Terms and Definitions
Last updated
Last updated
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:
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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.
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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 |
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. |
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 .