Assay data is captured in LabKey Biologics using
Assay Designs. Each Assay Design includes fields for capturing experimental results and metadata about them. Once a design has been created, many runs of data matching that format can be imported with the same design. This topic describes how administrators create and manage the Assay Designs available in the system.
Overview
Each field has a name and data type, for example, the following Assay Design captures data from a Titration experiment.
| SampleID | Expression Run | SampleDate | InjVol | Vial | Cal CurveID | Dilution | ResultID | MAb |
|---|
| 2016_01_22-C3-12-B9-01 | ER-005 | 2016-01-23 | 30 | 2:A,19 | 46188 | 1.0000 | 47836 | 0.2000 |
| 2016_04_21-C7-73-B6-02 | ER-005 | 2016-04-22 | 30 | 2:B,19 | 46188 | 1.0000 | 47835 | 0.2300 |
| 2015_07_12-C5-39-B4-02 | ER-004 | 2015-07-13 | 30 | 2:C,19 | 46188 | 1.0000 | 47834 | 0.3000 |
The fields in an Assay Design are grouped into categories:
- Run Fields: These are metadata fields that apply to one complete cycle of the experimental instrument or procedure. Possible run-level metadata fields would be: Operator (the lab technician who executed the experiment) or Instrument (the name of the lab instrument in which the experiment was performed).
- Results (Data) Fields: These fields capture the main results of your experiment, for example, see above.
- Other Categories: In some cases, there will be additional sets, such as Cell- or Analyte-level fields.
Assay Dashboard
Under
Assays on the main menu, you will see a listing of designs already created in your system. Click
Assays to open the dashboard.
The dashboard lists the assay design names and types, in a
Grid by default. You can also select a
Heatmap layout that will display the volume of runs imported for each assay over the past 12 months.
Note that when assay designs are created in the Biologics application, are scoped to the current folder. If your server includes any shared assays, you will also see them listed here. To create a shared or project scoped assay design, use the
LabKey Server interface.
Click the name of an existing design to see the assay properties and a grid of runs imported using it. Use the
to:
- Export Design
- Edit Design
- Copy Design
- Delete Design
- View Audit History
Create a New Assay Design
To create a new assay design in LabKey Biologics, follow this process.
- From the main menu, click Assays, then select Create > Assay Design.
- Select the Assay Type. For most cases, leave the Standard Assay tab selected.
- Click Choose Standard Assay.
- In the Standard Assay Designer, enter Basic Properties:
- Name field - this should reflect something about the nature of the assay and what is primarily being measured, for example, "Titer", "Immune Score", or "Cell Properties".
- Active: When this box is unchecked, the design is archived and hidden in certain views.
- Other fields are described in more detail in tooltips and in the topic: Assay Design Properties.
- Click to open the Run Fields panel. Add run-level metadata fields as desired.
- Click to open the Results Fields panel.
- If there are no result fields defined yet, you will have the options to infer them from an example data spreadsheet (the supported formats are listed), import a prepared JSON file as for run fields, or click Manually Define Fields and add them individually.
- Click Add Field to add new fields. Provide their Name and Data Type.
- Keep adding fields until your data can be adequately captured.
- To create a link between the assay data and the original samples, we recommend adding a SampleID field of type "lookup". See below for details.
- Click Save.
Linking Assay Data to Samples
To link assay data to the originating samples, you can add a field with the data type
Sample to your assay design.
- In your Assay Design, add a field, typically in the Run or Results Fields section. This field can be of any name, such as SampleID or SpecimenID. Use whatever name best matches your result data.
- In the Data Type column, choose the field type Sample.
- Click the icon to expand field details.
- Under Sample Options, select the desired Sample Type.
- To link to all samples across any Sample Type, select All Samples from the "Sample lookup to" dropdown.
- Click Save to confirm the changes.
To learn about connecting assay results to other kinds of entities, review this topic:
Biologics Admin: Assay Integration
Review or Edit Assay Design
To review the details or edit a design, select it from the main menu and select
> Edit Design.
You will see all the fields and properties set up when the design was created. If changes are needed, make them using the same method as for the
creation of a new design. Click
Finish Updating [Assay Name] to save changes.
Archive Assay Design
Assay Designs can be hidden from certain views by unchecking the
Active checkbox in the
Assay Properties. Archived, or inactive, designs are not shown on the main menu or available for new data entry through the Biologics application interface, but existing data is retained for reference. Note that you could still import new data for an archived assay in the LabKey Server interface if necessary.
Using the archive option can be helpful when a design evolves over time. Making the older versions "inactive" will ensure that users see the latest versions. An assay design may be reactivated at any time by returning to edit the design and checking the
Active box again.
When viewing all assay data for a sample, both the active and archived assays will be shown if there is any data for that sample.
On the main
Assays dashboard, you will be able to find inactive assays by switching to the
All tab.
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