This topic covers the management of samples and types of samples within the Sample Manager application.
Freezer Management Available

You can track the storage and usage of samples through the Freezer Management feature. Learn about storing samples in freezers here:

View All Sample Types

To view all the Sample Types defined in LabKey Sample Manager, click Sample Types on the main menu.

You can select between several ways to view all the samples in the system.

Grid

The grid view of all Sample Types lists the name, description, and other details about each type of sample in the system.

Click the name to open the set of individual samples of that type.

Heatmap

The heatmap shows a 12 box row for each type, representing 12 months of sample collection. Darker shades are used for months where more samples were collected. Hover over any square for more details.

Click a square to open a grid view of data filtered for that month and Sample Type.

Cards

The card view of all samples indicates the total number of samples for that type.

Click a card to see the grid of data for that Sample Type.

View Samples of One Type

You can open the grid of all samples of a specific type in several ways:

The grid of samples can be filtered, sorted, and searched using the omnibox selection field.

Manage Menu

Actions on the Manage menu for a Sample Type include:

  • Import Samples
  • Delete Samples
  • Edit Selected Samples in grid: Edit the selected rows in a grid.
  • Edit selected samples in bulk: Assign the same value to one or more fields of a batch of selected rows.
  • Add to Picklist

Jobs Menu

The Jobs menu offers the following options. Learn more at the links:

Storage Menu

The Storage menu offers the following options. Learn more at the links:

Menu

The menu in the upper right offers these options:

  • Edit Sample Type Design: Reopen the existing details and fields; edit using the same interface as you used to create the Sample Type. Note that you cannot edit the Name of the type, and use caution if you change the naming pattern that you will maintain unique names for each sample.
  • Delete Sample Type: Note this will delete all sample data as well
  • View Audit History: Administrators can view the audit history for this Sample Type from this link.

View Individual Sample Details

Click the Sample ID for any sample to view the details entered about it. Any description will be shown in the header and properties defined for that type of sample will be shown under Details with their values. From the (bars) menu you can create new samples of this type, delete this sample, check it out of storage, or upload assay data for this sample. You can also view the audit history for this specific sample.

Panels on the page include:

  • Storage Location: Shows the current location, checkout status, and storage details.
  • Aliquots: Details about any aliquots created of this sample.
  • Details: Details about this sample.
  • Source Details: Information about sources of this sample.
  • Parent Details: Information about parents of this sample.
The tabs along the top of the details page let you see the lineage, aliquots, assays, jobs, and timeline for this specific sample.

Edit Sample Details

To edit the details for this sample, click the (Edit) icon for that section. Make changes using dropdowns and selectors similar to when you originally assigned the values. Remember to click to Save your changes.

Edit Sample Lineage

You can edit the source and parent information (i.e. the lineage) for a sample directly from the sample details page. Use the (Edit) icon for the Source Details or Parent Details section as needed. Make changes using dropdowns and selectors similar to when you originally assigned the values. Remember to click to Save your changes.

Edit Details for Multiple Samples

To simultaneously edit the details for multiple samples, select them on a grid or picklist (using checkboxes), then choose either:

  • Manage > Edit Selected Samples in Grid, or
  • Manage > Edit Selected Samples in Bulk

Edit Selected Samples in Grid

When using the grid editor, there are two tabs available:

  • Sample Data: Enter new values for the selected samples; you cannot edit read-only fields like the Sample ID or Barcode value.
  • Storage Details: Edit the storage information for the selected samples.

Click Update Samples when finished editing.

Edit Selected Samples in Bulk

The sample details can be edited in bulk. Click to Enable the fields that you want to assign the same value for all the selected samples. Shown here, the "Project" will be changed but the other fields will be left unchanged.

Click Edit with Grid to make further adjustments to details or storage information in the grid editor.

Click Update Samples when finished editing.

Delete Samples

Deletion of samples may be necessary for a variety of reasons, and once completed, deletion cannot be undone. You can delete a single sample while viewing it's details page.

  • From the detail page for the sample to delete, open the (bars) menu on the right.
  • Select Delete Sample.
  • You will be asked to confirm the deletion.

You can also delete one or more samples from the grid view for the Sample Type. Note that you can only delete up to 10,000 samples at one time, so if you need to delete more than that, perform the deletion in batches.

  • From the grid view for the type of sample to delete, select one or more checkboxes for the sample(s) you wish to delete. To select all samples, use the checkbox at the top of the column.
  • Select Manage > Delete Samples.
  • You will be asked to confirm the deletion.

Note that if any of the samples you attempt to delete were used to derive other samples (i.e. are parent samples) or are associated with assay runs (i.e. linked as lookups from data you have imported) you will not be able to delete them. The popup will give you more details and ask you to confirm or cancel the partial deletion of any samples without dependencies.

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