Biologics: Projects and Folders

Documentation
The LabKey Biologics application is designed to run in a project or folder on LabKey Server. This topic covers considerations for designing your system.

Support Multiple Biologics Containers

Biologics runs in the context of a project or folder, collectively known as containers. Each container can have unique permissions assignments and data, supporting a secure and isolated workspace. If desired, many resources, including assay designs and sample type definitions, can also be shared across multiple containers. The Biologics administrator should determine the configuration that best represents the organization.

Example Scenarios:

1. You might have two groups doing distinct work with no need to share data or compare results. These two groups could each use a separate Biologics project or folder and keep all resources within it.

2. If two groups needed to use the same assay designs or sample types, but would not otherwise share or compare the actual data, those definitions could be placed in the Shared project, with all collection and analysis in separate folders for the two groups. Note that in this scenario, Samples created of those shared types would have the same naming pattern and if you used a container-specific prefix, it would not be applied to the samples of the shared type.

3. If multiple groups need to share and compare data, and also keep clear which data came from which group originally, you could apply a container prefix in each group's folder so that all data would be consistently identified. In this scenario, each container would need its own sample type definitions so that the naming patterns would propagate the prefix into the created samples.

4. Configure Biologics in a top level LabKey container, then add one or more sub-containers also of folder type "Biologics". These sub-containers are called Projects within Biologics. Bioregistry and Sample definitions can be shared among the Projects and permissions controlled independently. Users will see the entities and samples from Projects to which they have been granted "Read" permissions.

When in use, an additional Project menu will be show between the Biologics logo and the main menu. Users will see the contents of the application 'scoped' to the selected Project. Selecting the top-level container (BiologicsMultiVerse in this example) will show all data the user can access across all Projects.

5. Freezers can be shared among folders with different permissions. Users will only be able to see details for the stored samples to which they have been granted access. Learn more about shared freezer access in this topic: Biologics: Shared Freezers

Apply Naming Prefix

You can apply a container-specific naming prefix that will be added to naming patterns to assist integration of data from multiple locations while maintaining a clear association with the original source of that data.

This prefix is typically short, 2-3 characters long, but will not be limited. Prefixes must be unique site-wide, and should be recognizable to your users. Before setting one, make sure you understand what will happen to the naming patterns and names of existing entities in your project.

  • All Naming Patterns for Sample Types and Data Classes in the container will be updated to include the new prefix.
  • New samples and entities created after the addition of the prefix will have names that include the prefix.
  • Existing samples and entities created prior to the addition of the prefix will not be renamed and thus will not have the prefix (or might have a different previously-applied prefix).
  • Sample aliquots are typically created and named including the name of the sample they are aliquoted from. This could mean that after the prefix is applied, new aliquots may or may not include the prefix, depending on whether the originating sample was created before or after the prefix was applied. Learn more about aliquot naming here: Aliquot Naming Patterns.
To set a container prefix:
  • Select Administration from the user avatar menu.
  • Click the Settings tab.
  • Scroll down to the ID/Name Settings section.
  • Enter the prefix to use. You will see a preview of what a Naming Pattern with the prefix applied might look like using a representative example, Blood-${GenId}:
  • Click Apply Prefix to apply it.
  • This action will change the Naming Pattern for all new and existing Sample Types and Data Classes. No existing IDs/Names will be affected. Are you sure you want to apply the prefix?
  • Click Yes, Save and Apply Prefix to continue.

Force Usage of Naming Patterns for Consistency

To maintain consistent naming, particularly when using container-specific naming prefixes, you may want to restrict users from entering their own names for entities. This requires that every type of entity have a naming pattern that can be used to generate unique names for them.

When users are not permitted to create their own IDs/Names, the ID/Name field will be hidden during creation and update of rows, and when accessing the design of a new or existing Sample Type or Data Class.

Additionally:

  • Attempting to import new data will fail if an ID/Name is encountered.
  • Attempting to update existing rows during file import will also fail if an unrecognized/new ID/Name is encountered.
To disallow User-defined IDs/Names:
  • Select Administration from the user avatar menu.
  • Click the Settings tab.
  • Scroll down to ID/Name Settings.
  • Uncheck the box Allow users to create/import their own IDs/Names.
    • Note that to complete this change, all entities in the system must have a valid naming pattern. You will see a warning if any need to be added.

Shared Sample Types and Data Classes (Bioregistry Entities)

Any Sample Types and Data Classes (Bioregistry Entities) defined in the /Shared project will also be available for use in LabKey Biologics LIMS. You will see them listed on the menu and dashboards alongside local definitions.

From within the Biologics application, users editing (or deleting) a shared Sample Type or Data Class will see a banner indicating that changes could affect other folders.

Note that when you are viewing a grid for any Data Class, the container filter defaults to "Current". You can change the container filter using the grid customizer if you want to show all Data Class members in "CurrentPlusProjectAndShared" or similar.

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