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Terms and Definitions

The following table defines the terms used in BaseSpace Clarity LIMS and related documentation.

See also Understanding API Terminology (LIMS v5 and later).

Account

Not fully supported in BaseSpace Clarity LIMS v5.x. Support is planned for a future release. In v5.x, a workaround is to create an Account 'on the fly' from the Projects and Samples screen.

An organization with which your facility conducts business. You can record an account's address, client names, and other information. You can then associate clients with their applicable account (see Client).

In LIMS 2.1, the term Labs was replaced with Accounts. However, the API resource is still called lab.

Aggregation

See QC Aggregation.

AI node

See Automation worker.

As of BaseSpace Clarity LIMS v5.0, this term is deprecated. However, some of the API documentation may still refer to 'AI node'.

Analyte

See Derived Sample.

As of BaseSpace 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 that was generated by an earlier step. A derived sample or measurement is a type of artifact.

In the 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 BaseSpace Clarity LIMS user interface. Automations can be configured for steps and for derived samples.

Automation worker

A software component that runs automations. May be installed on the same server as the LIMS or on several other machines that all draw from the queues of one 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.

BaseSpace Clarity LIMS

The main web client used by lab scientists, lab managers, and system administrators to:

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 automations
Create and custom fields and presets
Create and configure instruments, reagent kits and lots, reagent labels, and control samples

Client

An individual within your laboratory, or an external individual who works with your laboratory, who is directly associated with a project in the LIMS.

In the LIMS user interface, the term Contact has been replaced with Client. However, the API permission is still called contact .

Collaborator

Not supported in BaseSpace Clarity LIMS v5.x. Support is planned for a future release.

LIMS user role assigned to external customers or other individuals who submit samples to the LIMS.

Contact

See Client.

Custom field

(formerly UDF)

A field that LIMS administrators can add to the user interface to collect information for a sample/group of samples, master step, step, client, account, or container.

For example, the administrator may wish to add a field allowing users 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; however, you can 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 BaseSpace 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 BaseSpace 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 your hard disk drive or in another piece of software.

File placeholder

(formerly shared ResultFile)

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 pre-populated master step fields that define values for step data at run time.

They eliminate the need for the user to manually enter this information, and ensure that the correct information is recorded 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 the 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.

You can add a label group for each reagent category used in your lab, and then add labels to the groups - where each label represents a reagent type within the group/category. See also Label Group.

Label group

A reagent category.

You can add a label group for each reagent category used in your lab, and then add labels to the groups - where each label represents a reagent type within the group/category. See also Label.

LIMS ID

A unique identifier assigned to all assets (samples, projects, containers, steps, etc.) in the LIMS.

IDs are assigned in a non-decreasing 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, LIMS IDs of sequentially uploaded samples, for example, will not necessarily have sequential LIMS IDs.
We reserve the right to change the algorithm that generates LIMS IDs in future versions of the LIMS. It is therefore not suggested to assume that IDs will be sequential. Instead, consider using a custom field and a script to set a sequential number for your purposes.

Master step

(formerly process type)

A technique or procedure performed on a sample. To be considered a 'master step' in the LIMS, the technique/procedure must be created and configured as such, and must have an input (not all steps have an output).

In the LIMS, master steps are created and configured on the Lab Work configuration screen. These master steps then 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.

Parse

The process of analyzing an input file and displaying it in BaseSpace Clarity LIMS.

Plug-in

A software component or module that adds functionality to a software program.

Preset

See Group of Defaults.

As of BaseSpace Clarity LIMS v5.0 this term is deprecated.

Process

See step.

As of BaseSpace Clarity LIMS v5.0, this term is deprecated. However, the API resource is still called process.

Process type

See Master step.

As of BaseSpace Clarity LIMS v5.0, this term is deprecated. However, the API resource is still called process.

Project

BaseSpace 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 you add samples to the LIMS, you must add them to a project.

Protocol

In BaseSpaceClarity LIMS, a protocol is a set of steps that must be performed in a specific sequence, as part of a lab's 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 together 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 BaseSpace Clarity LIMS v5.0, this term is deprecated.

Resultfile

See Measurements and File Placeholders.

As of BaseSpace 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 BaseSpace Clarity LIMS. Typically, the Researcher role is assigned to laboratory scientists who use the 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 BaseSpace 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 Understanding Master Step Types and Step Outputs.

Submitted sample

The original sample that is added to a project in BaseSpace Clarity LIMS.

Timestamp

The dates and times associated with a file.

User

An individual within your laboratory, or an external individual who works with your laboratory and has access to the BaseSpace Clarity LIMS system. Since each step performed in the 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 BaseSpace 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 the way in which work is performed in the lab.