Premium Feature — Available with LabKey Biologics LIMS. Learn more or contact LabKey.

LabKey Biologics offers a number of different ways to work with assay data in the system. Administrators can control which options are available and to which users.

Assay Dashboard

Click Assays on the main menu to go to the assay dashboard. You'll see a grid listing the Assay Designs in the system with name, description, type, and run count. A button to download a template is provided for each assay.

Any archived, or inactive, assay designs are only included when you click the All tab.

Assay Data Details

Click the name of an Assay Design to see it's summary page, with several tabs, showing various scopes of the data:

  • Batches (Shown only if any Batch fields are defined): View batches, the widest grouping of the data. Each batch generally groups together multiple runs of data.
  • Runs (Default): Runs are the mid-level grouping of the data, standing between the batches and the result data. Each run generally represents one file of data.
  • Results: Displays the result data of the assay, showing the data output of the instrument.

Hover over the Details link in the header to see creation information and status.

Custom grid views are available by clicking the Views button. Learn about customizing data grids in this topic: Biologics: Grids, Detail Pages, and Entry Forms.

If an administrator has added any charts to an assay, as detailed in the topic: Biologics Admin: Charts, they can be viewed by clicking the (Charts) button.

Edit Assay Runs and/or Results

If your assay design provides for editable runs and/or results, and you have sufficient permission, you can edit run properties and results in bulk:

  • To edit run properties, start from the Runs tab and select the runs to edit.
  • To edit assay result rows, either click the run name or the results page for the assay (to see results from any run).
    • Note that including the Created/CreatedBy/Modified/ModifiedBy fields in the assay result grid view will help track the time of creation and edit.
Select the rows of interest and select your option from the Edit menu. If you don't see this menu, it may be because the assay design does not support editable runs or results.
  • Edit in Grid: Start from a grid view of all the data for the selection; manually adjust as needed.
  • Edit in Bulk: Assign one value for a field to all the selected rows. For example, if an incorrect Day was entered for a set of runs, you could correct it in one step.

For details about using the editors for these two methods of updating run properties and/or results rows, see the documentation for the same feature in LabKey Sample Manager

Move Assay Runs Between Projects

If you are working with multiple Biologics Projects, you can move assay runs between them by selecting the desired run(s) on the Runs tab and choosing Edit > Move to Project. This option is only shown when Projects are in use.

Learn more in the Sample Manager documentation for moving data between projects.

Delete Assay Results

Specific results rows within a run can be deleted from either the grid for a specific run, or for the results page for the assay as a whole. If you want to delete an entire assay run, learn how in this topic: Biologics: Upload Assay Data.

From the results grid, select the rows to delete and select Edit > Delete.

You will be reminded that deletion of rows is permanent and cannot be undone. You can enter a comment about the Reason(s) for deleting that will be audited. Click Yes, Delete in in the popup to actually delete the results.

Work with Samples Associated with Assay Data

When your assay data is linked to samples, you can select a desired set of rows and then use the Samples menu to work with the set of samples mapped to those results.

Assay Quality Control

Visibility of assay data in Biologics can be controlled by setting quality control states. While an admin can edit assay designs to use QC states within the Biologics application, the actual states themselves cannot be configured in the application.

Set Up QC States (Admin)

To configure states, an admin must:

  • Open the Assay Design where you want to use QC. Select > Edit Design.
  • Confirm that the QC States checkbox is checked. If not, check it and click Finish Updating [Assay Design Name].
  • Use > LabKey Server > [current Biologics project name] to switch interfaces.
  • Configure the available QC states in the system, using this topic: Assay QC States: Admin Guide.
    • Select (Admin) > Manage Assays.
    • Click the name of your assay design.
    • Select QC State > Manage states.
    • Define the states you want to use.
  • Once complete, use > LabKey Biologics > [current Biologics project name] to return to Biologics.

Use QC States (Users)

Once QC states have been configured in the system, users (with the appropriate roles) can assign those states to assay run data. Users can update QC states in the following cases:
  • when a user has both Reader and QC Analyst roles
    • OR
  • when a user has either Folder, Project, or Site Admin roles
To assign QC states within the Biologics application:

  • Navigate to the assay run view page. (Cell Viability runs are shown below.)
  • Select one or more runs.
  • Select Edit > Update QC States.
  • In the popup dialog, use the dropdown menu to select the QC state. This state will be applied to all of the runs selected.
  • Optionally add a comment.
  • Click Save changes.
  • The QC states will be reflected in the runs data grid. Admins and QC Analysts will see all of the runs, as shown below.
  • It should be noted that if some of the QC states are not marked as "Public Data", they will not be included in the grid when viewed by non-admin users. For example, if "Not Reviewed" were marked as not public, the reader would see only the runs in public states:

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