Table of Contents

guest
2018-12-11
   Tutorials
     Set Up for Tutorials: Trial
     Set Up for Tutorials - Non-Trial
     Navigation and UI Basics

Tutorials


Tutorials provide a "hands on" introduction to the core features of LabKey Server, giving step-by-step instructions for building solutions to common problems. They are listed roughly from simple to more complex, and you can pick and choose only those that interest you.

In order to run any tutorial, you will need:

This icon indicates whether the tutorial can be completed on a Hosted trial server or a Virtual Machine trial server.

New User Tutorials

Title Description Works on Hosted Trial Server? Works on VM Trial Server?
Data Grid TutorialTake a quick tour of data grids and visualizations. No trial server necessary.  
Tutorial: SecurityLearn how to organize and secure your data using LabKey Server.
Tutorial: File RepositoryManage, search, and share file resources.
Tutorial: Collaboration ToolsLearn how to use LabKey Server's secure, web-based collaboration tools.
Tutorial: ListsWork with data tables.
Tutorial: Electronic Lab NotebookSet up a basic electronic lab notebook and sample inventory system.


Study Tutorials



Assay Tutorials

Title Description Works on Hosted Trial Server? Works on VM Trial Server?
Tutorial: Design a General Purpose Assay Type (GPAT)Import, manage, and analyze assay data. Add assay data to a study.
Tutorial: NAb AssayWork with NAb experiment data from 96-well or 384-well plates 
Tutorial: ELISA AssayImport and analyze ELISA experiment data. 
Tutorial: ELISpot Assay TutorialImport and analyze ELISpot experiment data. 
Discovery Proteomics TutorialStorage and analysis for high-throughput proteomics and tandem mass spec experiments. 
Tutorial: Import a Flow WorkspaceLearn about using LabKey for management, analysis, and high-throughput processing of flow data. 
Tutorial: Perform a LabKey Flow AnalysisAnalyze flow data. 
Tutorial: Import Flow Data from FCS Express  
Tutorial: Set Flow BackgroundLearn about setting metadata and using backgrounds with flow data. 
Luminex Assay Tutorial Level IManage, quality control, analyze, share, integrate and export Luminex immunoassay results. 
Luminex Assay Tutorial Level IIUse advanced features for quality control and analysis. 
Microarray Assay TutorialWork with sample microarray data. 
Expression Matrix Assay TutorialTry an example expression matrix assay. 


Developer Tutorials



Biologics Tutorials






Set Up for Tutorials: Trial


This topic covers the quickest and easiest way to set up to run LabKey tutorials using a free trial of LabKey Server. If you want to run tutorials not supported in the trial environment, or already have access to LabKey Server, see Set Up for Tutorials - Non-Trial.

Tutorials you can run using a free trial of LabKey Server are marked with this badge.

LabKey Trial Server

To run the LabKey Tutorials, you need three things:

1. An account on a running LabKey Server instance. It only takes a few minutes to create your own LabKey Trial Server:

2. A basic familiarity with navigation, folder creation, and utilities like web parts. Use this topic alongside your new instance: 3. A tutorial workspace project where you are an administrator and can create new folders.

  • On the home page of your trial server, click Create.
  • Enter the Name "Tutorials".
    • If you plan to share this trial server with other users, consider using "Tutorials-Username" so you can each have your own workspace.
  • Leave the default folder type selection, "Collaboration," and click Next.
  • Leave the default permission selection, "My User Only," and click Next.
  • Skip the advanced settings and click Finish.
  • (Optional): To enhance this project, you can add some custom content making it easier to use.

Finished

Congratulations, you can now begin running tutorials in this workspace on your trial server.

I'm Ready for the Tutorial List




Set Up for Tutorials - Non-Trial


This topic explains how to set up for the LabKey Tutorials on a non-trial instance of the server. If you are using a hosted trial server, use this topic instead: Set Up for Tutorials: Trial.

To run the LabKey Tutorials you need:

  1. An account on a running LabKey Server instance.
  2. A tutorial workspace project on that server where you are an administrator and can create new folders.
  3. A basic familiarity with navigation, folder creation, and utilities like web parts.
If running tutorials on a 30 day free trial instance of LabKey Server does not meet your needs, the other options for creating a tutorial workspace are:

Local VM Installation

1. You can download and install your own server on a local machine using VM image of the server. Follow the instructions in this topic to register, download, install, and start using LabKey Server.

2. You will be the site administrator on this server. To create a tutorials project:
  • Select (Admin) > Site > Create Project.
  • Enter the name "Tutorials" and choose folder type "Collaboration".
  • Accept all project wizard defaults.

3. Learn the navigation and UI basics in this topic:

Existing Installations

1. & 2. If your organization is already using LabKey server, contact your administrator about obtaining access as an administrator to a project or folder to use. For example, they might create and assign you a "Tutorials-username" project or subfolder. They will provide you the account information for signing in, and the URL of the location to use.

LabKey Server installations in active use may have specialized module sets or other customizations which cause the UI to look different than tutorial instructions. It's also possible that you will not have the same level of admin access that you would have if you installed a local demo installation.

3. Learn the navigation and UI basics in this topic:

The location given to you by your administrator is your tutorial workspace where you can create a subfolder for each tutorial that you run.

Full Local Installation

1. If none of the above are suitable, you may need to complete a full manual installation of LabKey Server. Detailed instructions are provided here:

If you encounter difficulty during this installation, you may find help in our Installation Forum.

2. You will be the site administrator on this server. To create a tutorials project:

  • Select (Admin) > Site > Create Project.
  • Enter the name "Tutorials" and choose folder type "Collaboration".
  • Accept all project wizard defaults.

3. Learn the navigation and UI basics in this topic:

Finished

Congratulations, you can now log in, navigate to your workspace, and begin running tutorials.

Learn More

I'm Ready for the Tutorial List




Navigation and UI Basics


Welcome to LabKey Server!

This topic helps you get started using LabKey Server, understanding the basics of navigation and the user interface.

If you are using a LabKey Trial Server, use this topic instead: Learn About LabKey Server: Trial.

Projects and Folders

The project and folder hierarchy is like a directory tree and forms the basic organizing structure inside LabKey Server. Everything you create or configure in LabKey Server is located in some folder. Projects are the top level folders, with all the same behavior, plus some additional configuration options; they typically represent a separate team or research effort.

The Home project is a special project. It is the default landing page when users log in and cannot be deleted. You can customize the content here to suit your needs. To return to the home project at any time, click the LabKey logo in the upper left corner.

The project menu is on the left end of the menu bar and includes the display name of the current project.

Hover over the project menu to see the available projects, and folders within them. Click any project or folder name to navigate there.

Any project or folder with subfolders will show / buttons for expanding and contracting the list shown. If you are in a subfolder, there will be a clickable 'breadcrumb' trail at the top of the menu for quickly moving up the hierarchy. The menu will scroll when there are enough items, with the current location visible and expanded by default.

The project menu always displays the name of the current project, even when you are in a folder or subfolder. A link with the Folder Name is shown near the top of page views like the following, offering easy one click return to the main page of the folder.

For more about projects, folders, and navigation, see Project and Folder Basics.

Tabs

Using tabs within a folder can give you new "pages" of user interface to help organize content. LabKey study folders use tabs as shown here:

When your browser window is too narrow to display tabs arrayed across the screen, they will be collapsed into a pulldown menu showing the current tab name and a (chevron). Click the name of the tab on this menu to navigate to it.

For more about adding and customizing tabs, see Use Tabs.

Web Parts

Web parts are user interface panels that can be shown on any folder page or tab. Each web part provides some type of interaction for users with underlying data or other content.

There is a main "wide" column on the left and narrower column on the right. Each column supports a different set of web parts. By combining and reordering these web parts, an administrator can tailor the layout to the needs of the users.

For a hands-on example, try the Tutorial: Collaboration Tools.

To learn more, see Add Web Parts and Manage Web Parts. For a list of the types of web parts available in a full installation of LabKey Server, see the Web Part Inventory.

Header Menus and URLs

In the upper right, icon menus offer:

  • (Search): Click to open a site-wide search box
  • (Admin): Shown only to Admins: Administrative options available to users granted such access. See Admin Console for details about options available.
  • (User): Login and security options; help links to documentation and support forums.


Watch the URL at the top of the page as you navigate LabKey Server and explore features on your server. Many elements are encoded in the URL and programmatic access via building URLs is possible with APIs. Learn more here: LabKey URLs.

Security Model

LabKey Server has a group and role-based security model. Whether an individual is authorized to see a resource or perform an action is checked dynamically based on the groups they belong to and roles (permissions) granted to them. Learn more here: Security.

What's Next?