This topic is under construction.

This topic is intended to be used with a LabKey Trial Server.

LabKey provides a customizable framework for longitudinal study data. A study tracks information about subjects over time. Explore a read-only example here:

This topic assumes you have your own time series data about some study subjects and helps you create your own study where you can upload and analyze data of your own. To do that, you will use a cloud-hosted trial version of LabKey Server. It takes a few minutes to set up and you can use it for 30 days. If you already have a Trial Server to use, you can log in to it and skip ahead.

Start a Trial Server

Log In Here

To start a trial, you need a free account on www.labkey.org.

Start a Trial Server

  • Logged in to your www.labkey.org account, click here. It will open in a new tab:
  • Use that new tab in parallel with this topic to complete the process:
    • Click Add Product.
    • Under LabKey Server - Trial, click Create Site.
    • Give your site a Name: This will be shown in the header (where you see "LabKey Support" on this page).
    • Select your unique URL: Something short and memorable that will be the first segment of your URL.
    • Leave the Product, "LabKey Server - Trial" selected.
    • Click terms of use to open it in the panel. After reviewing, check the box agreeing to the terms.
    • Click Create Site.
Site creation takes approximately 5 minutes. While you wait, let's plan the design of your study and gather information.

Plan Your Study Framework

You may already have data you plan to upload. If not, we will provide example files to get you started.

Identify your Study Subjects

The subjects being studied, "participants" by default, can be humans, animals, trees, cells, or anything else you want to track.

Look at a dataset you plan to use. How are subjects under study identified. What column holds identifying information?

Decide How To Track Time

Time Based: The example study to explore tracks time using dates. The date of each data collection are entered and the study is configured to break these into month-long timepoints, labeled as "Month 1", "Month 2" etc.

Visit Based: You can also track time in a visit-by-visit manner. If the elapsed time between events is not relevant but you have a fixed sequence of visit events, a visit-based study may be appropriate. Visits are identified by sequence numbers.

Continuous: A continuous study is used when there is no strong concept of visits or fixed buckets of time. Data is entered and tracked by date without using timepoints.

Specimen Integration

If your study will integrate with data from analysis of specimens, you can incorporate that information. This walkthrough does not cover that scenario - you can learn more in this topic: Specimens: Administrator Guide.

Security

Identify your security requirements and how you plan to use the data in your study. Who will need access to what data

Create Your Study

  • Once your trial server has been created, you will receive an email notification with a direct link to it, or you can click Go To Site in the trial manager.
  • Click the Create Project button on the home page.
  • Enter Name "Tutorials", leave the default folder type and click Next, then Next and then Finish to create the new project with all the default settings.
  • In the new project, click Create New Subfolder.
  • Enter the Name you want. In our example, it is named "My New Study".
  • Select the folder type Study and click Next.
  • Click Finish to create the folder.
  • Click Create Study.

  • Under Look and Feel Properties:
    • Study Label: Notice your folder name has the word "Study" added; you can edit to remove redundancy here if you like.
    • Subject Noun (Singular and Plural): If you want to use a word other than "Participant/Participants" in the user interface, enter other nouns here.
    • Subject Column Name: Look at the heading in your dataset for the column containing indentifiers. Edit this field to match that column.

  • Under Visit/Timepoint Tracking:
    • Select the type of time tracking you will use. Dates, Assigned Visits, or Continuous.
    • If needed for your selection, enter Start Date and Default Timepoint Duration.

  • Under Specimen Management:
    • Leave the default selection. You can change it later if you decide to add specimen data to the study.

  • Under Security Mode:
    • Select whether to use basic or advanced security and whether to make datasets editable or read-only.
    • To maximize the configurability of this study, choose advanced security with editable datasets.

  • Click Create Study.
  • You will now be on the Manage tab of your own new study. This tab exists in the read-only exploration study we provided, but you cannot see it there. It is visible only to administrators.
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Upload Your Data

TBD

Discussion

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