Biologics: Create Samples

2024-03-29

Premium Feature — Available with LabKey Biologics LIMS. Learn more or contact LabKey.

To create new samples within LabKey Biologics, you must first create the Sample Type to describe the properties this kind of sample will have.

Once the type exists, you can create or import data for new samples, using grid and file import interfaces described here.

Topics

Create Sample Type

The Sample Type defines the fields and properties of samples. You can create Sample Types either inside or outside the LabKey Biologics application.

To create Sample Types inside the Biologics Application, click Sample Types on the main menu, then select Create Sample Type.

Follow the Sample Type creation process, as described in this topic for the LabKey Sample Manager application:

Built in system fields, such as Sample Status, Storage Amount and Units, and Expiration Dates are always available in a Sample Type by default. You can disable unneeded default fields and add additional custom fields as well. Once you specify all the properties and fields, click Finish Creating Sample Type and it will be available for use in the application.

Learn about about the different field types available in this topic: Field Types and Properties Special behavior for File fields in Sample Types is described in this topic: Attach Images and Other Files

Naming Patterns

Samples must have unique names (SampleIDs). These can be provided by you or generated by the system using a Naming Pattern as part of the definition of the Sample Type. Naming patterns can incorporate column values, dates, strings, and lineage details. Learn more in this topic:

Aliquot Naming Patterns are also defined for the sample type. The default is the parent sample name (AliquotedFrom) followed by a dash and incrementing counter:
${${AliquotedFrom}-:withCounter}

If instead you wanted to use a dot between the sample name and aliquot number, you'd use the pattern:

${${AliquotedFrom}.:withCounter}

Learn more about customizing aliquot naming patterns here: Aliquot Naming Patterns

Both Sample and Aliquot naming patterns will be validated during sample type creation, giving administrators a chance to correct any syntax errors. Users will be able to hover over the to see an example generated ID in a tool tip within the application when creating new samples or viewing the details for a sample type.

Sample Name Changes

Note that you cannot edit the SampleID (Name) later using any grid, bulk or file import method. To change the SampleID, you can edit the individual sample's details. Keep in mind that sample names must remain unique.

Note that an administrator can restrict the ability to edit sample names if desired.

Sample and Aliquot Fields

The Fields in a Sample Type define the data and metadata you can store about the sample.

An administrator can configure each field to be:

  • Editable for samples only (default): Aliquots will inherit the value of the field from the sample.
  • Editable for aliquots only: Samples will not display this field, but it will be included for aliquots.
  • Separately editable for samples and aliquots: Both samples and aliquots can set a different value for this property.

Add Samples

There are several ways to add samples to the system.

  • From the grid of the type of samples you're adding, select Add > to add them manually or import from a file. Learn more here.
  • From the home page or Sample Types dashboard, click the Add Samples menu and choosing either import method, then select the sample type to add. When importing from a file, you can also elect to add samples of multiple types and optionally create storage for the new samples. Learn more here.
  • From the detail page for any Registry Source: Select Manage > Create Samples > [Type of Sample] to create samples of any type. See below.
  • From a Registry Source or Media type that you want to include as the parent of new samples, select the desired parent rows, then choose Create Samples > [Type of Sample].

You can also create new samples from other entities or parent samples as described in the next section.

Derive Samples from Selected Parent(s)

To create new samples of any type by deriving them from one or more parent sample(s), start from the grid of the parent sample type.

Select the parent(s) using checkboxes, then choose Derive > and one of the options. Note that on narrower browsers, the "Derive" section will be under the More menu.

Derive From Selected

When you select one or more parent samples and choose Derive > Derive from Selected > [Type of Sample], you can create one or more output samples per parent, potentially with different properties.

Enter how many new samples per parent you want to create, then click Go To Sample Creation Grid.

You'll see the parent entity prepopulated, can edit this if necessary, and provide other details before finishing sample creation.

Learn more in the companion topic for Sample Manager:

Aliquot or Pool Selected Samples

Selecting one or more samples, then choosing either Aliquot Selected or Pool Selected will let you create a selected number of new samples with the given parent(s).

Provide the number to create (for derivatives and aliquots this is the number per parent), then click Go To Sample Creation Grid to continue creating the new samples with prepopulated parents.

Learn more in the companion topic for Sample Manager:

Sample Creation Wizard

The fields required for creating new samples will vary based on the Sample Type.

  • All new samples require:
    • Sample Type: May be prepopulated, or need to be selected.
    • Quantity to create.
  • You can provide values for other system fields like the expiration date, storage amount and units, etc.
You can either add samples manually or import their data from a file. More details for both options are found in the companion topic for the LabKey Sample Manager application:

Parents

If desired, one or more parents of the new sample can be added here. Click Add Parent, then select the type of parent to be added from the list of Registry Source Types and Sample Types available. More than one type of parent may be selected if needed, and there is no requirement that each new sample have parents from every type selected.

If you are generating new sample IDs from an existing sample or entity, it will already be prepopulated as a parent, with the type of entity preselected as a parent type.

Generating Samples

Once the fields in the wizard are completed, click Finish Creating # Samples to generate the new samples.

Upon successful submission, you will see the sample type filtered to show only your newly created samples.

Import Samples from File

Access this option by navigating to the type of sample you are importing and choosing Add > Import from File. Note that this option is only for adding new rows. If you want to update existing rows, select Edit > Update from File instead.

Using a downloaded template for your Sample Type makes it easy to import data in the expected format from file.

Follow the steps in the companion topic for Sample Manager:

Click Import to create the samples.

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