This tutorial provides a guided tour of LabKey Biologics' user interface and search functionality, including:
  • How to use the main dashboard and menus
  • How to search for entities of interest
  • How to view and interpret detailed views of those entities
  • How to navigate to related entities
  • How to browse and refine registry grid views

Set Up Trial Server

  • This tutorial assumes that you have registered and created a Biologics Trial instance of the server.
  • If you have already created a biologics trial server, select it, and login: Your Sites
  • On your site, click Explore.

Main Dashboard and Menus

This section provides a quick tour of LabKey Biologics. Click along as directed to see different aspects of the data and the available tools.

Biologics Home Page

  • Navigate to your Biologics home page.
  • The top header bar is available throughout the application and includes:
    • The clickable logo, for returning to this dashboard at any time.
    • A main Menu button, giving access to all of your data and activities.
    • A set of additional menus in the upper right:

On the dashboard, you'll also see panels displaying:

  • Dashboard Insights: A selectable set of visualizations, defaulting to the Sample Count by Sample Type.
  • Recent Assay Data: Quick access to the most recently imported assay runs. Use the selector to narrow to a specific assay.

Notifications

In the header, the Notifications menu will report when background imports are completed.

Large imports will be completed in the background, freeing the user to work on other tasks in the system. While an import is underway, the bell icon will be replaced with a spinner icon. The number superimposed on the menu indicates how many notifications are available.

Registry Dashboard

In the main header Menu, click Registry.

The Registry section is where you will find all the different Entities in the system: Molecule Sets, Molecules, etc.

Data Grids

  • Click Molecules.
The Molecules page shows a data grid of all of the registered Molecules.

Detail Pages

  • Click M-3.
  • The M-3 Details page shows properties, components, related entities of this molecule.
  • Scroll down to view the related entities.
  • Return to the Molecules grid page by clicking Molecules in the submenu bar. You can also use the main menu.

Search Biologics

  • In the header search panel, enter:
    IgG1
  • While there are only a few results, explore filtering them:
    • Click Advanced
    • Open the dropdown menu and select Molecule.
    • Click Search.
  • Click the M-1 search result.
  • Scroll to the Molecule Components and click PS-17.
    • If you click anywhere in the bar, the section will expand. Click the actual name link "PS-17" to switch to that entity's details.
  • Click Sequence. The Sequence tab shows sequence annotations (the results of the sequence analysis engine).
  • Click Protein Sequences.
  • You are taken to a data grid of the registered protein sequences.
  • Clicking in the "Select..." omnibox above any grid brings up a dropdown of options: filter, keyword search, sorting, and selecting grid views by name (when any are defined).
  • If you type directly into the box, you will search. Enter the following text in the search bar:
    IgG4
  • The search returns 3 results.
  • Sort by clicking the menu icon in the column header Avg. Mass and selecting Sort ascending.
  • Modifications of the grid accumulate in the search bar in lozenge boxes.
  • Clear the modifications to return the grid to its original state. To reveal the 'X' for deleting, hover over the lozenge.

The guided tour continues in the following topic: Biologics Tutorial: Add Sequences to the Registry

Next Tutorial

Biologics Tutorial: Add Sequences to the Registry

Discussion

Was this content helpful?

Log in or register an account to provide feedback


previousnext
 
expand all collapse all