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DBM - Spirit Data Migration

This page is intended solely for users from DBM research groups who are migrating their data from SPIRIT to LabKey Sample Manager. If you are not involved in this migration, please disregard this page.

Due to the decommissioning of SPIRIT, DBM users need to take action and migrate their data into new solutions. LabKey Sample Manager is a recommended tool. This page outlines the transition plan from Spirit to LabKey Sample Manager. Below, you’ll find a visual timeline that highlights the key phases of this migration, along with important milestones and deadlines. Be sure to review the steps carefully and reach out for support if needed.

Spirit Data Migration

Next Steps for migrating to LabKey Sample Manager

Once you’ve decided to migrate your data from Spirit to LabKey Sample Manager, follow this step-by-step guide for the final import of data into the main LabKey server.

Actions Performed by
Step 1. Contact the sciCORE LabKey Team at: scicore-admin@unibas.ch.

The sciCORE team will support the DBM users with data migration planning and execution from SPIRIT to LabKey Sample Manager.		 Users
Step 2. Onboarding email to the users.

The onboarding email includes:
  1. A link to the newly created project in the LabKey Dev environment (named after the PI of the group).
  2. Available time slots for an onboarding Zoom call to schedule a discussion.
  3. Instructions for exploring the Sample Manager module, including links to relevant documentation.
  4. Information about project access:
    • Login instructions using UniBas credentials.
    • User roles and pre-configured permission groups (e.g., Admins, Editors).
    • Guidance on modifying or adding permission groups if needed.
 sciCORE
Step 3a. Onboarding Zoom Call.

This call is an interactive session between the user and the sciCORE LabKey team to align on data structure, privacy, and platform usage.
  1. Review the SPIRIT data structure with the user.
  2. Explain LabKey’s data privacy guidelines.
  3. Provide a live demo of LabKey Sample Manager, covering:
    • Sample types and relationships
    • Data lineage
    • Metadata and file attachments
    • Search and filter features
 sciCORE
Step 3b. Onboarding Zoom Call.
  1. Share an overview of the current SPIRIT data structure.
  2. Confirm understanding of data privacy requirements (e.g., anonymization).
 Users
Step 4. Prepares and Sends Curated Data.
  1. Export data from SPIRIT in CSV, Excel, or TSV format. For technical support with the export of the data from SPIRIT, contact support-dbm@unibas.ch.
  2. Define sample types and source types, including lineage relationships (recommended).
  3. Perform Data Cleanup and Standardize values (e.g., dates, categorical fields)
  4. Send curated data to the sciCORE LabKey team for review.
 Users
Step 5a. Data import into LabKey Dev Environment.
  1. Review the curated dataset.
  2. Perform a pilot import into the LabKey Dev environment.
  3. Validate structure and usability with the user.
 sciCORE
Step 5b. Data import into LabKey Dev Environment.
  1. Participate in the validation process.
  2. Confirm that the data is accurate, functions as expected, and is ready for final migration to the main LabKey server.
 Users
Step 6. Final Migration to Main LabKey Server.
  1. Perform the full migration of curated data to the production LabKey server.
  2. Configure user access and permissions.
  3. Notify users when the production project is ready for active use.
 sciCORE

More information about LabKey Sample Manager can be found here.