- 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
An Advanced (External) Specimen Repository
can act as a specimen request and tracking system. This topic will walk through some of the Specimen Request Settings
a coordinator would use to customize the interface for their users. For more information about all of the options available, see Specimen Coordinator Guide
The configuration of the repository is done by an adminstrator as in the previous step in this tutorial. The tracking system can also be managed by an administrator, or these steps can be done by a user granted (or impersonating) Specimen Coordinator
Set Up Specimen Request Tracking
Within your study, click the Specimen Data
tab and click Settings
in the Specimen Tools
- Statuses: Define the different stages of the request approval process.
- Actors: Define people or groups who might be involved in a specimen request.
- Request Requirements: Define default requirements for new requests.
- Request Form: Customize the information collected from users when they generate a new specimen request.
- Notifications: Configure emails and notifications sent to users during the specimen request workflow.
- Requestability Rules: Manage the rules used to determine specimen availability for request.
A specimen request goes through a number of states from start to finish. Request statuses help a specimen coordinator organize and track requests through the system and communicate progress to requesters. States are numbered sequentially, but not all requests need to pass through all states.
- From the Specimen Request Settings panel, click Manage Request Statuses.
- If they are not already defined, add the following new status options:
- "Processing Request"
- "Pending Approval"
- Click Save after each addition.
- Set the checkmark columns to the right as shown in the following screencap. "Completed" and "Rejected" are Final States; all states except "Rejected" lock the associated specimens so that they cannot be requested by others.
Notice the option to Allow requests to be built over multiple searches before submission
. This is a convenience for requesters, but requires the coordinator to watch for abandoned unsubmitted requests that may have locked specimens needed by others.
- When finished, click Done.
Each person or group involved in processing a specimen request should have an Actor
defined to represent them in the specimen repository tracking system. Examples include:
- Specimen requesters, such as lab technicians or principal investigators
- Reviewers of requests, such as oversight boards or leadership groups
- Those responsible for storing and shipping specimens, such as repository owners
Actors can be of two types:
- One Per Study: There is one group of people representing this actor in the study, specified by a single list of email addresses.
- Multiple Per Study (Location Affiliated): There may be multiple groups representing this actor at multiple sites. Each site/actor combination has a separate list of member email addresses.
For this tutorial, it is helpful to define a few fictional "users" and "locations" to demonstrate assignments. An administrator
can add new site users as follows.
- Click Stop Impersonating if you are impersonating a specimen coordinator.
- Select (Admin) > Site > Site Users > Add Users.
- This tutorial uses the following. Enter each email on its own line.
- Uncheck the Send password verification emails to all new users box for this tutorial.
- Click Add Users.
- Click Done.
Learn about defining locations
and setting location types in this topic: Manage Locations
Return to the specimen tutorial study folder. The following steps can be completed by a specimen coordinator, so resume impersonation of roles "Specimen Coordinator" and "Reader" using the (User)
- Click the Specimen Data tab and click Settings.
- Click Manage Actors and Groups.
- Fill out the form as shown below. Click Save after each addition.
- Click Update Members on the Scientific Leadership Group row and add a (ficticious) user email such as the "email@example.com" we just added as a site user.
- Uncheck the Send password verification emails to all users box for this tutorial.
- Click Update Members.
- Click Update Members on the Institutional Review Board row. Because we defined this as an actor with multiple instances per study (location affiliated), you Choose Site before adding members.
- Click High Point Clinic and you will see the same panel for adding users as for the scientific leadership group.
- Enter the email "firstname.lastname@example.org".
- Uncheck the Send password verification emails to all users box.
- Click Update Members.
- By clicking Update Members again for any actor or actor/site combination, you can review the current list, remove, or add new members, such as "email@example.com".
- Click Update Members.
- Click Done.
Request Requirements, Form, Notifications, and Rules
The coordinator can also configure the other Specimen Request Settings
- Manage Default Requirements: Default requirements for new specimen requests, such as approval from a given actor.
- Manage New Request Form: Customize the request form itself to gather required information from requesters.
- Manage Notifications: Define the email notification process and content
- Manage Requestability Rules: Set your own rules for when specimens are shown as unavailable.
For this tutorial, simply use the default settings. For more information, see Specimen Coordinator Guide
Now your basic repository is ready for users to make some sample requests. You can continue to the next tutorial step as an Admin, Specimen Coordinator, or impersonate the role of Specimen Requester
(remember to also impersonate the Reader role). After some requests are made, you can return to the role of coordinator to track and approve them.