Tutorial: Design a General Purpose Assay Type (GPAT)

Documentation

Overview

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, allowing you to confirm a valid run.
  • Integrate quality controlled 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 a "general purpose assay type", or "GPAT", one of LabKey Server's many tools for working with instrument data. This assay type provides a flexible format for describing your experimental results, so that many sets of experimental results can be imported to LabKey Server using the pattern specified in the design. The structure of an assay design may include:

  • the type and format of experimental result files
  • contextual information about the experiment
  • the definition of summaries or visualizations appropriate for sharing
Assay designs also help to ensure that appropriate data points are collected for each experimental run loaded into the server. For any manual data entry steps, LabKey Server automatically generates the appropriate data entry pages based on the assay design. The design can specify required and optional data fields, default values for fields, as well as pick-lists of standard values, thereby reducing the incidence of errors when entering data.

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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