Introduction to LabKey Biologics

Documentation: Version 22.3

LabKey Biologics aims to speed the discovery of biologic therapies by providing key tools for research teams, including:

  • A consolidated knowledge base to store and organize everything you need to make scientific decisions
  • Efficient and reproducible capture and integration of your data, from samples, assays, and experiments
  • Tools promoting collaboration among teams for smooth handoffs and reproducible procedures
  • Media management for clear tracking of ingredients and mixtures.
  • A data-integrated electronic lab notebook (ELN)
  • Freezer management aligning your physical storage with digital storage and tracking.
This topic provides an introductory tour of these key features.

Knowledge Base

Bioregistry

The Bioregistry forms the team's shared knowledge base, containing detailed information on your sequences, cell lines, expression systems, and other research assets. The Bioregistry recognizes nine entity types:

  • Cell Lines
  • Constructs
  • Expression System
  • Molecules
  • Molecule Sets
  • Molecule Species
  • Nucleotide Sequences
  • Protein Sequences
  • Vectors
If desired, these entity types are customizable to reflect the focus of your research project or simply to suit the terminology preferred by your organization.

Data Grids

Each entity type is organized into data grids that can be filtered, sorted, and searched to find items of interest. A search bar above each data grid provides intuitive querying for entities. Data grids are customizable to show those columns that are most relevant to the research effort.

Entity Details

Click an entity in a grid to see its details page. Each details page shows the entity's properties and relationships to other entities. All details pages can be configured to show the most relevant data. For example, the details page for a protein sequence shows the chain format, average mass, extinction coefficient, the number of S-S bonds, etc., while the details page for a expression system shows the cell lines, constructs, and target molecule, as well as the samples drawn from it.

Entity Relationships

Each details page contains a panel of relationships to other entities. For example, for a given protein sequence, the relationship panel shows:

  • which expression systems it is included in
  • which molecules it is a part of
  • which nucleotide sequence encodes for it
Entity relationships are shown as links to other details pages, making it easy to follow lineage lines and to track down associated samples and experimental data.

To get a sense of how the Registry knowledge base stores entities and their relationships, follow the tour steps below on your Biologics Trial Server. You should have another browser window open on the home page of your trial.

This series of clicks navigates through entities related to a particular protein sequence (the Nivolumab Light Chain).
  • Navigate to the Biologics home page.
  • Click the Menu.
  • Under Registry, click Protein Sequences.
  • In the data grid, click PS-24. Notice the detailed information about the Nivolumab Light Chain protein sequence.
  • Scroll down to the Related Entities panel and click M-3. Notice the detailed information about the Nivolumab molecule.
  • Scroll down to the Related Entities panel and click ES-3. This expression system is linked to assay result data, as shown below.

Capture and Integration

Data about your samples, experiments, and instrument assay results can be integrated to provide a full data landscape. Design customized methods for representing and linking your information.

Inventory

Samples, media stocks, and other lab assets are stored in an inventory, organized into data grids and detail pages, similar to the way entities are stored in the Registry. Names for newly created samples are generated according to a pre-defined pattern controlled by administrators. Sample names can be built up from elements such as dates, incrementing numbers, static text, project names, etc. For example:

  • vial-0001
  • S-11.22.2019-0001
  • BarCode-20191122.0001
Existing sample inventories can be easily imported into the system.

Sample Lineage

The inventory system also understands sample vial relationships and lineage, that is, parent and child vials. A graphical view shows the upstream and downstream lineage of the current sample. The same information is also available in a grid form, which allows you to navigate via the parentage lines to related sample vials.

Media Recipes and Batches

The inventory also lets you define both media recipes and real batches of media, so you can track current state of your lab stocks.

To get a sense of how experiments link together samples and result data, follow the tour steps below on your biologics trial server. This series of clicks navigates from assay result data (for Cell Viability) to related sample information and lineage.
  • Click the Menu in the header.
  • Under Assays, click Cell Viability.
  • Click the Results sub-tab. This data grid shows all of the Cell Viability data in the registry.
  • Click the sample S-001. This sample was used to generate one row of the Cell Viability data.
  • Click the Lineage sub-tab. Notice the graph showing the parent expression system from which the sample was drawn.

Analytics and Visualizations

Analytics and visualizations can be included throughout LabKey Biologics to provide key insights into the large molecule research process.

Protein Classification Engine

When new protein sequences are added to the Registry, they are passed to the classification and annotation engine, which calculates their properties and identifies key regions on the protein chain, such as leader sequences, variable regions, and constant regions. (Researchers can always override the results of the classification engine, if desired.) Results are displayed on the Sequence tab of the protein's detail page. Identified regions are displayed as multicolored bars, which, when clicked, highlight the annotation details in the scrollable section below the sequence display.

On your biologics trial server, you can reach this same sequence:
  • Click the Menu in the header.
  • Under Registry, click Protein Sequences.
  • In the data grid, click PS-24.
  • Click the sub-tab Sequence. Notice the sequence analysis panel which displays multi-colored sub-sequences and associated annotations.

Collaboration Among Teams

A fully customizable task-based workflow system is included in LabKey Biologics. Individual users can all be working from the same knowledge base with personalized task queues and priorities. While no example tasks or templates are included with your trial, you can create your own.

  • Click the Menu in the header.
  • Click Workflow.
  • Click Create.
  • Under Workflow, you have two options:
    • Job: Design a job with subtasks, assignments, connections to entities and samples, etc.
    • Job Template: Design a template for creating many similar jobs.

Media Management

In the Media section of the main menu, you will find sections for tracking:

  • Batches
  • Ingredients
  • Mixtures
  • Raw Materials
Careful tracking of media and components will help your team develop quality production methods that are reproducible and scalable.

Electronic Lab Notebook

Our data-integrated ELN (electronic lab notebook) helps you record results and support collaboration and publication of your research. Directly link to relevant registry entities, specific result runs, and other elements of your biologics research. Submit for review and track feedback and responses within the same application.

Learn more in this section:

Freezer Management

When you use Freezer Management tools within LabKey Biologics, you can directly track the locations of samples and media in all the freezers your team uses. Create an exact digital match of your physical storage and record storage details and movements accurately. Sample data is stored independently of storage data, so that all data is retained even after a sample is consumed or removed from storage.

Learn more in the Sample Manager documentation here:

Discussion

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