Tutorial: Design a General Purpose Assay Type (GPAT)

Documentation
This tutorial can be completed using a free 30-day trial version of LabKey Server.

This tutorial walks you through importing, annotating and interpreting the tabular results (often provided in a spreadsheet) of a custom assay. You will:

  • Set up a new assay design, to capture both the core data and the contextual information ("metadata") about the experiment.
  • Perform validation as you upload sample data.
  • Quickly visualize the data, to confirm a valid run.
  • Integrate selected assay data with other information in a study.

The "General Purpose" Assay Type (GPAT)

As part of this tutorial, we will create an assay design based on the "general purpose assay type", or "GPAT", the most flexible of LabKey Server's tools for working with instrument data. This assay type gives you complete control over the format for mapping your experimental results into LabKey Server. The structure of an assay design may include:

  • The type and format of experimental result files
  • Contextual information about the experiment provided by a user
  • The definition of summaries or visualizations appropriate for sharing
Assay designs can also ensure that all necessary information is collected for each experimental run loaded into the server. For any manual data entry steps, the design can specify required fields, offer sensible default values, build in immediate range or regular expression validation, and offer pulldown menus of acceptable values, thereby reducing the incidence of data entry errors.

Example

The original Excel spreadsheet looks like this:

The data grid within LabKey Server will look like this, offering many built in analysis options:

Tutorial Steps

First Step

Discussion

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