LabKey Biologics represents materials in various phases of bioprocessing using Samples
. Samples of many different types can be defined to represent your development process. They can be standalone compounds, they can have parentage/lineage, they can be aliquoted, used to derive new samples, or pooled. The lineage of samples you track may be both concretely real (such as a parent material or vial) and virtual (such as a Recipe and/or an Expression System used).
Sample Types define the fields and properties for the different kinds of samples in your system.
Sample Types Dashboard
In the LabKey Biologics application, the Sample Types
dashboard displays an overview of all the samples known to the system.
Sample Types can be created and edited either inside or outside of the Biologics Application
Click the name of a Sample Type to see details about the type, including how new names will be generated, plus a panel of sample type Insights
and a grid of all SampleIDs registered of this type. Menus are provided for:
- Create: Presents the list of what you can create from here, including new Samples of any existing type.
- Manage Samples: Actions available here include importing samples from file, deleting, and editing in grid or bulk.
- Jobs: Start a workflow job. If any samples are selected, you can also add them to a new or existing job.
- Charts: If charts are defined for this kind of sample, you can open them from here.
- Paging controls.
- : Download
- Grid Views: Select from any custom grid views offered for this kind of sample.
- Sample/Aliquot Selector: Choose from:
- All Samples (Samples and Aliquots)
- Samples Only
- Aliquots Only
Below the menus, the omnibox
offers searching, sorting, and filtering like other grids in the system.
Sample Type Insights
The panel of Insights
gives a quick visual summary of Storage Status
, Sample Status
, and Aliquots
. Color coded bars show the relative prevalence of each state. Hover for details, shown here, how many samples are checked out. Click any bar segment to filter the samples grid to show only those samples.
Learn more in the companion topic for Sample Manager
Click an individual Sample Id to see its details. A sample details page
shows five tabs:
- Overview: Summary of sample and parent information.
- Lineage: Shows the parents and children of the current sample.
- Aliquots: Shows all aliquots created from this sample (if any).
- Assays: Displays any assay data associated with this sample.
- Jobs: Shows all jobs involving this sample.
A brief summary of each is shown below. More details are available in the Sample Manager documentation
The overview tab shows the values of all properties for the sample.
- Create Samples (of any Sample Type): Only creation of derivatives is supported here. By default this sample will be a parent of the new one(s).
- Create Workflow Job: By default this sample will be automatically assigned to the job.
- Upload Assay Data (for any Assay)
- Delete Sample: Available only when samples do not have dependents like derived samples, assay data, or status that prevents deletion.
Below the panel of details about this sample, you will see a panel of Parent Details
giving the type and property values for the parent from which this sample was created. Shown above, "ER-005", one of the expression runs.
Users with appropriate permissions can edit the parent details here when appropriate, changing parents, adding additional "parents" of other types, etc.
Sample lineage is available as a graphical view by default, as shown below. Hover over any node for more information, click any node to see details. Click Go To Lineage Grid
to see the same information as a grid. Learn more in the topic: Entity Lineage
A grid of all the aliquots created from this sample. Learn more about creating aliquots in the Sample Manager documentation
The Aliquot Naming Pattern
is part of the sample type definition
. The default is the parent sample name (AliquotedFrom
) followed by a dash and incrementing counter:
If instead you wanted to use a dot between the sample name and aliquot number, you'd use the pattern:
Learn more about customizing aliquot naming patterns here: Aliquot Naming Patterns
On the Assays
tab, you can see all the assay data available for that sample, as well as for all aliquots (and subaliquots) created from it. Click the assay name to see all results for that assay for the sample you are viewing. Select whether grids include data for samples, aliquots of those samples, or both.
A grid of links to all the jobs that involve this sample, if any. Click Start a New Job
to create a new one with this sample as an input.
The status of samples can be tracked using customizable Sample Status
values. There are three main types of status:
- Available: Can be used.
- Consumed: Used up, and can longer can be aliquoted or checked out, but remains in the system for analysis and tracking.
- Locked: Not currently available; some actions are prevented.
Learn more in the Sample Manager companion topic for this feature
Use Status Settings
Users can assign statuses to their samples throughout the system:
- At sample creation
- During file import of new or updated samples
- When updating a single sample's details
- In a bulk sample update
Aliquots can have status values separate from their parent sample.
Manage Status Options
From the main menu, click Sample Types
then click Manage Sample Statuses
. Scroll down to find the current status settings defined.
Sample Status Legend
In many places in the application, users can access a legend of available status values. Hover over the
for the Status
column or field to see a legend listing all the available status values and their color coding.
When working with samples, it can be convenient to create user-defined picklists
for gathering a set together for some operation like adding to a workflow job, adding to storage, performing bulk operations, etc. You can add samples to picklists from many places in the application, and create new ones as needed on the fly. A user can build a picklist privately, adding and removing samples until the correct set are defined, or share with the team so that everyone can work from the same list.
Access the picklists dashboard from the user menu:
Sample Grids Containing Samples of Several Types
Some sample grids, including picklists, workflow sample lists, and lineage listings of descendent samples, may contain samples of more than one sample type. These grids will offer a set of tabs:
- All Samples: A listing of all samples on the list, with system fields common to any sample type.
- Specific Sample Types: The type-specific listings will show, and allow updating of, properties of the specific sample type.
For example, menus on the picklist grid offer:
- Jobs (on all tabs)
- Storage (on all tabs)
- All Samples: The sample selection for the grid lets you select whether to show aliquots, samples, or both.
LabKey Server Documentation about Samples