When you import instrument data into LabKey server, assay tools allow you to create a detailed assay design, which tells the server how to interpret complex information. An assay design can be partially inferred by reading the spreadsheet itself, but you might need to make modifications, and might also want to track who generated that spreadsheet and with what instrument settings. Your design would specify what information to gather from an operator at the time of upload, and how best to store both the data and the additional metadata about it.

Create a New Assay Design by Inference

LabKey Server can give you a head start on creating your assay design by inferring column names and types from a sample data file, in this case an Excel spreadsheet.

  • In the Files web part, click the (Folder Tree) icon to open the folder tree.
  • Open the Assays > Generic folder and check the box for "GenericAssay_Run1.xls".
  • Click Import Data.
  • In the Import Data popup, locate the Text or Excel Assay section, select Create New General Assay Design and click Import.
  • Enter the name GenericAssay.
  • Select the Location: "Current Folder (Assay Tutorial)"
  • Review the inferred columns.
  • Uncheck the boxes for column5 and column6. These empty columns are not needed for this tutorial.
  • Click Show Assay Designer at the top of the page.
  • The inferred column information can be seen in the assay designer UI by opening the various sections. Review but do not change the information here for this tutorial.
  • Click Save.
  • The assay design you needed has now been created and saved. You will now be on the "Data Import: Batch Properties" page. To continue without importing the run you used for inferral, click Cancel.
  • Click Assay Tutorial to return to the main folder page. You will now see GenericAssay on the assay list.

Add Fields to the Assay Design

At this point, we have a skeleton design capable of uploading any spreadsheets of the same format. For this tutorial, we'll add our own fields, in order to capture information about who was operating the instrument and with what settings.

An assay design is composed of different fields. There are three types of built-in fields:

  • Data Fields: Can be read from the uploaded file.
  • Run Fields: Are specific to a single file and will be populated by the operator for each file, or run of data.
  • Batch Fields: Apply to groups of runs and are typically populated by the operator once per batch.
For any fields requiring user entry, we can clarify what users are supposed to enter by customizing the description. It is also possible to make user entry more reliable by constraining fields to known sets of values (such as specific machines present in a given lab) and defining data validators and formats to catch common entry errors.

  • Open your new design for editing:
    • Click GenericAssay in the Assay List web part.
    • Select Manage Assay Design > Edit Assay Design.
  • Click the heading for the section Batch Fields.
    • Click Add Field, enter the Name "OperatorEmail".
    • Click Add Field again, enter the Name "Instrument".
    • Click the (expansion) icon on the right and enter the Description: "The diagnostic test instrument."
  • Scroll down and click the heading for the section Run Fields:
    • Click Add Field.
    • Enter the Name "InstrumentSetting".
    • Select Integer for the Data Type field.
    • Click the (expansion icon) to open the panel.
    • Enter the Description: "The configuration setting on the instrument."
  • Note: if you add an extra blank field, or any field you want to delete, you will need to open the editor panel for it by clicking the (expansion icon), then clicking Remove Field to delete it.
  • Click Save in the lower right.
  • Your new assay design is now ready to use. We can use it to import as many runs as we like from spreadsheets with the same structure and gather instrument information from the operator.

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