You design an assay by creating a named instance of a built-in assay type, adding and modifying fields, or properties, as needed. This topic covers properties and fields pre-defined (but still optional) for all assay designs.

Assay Properties

These assay properties are included in all assay designs:

  • Basic Properties:
    • Name: Required text. Each assay design must have a unique name.
    • Description Optional text.
    • QC States: (Premium Feature/Available in GPAT assays) Check to enable defining and using assay QC states for this assay design.
  • Editing Settings:
    • Editable Runs: If enabled, users with sufficient permissions can edit values at the run level after the initial import is complete. These changes will be audited.
    • Editable Results: If enabled, users with sufficient permissions can edit and delete at the individual results row level after the initial import is complete. These changes will be audited. New result rows cannot be added to existing runs.
  • Import Settings:
    • Auto-copy Data to Study: If a target study is selected, then when new runs are imported, data rows are automatically copied to the specified target study. Only rows that include subject and visit/date information will be copied. For details, see Copy Assay Data into a Study.
  • Import in Background: If enabled, assay imports will be processed as jobs in the data pipeline. If there are any errors during import, they can be viewed from the log file for that job.
    • Transform Scripts: For details, see Transformation Scripts.
    • Save Script Data for Debugging: Typically transform and validation script data files are deleted on script completion. For debug purposes, it can be helpful to be able to view the files generated by the server that are passed to the script. If this checkbox is checked, files will be saved to a subfolder named: "TransformAndValidationFiles", located in the same folder that the original script is located.

Batch Fields

The user is prompted for batch properties once for each set of runs during import. The batch is a convenience to let users set properties once and import many runs using the same suite of properties. Typically, batch properties are properties that rarely change. Default properties:

  • Participant Visit Resolver This field records the method used to associate the assay with participant/visit pairs. The user chooses a method of association during the assay import process. See also Participant/Visit Resolver Field.
  • TargetStudy. If this assay data is copied into a study, it will go to this study. This is the only pre-defined Batch property field for General Assays. It is optional, but including it simplifies the copy-to-study process. Alternatively, you can create a property with the same name and type at the run level so you can then publish each run to a different study. Note that "TargetStudy" is a special property which is handled differently than other properties.

Run Fields

Run properties are set once for all data records imported as part of a given run.

  • No default run properties are defined for General Assays.

Results Fields

Results fields (sometimes called data properties) apply to individual rows within the imported run.

The pre-defined Results Fields fields for General Assays are:

  • SpecimenID
  • ParticipantID
  • VisitID
  • Date
These properties are used to associate assay data with other data from the same source material. For more, see Participant/Visit Resolver Field.

Files and Attachments

Assay datasets can associate a given row of data with a file using a field of one of these types:

  • File: A field that creates a link to a file. The file will be stored in the file root on the server, and will be associated with an assay result.
  • Attachment: A field that will associate an image file with a row of data in a list.
These files might contain images or rectangular data. For example, to index microscopy files, you might create an assay design with metadata and descriptive fields (such as content, timing, staining) and then include an attachment file with the image.

Related Topics

For assay-specific properties and fields see the following pages:

Discussion

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