Premium Resource - Specimen functionality is a legacy feature available with Premium Editions of LabKey Server. For new installations, we recommend using Sample Manager instead. Learn more or contact LabKey.

The tutorial begins by importing example research and vial data and configuring the specimen repository system, tasks done by the folder administrator.

To be able to use this tutorial, you must have the specimen module installed on your server and enabled in the /Tutorials/HIV Study folder before you import the study to it.

Example Data Set Up

The tutorial makes use of example data contained in an example study. Note that if you are working on a LabKey Server trial instance, you cannot use the pre-loaded Example Project to complete this tutorial.

Locate your Tutorials/HIV Study folder. If you don't have one, or it is not yet populated, follow the instructions on this page, remembering to first enable the specimen module:

Navigate to the Overview tab of your /Tutorials/HIV Study folder.

When you import our tutorial study, it includes a specimen repository with vial data pre-loaded. More about importing archives and other administrative tasks can be found in Specimens: Administrator Guide.

Set Specimen Repository Settings

Basic options like the repository type, display and behavior of your repository are covered by the options in the Specimen Repository Settings section of the Manage Study page.

Change Repository Type

  • In your study folder, select (Admin) > Manage Study.
  • Under Specimen Repository Settings, click Change Repository Type.
  • Select Advanced (External) Specimen Repository (if it is not already selected). Two advanced options are available:
    • Specimen Data options are:
      • Read-only: Specimen data is read-only and can only be changed by importing a specimen archive.
      • Editable: Specimen data is editable.
    • Specimen Requests options are:
      • Enabled: The system will allow users with appropriate permissions to request specimens, and will show counts of available specimens.
      • Disabled: Specimen request features such as the specimen shopping cart will not appear in the specimen tracking user interface.
  • For this tutorial, Advanced Specimen Repository, Read-only, and Enabled should be selected.
  • Click Submit.

Edit Specimen Table Fields

Specimen information is stored in three linked tables, each of which has a set of Fields that can be customized as needed.

  • Specimen: top level information for the specimen (which may have been aliquoted into several vials)
  • Vial: holds information about each individual vial
  • SpecimenEvent: holds information about each event for a vial, such as processing or change of location
  • Click Edit Specimen Fields.
  • Review the default specimen fields.
    • Options available for fields in each table include reordering, adding new ones, and removing any unnecessary fields. Some fields are required parts of the specimen tables and cannot be removed.
    • Expand any field using the icon on the right. Options for individual fields include assigning custom labels, defining import aliases, and adding automated validation or conditional formatting.
  • For this tutorial, make no changes.
  • Click Cancel to avoid saving accidental changes.
  • Repeat the above for the Edit SpecimenEvent Fields and Edit Vial Fields tables, making no changes.

For more information about editing fields in the three specimen tables, see Specimen Fields and Rollup Rules.

Manage Display and Behavior

Specimen display settings available:

  • Comments and Quality Control:
    • Default Mode: The specimen system can function in two modes. Users with appropriate permissions can always manually switch modes.
      • Request Mode: Vials are requested and requests are managed.
      • Comments Mode: Vial information itself can be modified.
    • Manual QC flagging/unflagging: Vials are automatically flagged for QC at time of import if a vial's history contains conflicting information. Enable manual QC flagging/unflagging to allow these states to be changed without updating the underlying specimen data. Once a vial's QC state is set manually, it will no longer be updated automatically during the import process.
  • Low Vial Warnings. If enabled, the specimen request system can display warning icons when supplies of any primary specimen are very low (zero or one available). An icon will appear next to all vials of that primary specimen.
    • Display one available vial warning: Select whether to show for all users, administrators only, or never.
    • Display zero available vial warning: Select whether to show for all users, administrators only, or never.
  • Return to the Manage tab.
  • Click Manage Display and Behavior.
  • Review options available.
  • For this tutorial, make no changes.
  • Click Cancel to avoid saving accidental changes.

Configure Specimen Groupings

You can decide which specimen groupings to display by default in the Specimens web part. The default groupings are sufficient for this tutorial. To read about the options available, see Customize Specimens Web Part and Grid Views.

Populate the Repository

The administrator loads specimen data into the repository, either from a spreadsheet or from a specimen archive. For this tutorial, the specimen archive has already been imported with the sample study. For more about uploading data, see Import a Specimen Archive.

Assign Specimen Requester and Coordinator Permissions

Specimen data can be made available to others via the usual read or edit permissions within the given study folder. Two additional permission levels are provided to support specimen request tracking:

  • Specimen Requester permission is required to place a request or view the status of requests in process.
  • Specimen Coordinator permission is offered as an intermediate administrative level for the individual tracking requests through the approval and fulfillment process without requiring full administrative permissions throughout the study.
These specialized roles do not automatically include any other access to resources, so users must also be assigned at least Reader permission on the folder in order to use them.

To complete the tutorial, you can continue with admin permissions, or choose to explore the other permissions levels using role impersonation.

  • Click the Specimen Data tab (so you start on a tab that a Specimen Coordinator can view).
  • Select (your user name) > Impersonate > Roles.
  • In the popup, click the boxes for both Reader and Specimen Coordinator.
  • Click Impersonate.
You will now to see your project and folders through the eyes of a user assigned the "Specimen Coordinator" role.

For details about defining users and granting permissions, see Configure Permissions.

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