Terms and Definitions

Replicate(s)The following table defines the terms used in Clarity LIMS and related documentation.

Account	Not fully supported in Clarity LIMS v5.x and later. Support is planned for a future release. A workaround is to create an account quickly from the Projects and Samples screen. An organization with which the facility conducts business. Includes account address, client names, and other information. Associate clients with their applicable account (see Client). NOTE: In Clarity LIMS v2.1, the term labs was replaced with accounts. However, the API resource is still called lab.
Aggregation	See QC Aggregation.
Analyte	See Derived Sample. As of Clarity LIMS v5.0, this term is deprecated. However, the API resource is still called analyte.
Artifact	A generic term for an item at the beginning of a step generated by an earlier step. A derived sample or measurement is a type of artifact. NOTE: In the Clarity LIMS user interface, the term artifact has been replaced with derived sample or measurement. However, the API resource is still called artifact.
Automation	Used to trigger scripts from the Clarity LIMS user interface. An automation can be configured for steps and for derived samples.
Automation worker	A software component that runs automation. May be installed on the same server as Clarity LIMS or on several other machines that all draw from the queues of one Clarity LIMS instance.
Batch processing	Operations performed on more than one object at a time. For example, adding multiple samples to the system, rather than adding them individually.
BClarity LIMS	The main web client used by lab scientists, lab managers, and system administrators to complete the following tasks: Access information about the work currently underway in the lab. Create projects and upload samples. Record work completed in the lab. View project and sample status. Create and configure workflows, protocols, and steps. Create and configure automation. Create and custom fields and presets. Create and configure instruments, reagent kits and lots, reagent labels, and control samples.
Client	An individual within the laboratory, or an external individual who works with the laboratory, who is directly associated with a project in Clarity LIMS. NOTE: n the Clarity LIMS user interface, the term contact has been replaced with client. However, the API permission is still called contact.
Cloud hosted deployment	Clarity LIMS deployed with Illumina automation scripts to the Illumina Amazon AWS environment.
Collaborator	Clarity LIMS user role assigned to external customers or other individuals who submit samples to Clarity LIMS.
Contact	See Client.
Custom field (formerly UDF)	A field that Clarity LIMS administrators can add to the interface to collect information for a sample (or group of samples), master step, step, client, account, or container. For example, the administrator may wish to add a field to record whether a sample is toxic or safe to handle.
Derived sample	A sample that was generated (output) by a step. All derived samples trace back to submitted samples. By default, a step generates one derived sample. Configure some step types to output multiple derived samples (also referred to as derivatives)
Derivative	One of multiple samples generated by a step. See Derived Sample.
External Program Integration Plug-in (EPP)	See Automation. As of Clarity LIMS v5.0, this term is deprecated. However, some of the API documentation may still refer to EPP.
EPP node	See Automation worker. As of Clarity LIMS v5.0, this term is deprecated. However, some of the API documentation may still refer to EPP node.
Export	To copy a file and place it on the hard disk drive or in another piece of software.
File placeholder (formerly shared ResultFile)	A placeholder configured on a step that is replaced by a file at a run time. The file may be automatically generated or manually uploaded.
Group of defaults	A collection of prepopulated master step fields that define values for step data at run time. This eliminates the need to manually enter and make sure that information is recorded correctly every time a step is run. Groups of defaults are configured on the Custom Fields > Master Step Fields tab.
Import	To bring a file into Clarity LIMS and attach it to a placeholder or step.
Index	See Reagent Label and Label Group.
Input	An item that is consumed, processed, or analyzed by a step.
Label Also referred to as Reagent Label	Also referred to as reagent type, index, or molecular barcode. Add a label group for each reagent category used in the lab, and then add labels to the groups. Each label represents a reagent type within the group/category. See also Label Group.
Label group	A reagent category. Add a label group for each reagent category used in the lab then add labels to the groups. Each label represents a reagent type within the group or category. See also Label.
LIMS ID	A unique identifier assigned to all assets (samples, projects, containers, steps, and so on) in Clarity LIMS. IDs are assigned in a nondecreasing sequence. To prevent duplicate IDs being created by different applications in the suite in a race condition, each application allocates a group of IDs to itself when more are needed (currently in chunks of 50, which is not configurable). Therefore, Clarity LIMS IDs of sequentially uploaded samples, for example, may not have sequential Clarity LIMS IDs. We reserve the right to change the algorithm that generates Clarity LIMS IDs in future versions of Clarity LIMS. It is not suggested to assume that IDs are sequential. Instead, consider using a custom field and a script to set a sequential number.
Master step (formerly process type)	A technique or procedure performed on a sample. To be considered a master step in Clarity LIMS, the technique/procedure must be created and configured as such, and must have an input (not all steps have an output). Master steps are created and configured on the Lab Work configuration screen. These master steps act as templates from which individual steps are created and configured.
Measurement (formerly ResultFile)	Data that is generated during a step for each sample input to the step. Measurements can either be data written to measurement fields and/or files attached to the step inputs.
On premise deployment	Clarity LIMS deployed to your on-premise server or another non-Illumina cloud hosted environment, such as your own Amazon AWS environment.
Parse	The process of analyzing an input file and displaying it in Clarity LIMS.
Plug-in	A software component or module that adds functionality to a software program.
Preset	See Group of Defaults. As of Clarity LIMS v5.0 this term is deprecated.
Process	See step. As of Clarity LIMS v5.0, this term is deprecated. However, the API resource is still called process.
Process type	See Master step. As of Clarity LIMS v5.0, this term is deprecated. However, the API resource is still called process.
Project	Clarity LIMS uses projects as the basis for all work performed in the system. A project stores the information about the user who created it, the account and client with which they are associated, samples submitted to the project, significant dates, associated files, and so on. When adding samples to Clarity LIMS, they must add them to a project.
Protocol	In Clarity LIMS, a protocol is a set of steps that must be performed in a specific sequence, as part of a lab workflow.
QC aggregation	QC aggregation refers to a configured step that assembles sample QC measurements, evaluates them based on priority, determines overall QC results, and then assigns QC flags.
Queue	Queues allow the grouping of a collection of samples that are all waiting to be processed at a specific stage (protocol) in the lab workflow.
Reagent label	See Label.
Replicate(s)	See Derivative. As of Clarity LIMS v5.0, this term is deprecated.
Resultfile	See Measurements and File Placeholders. As of Clarity LIMS v5.0, this term is deprecated. However, some of the API documentation may still refer to ResultFile outputs.
Researcher	A role that can be assigned to a user in Clarity LIMS. Typically, the researcher role is assigned to laboratory scientists who use Clarity LIMS to manage and record their work as samples are processed in the lab.
Step	A lab procedure that has been configured and included as part of a protocol. All steps have a master step as their foundation.
Step type	In Clarity LIMS, steps and master steps are categorized based on the requirements and goals of the step, its inputs, and its outputs. For details, see About Step Types and Outputs.
Submitted sample	The original sample that is added to a project in Clarity LIMS.
Timestamp	The dates and times associated with a file.
User	An individual within the laboratory or an external individual who works with the laboratory and has access to the Clarity LIMS system. Because each step performed in Clarity LIMS is associated with a user, you can use this feature to track work through the lab.
User-defined field (UDF)	See Custom Fields. As of Clarity LIMS v5.0, this term is deprecated. However, the API resource is still called UDF and some API documentation may still refer to UDFs.
Workflow	A set of protocols arranged in a sequence that corresponds to how work is performed in the lab.