searchable and filterable metadata: Enables faster data discovery.
  • Custom views and export options: Facilitates collaboration and analysis.

What is available in LabKey for GFB users?

All metadata associated with sequencing runs at GFB is centralized in a single LabKey table called GFB_Dataset. This includes:

  • Sample & experiment identifiers
  • Sequencing parameters and equipment
  • File names and storage paths
  • Sample type and organism info
  • Quality control (QC) plots and reports

Preview:

GFB metadata repository in LabKey

Key features for GFB users

Intuitive User-Level Views

  • Filters for specific values (e.g. Sample ID)

Filters on table values

  • Sorting by multiple metadata fields
  • Custom views per user needs
  • Table reports and count summaries
  • Integrated QC plots

QC plots

Easy Data Export

Metadata from the GFB metadata repository can be exported in several formats: - Excel sheet (for offline use or sharing)

Export as Excel table

  • Text file (for downstream processing)
  • Code snippet (R or Python for scripting)

Export as script

Accessing the GFB Metadata

To access the GFB Metadata:

  1. Log in to LabKey server using the following url: https://labkey.scicore.unibas.ch/
  2. Open your group space.
  3. Navigate to the Facilities folder.
  4. Open the GFB_Dataset table to browse metadata.

Access GFB_Dataset table

Tip

Users do not need to export or upload anything unless they wish to work e.g. on the data locally.

How to apply for a LabKey metadata repository

If you’re accessing LabKey with GFB metadata for the first time, follow the steps below to get started:

Steps to Enable the GFB Metadata Service

Step Description Performed by
1. Contact sciCORE Email scicore-admin@unibas.ch and include the following information:
- Group admins: Specify one or more group members who should be assigned as LabKey space administrators. Please include their email addresses.
- Contact persons for demo: one or more group members who should be contacted by sciCORE for a demonstration of the service’s functionality. Please include their emails.
- PI name and email: PI name will be used to create a space in the LabKey (or access the space if it already exists), PI email address is a key to find the corresponding data for the GFB metadata repository		 PI
2. LabKey Space Setup sciCORE will set up your group space and integrate the GFB metadata repository. A welcome email will follow with:
- Project space URL
- Link to documentation
- Suggested times for a demo meeting		 sciCORE
3. Zoom Introduction sciCORE will walk you through:
- GFB metadata repository structure
- Filtering and viewing options
- Optional API usage (for advanced users)
Q&A session included		 sciCORE & Users

Summary of Benefits

  • Automated integration with GFB sequencing data
  • Fast access to metadata
  • Intuitive filters, exports, and custom reports
  • Collaborative environment for research groups

Info

If you have further questions or are not sure whom to contact, please reach out to: scicore-admin@unibas.ch