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This section describes how to batch create reagent kit lot to the LIMS by importing a Reagent Kit lot list - a Microsoft® Excel® *.xls or *.xlsx spreadsheet file.
The reagent kit lot list must be in *.xls or *.xlsx format.
The following column header names and its row position cannot be changed: Reagent Kit Name, Lot Name, Lot Number, Expires, Location, Notes and Lot Status.
The following columns must be populated: Reagent Kit Name, Lot Name and Lot Number fields.
The reagent kit name provided must correspond to a pre-existing and unique reagent kit in Clarity LIMS.
Updating of existing reagent kit lot information is currently not supported.
Download the reagent kit lot list template from the Configuration > Reagents page in Clarity LIMS.
Open the reagent kit lot list template.
By default, the template contains the following information:
Column headers (Row 4)
These headers must reference the names of the fields containing the information to capture for a reagent kit lot. Editing the column headers or creating additional headers will results in reagent kit lot manifest file import error.
Populate the columns with the information associated with the reagent kit lot. Enter the data starting from row 5 onwards.
Save the file and import it to reagent kits.
The import process aborts, if the reagent kit lot list contains one of the following
specifies a reagent kit name that does not exist in Clarity LIMS
specifies a reagent kit name that has more than one reagent kits with the same name in Clarity LIMS
An asterisk indicates a *mandatory field.
Regular font, without an asterisk, indicates an optional field.
The following column headers can be used in the sample list:
*Reagent Kit Name —Specify the name of the reagent kit. When specifying a value for this column, verify it exists in the system already. For instance, you can specify Illumina DNA PCR-Free Prep as a value, provided this reagent kit is configured in the system.
*Lot Name —Specify the name to use for this reagent kit lot. If there are duplicate lot names for the same lot number in the spreadsheet or already existed in the system, expect an error message. The message provides information on this error condition. No reagent kit lot is imported until duplicate names are resolved.
*Lot Number —Specify the lot number of the reagent kit to use for this lot.
Expires —Add an expiration date (Date format required) to this reagent kit lot number. Values for this column are optional. However, if Lot Status is set to Active or Archived for corresponding row that is missing value in Expires column, expect an error message. The message provides information on this error condition.
Location —Add a storage locate to this reagent kit lot. Values for this column are optional.
Notes —Add a description/note to this reagent kit lot. Values for this column are optional.
Lot Status —Add a status to this reagent kit lot by selecting Pending, Active or Archived from the drop-down list. Empty value will be defaulted to "Pending" status.
This section describes how to add and configure the instruments and equipment used in your lab, and associate these items with master steps.
Add the instruments and equipment used in your lab to Local Analysis Software, and associate these items with specific steps. When running steps in the LIMS, lab scientists can record the instruments and equipment used.
All users logged into the LIMS can access the Instruments configuration screen. However, what they are allowed to do in this screen is determined by their user permissions.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.
When adding instruments to Clarity LIMS, there are two main steps involved:
Add a new instrument type (Configuration:update permission required).
Select an instrument type and then add a new instrument of that type. You cannot add an instrument without first selecting an instrument type
When initially setting up the system, add all the instrument types used in the lab. For example, HiSeq 3000, 2100 Bioanalyzer, NanoDrop 2000. Any logged in user can then add specific instruments to each type.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Instruments.
On the Instruments configuration screen, select New Instrument Type.
In the Instrument Type Details area, complete the following required information:
Enter the name of the type of instrument or equipment you are adding.
In the Vendor drop-down list, select an existing vendor from the list, or select Create new and type the new vendor name into the field. After you create a vendor, it is added to the list and can then be selected when creating other instrument types.
In the drop-down list that displays, select one or more master steps on which to enable this instrument type.
To remove a step from this field, select the X to the left of the step name.
The instrument type is made available for use on all steps that are created from the selected master steps. When running those steps in the LIMS, the appropriate instrument can be selected from the Record Details screen. This configuration is bidirectional - when configuring a master step, you can select instrument types to associate with that master step.
Select Save.
The new instrument type displays in the Instrument Types area. The 'zero instruments' label indicates that no instruments of this type have yet been added.
On the Instruments configuration screen, in the Instrument Types area, select the appropriate instrument type.
Select New Instrument.
In the Instrument Details area, enter the details for this instrument.
Instrument Name: Enter the name of the instrument. (This is the only required field.)
Serial number: Enter the serial number of the instrument, or other instrument-specific information.
Expires: Select the expiry date (or calibration date) of the instrument or equipment.
Valid dates are the current date or any date in the future.
After an instrument has been saved, a label displays next to this field. The label shows the number of days, and then hours, remaining before the instrument expires, or warns that the instrument has expired.
The LIMS automatically archives the instrument when the expiry date is reached (see#instrument-status).
Software Name: Enter the name of the instrument software.
Software Version: Enter the instrument software version number.
Select Save.
In the Instrument Types area, the new instrument is nested under its instrument type.
To create another instrument of the same type, select Add Another New Instrument.
When creating instruments, note the following:
A LIMS ID is automatically assigned to the instrument.
The instrument record Created date is automatically populated.
The instrument record Modified date is automatically populated; this field keeps track of any changes made to the instrument details.
By default, the instrument status is set to Active. See #reactivate-an-archived-instrument.
The instrument Status toggles between Active and Archived. By default, when adding a new instrument, its status is Active.
These instruments are in use, or available for use, in your lab workflows; they can be selected by lab users as they record work for a protocol step.
Users may edit the details of Active instruments.
These instruments are not currently in use in lab workflows (for example, they may be expired or under repair), and are not available for selection by lab users working in the LIMS.
When the expiry date for an instrument has passed, the LIMS automatically archives the instrument.
The details of Archived instruments are read-only. They may be viewed, but not edited.
Archived instruments are listed together in a single Archived Instruments group (no subgrouping by type), at the bottom of the Instrument Types area. If an archived instrument is reactivated, it once again displays under its respective instrument type.
When editing instrument types and instruments, keep the following in mind:
Only users with the Configuration:update permission type can edit instrument types.
Changes made to an instrument type, or to any instruments of that type, are reflected on all future steps on which the instrument type is enabled.
Steps that have already been run are not affected by changes made to instrument types or instruments.
When deleting instrument types and instruments, keep the following details in mind:
To delete instrument types, the Configuration:update permission is required.
When deleting an instrument type, all instruments of that type are also deleted and are no longer available for selection on steps.
You cannot delete an instrument type if any instruments of that type are in use.
You cannot delete an instrument if that instrument has been used in a step.
In the Instrument Types area, expand the Archived Instruments section and select the instrument to reactivate.
If the instrument has not expired, select Activate.
If the instrument has expired, reset the expiry date to a date in the future, and then select Activate.
Select Save.
In the Instrument Types area, the reactivated instrument displays under its instrument type. The instrument may now be selected when running steps.
This section describes how to add and configure label groups (reagent categories) and labels (reagent types or molecular barcodes), and enable them for use on specific master steps.
Add a label group for each reagent category used in your lab, and then add labels to the groups. Each label represents a reagent type (or molecular barcode) within the group/category.
Select the label groups to be used in the step when configuring the properties of steps generated from an Add Labels master step type.
To access the Labels configuration screen, the Configuration:update permission is required. Users who do not have this permission do not see the Labels option displayed under the Consumables tab.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.
When adding label groups and labels to the LIMS, there are several main steps involved:
Add a new label group.
Then, to add labels to the group:
Download a template label list (Microsoft® Excel® file) from the Labels configuration screen.
Add reagent type details to the downloaded template.
Upload the completed label list.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab and then select Labels.
On the Labels configuration screen, select New Label Group.
In the Label Group Details area, enter the name of the label group you are adding.
Numeric names are not permitted.
Duplicate names are not permitted.
You may use the name of a previously deleted label group.
Select Save.
The new label group is listed in the Label Groups list. Because there are no labels in the group, no count displays.
The Upload Label List and Download Label List buttons display in the Label Group Details area.
On the Labels configuration screen, in the Label Groups list, select the label group to which you want to add labels.
In the Label Group Details area, select Download Label List to download the template.
Open the template in Excel. It has two example label entries containing the following information:
Group Name (column A): Prepopulated with the name of the label group you selected in the LIMS.
Label ID (column B): No information is provided in this column as it is populated by the LIMS.
Label Name (column C): Provides examples of label name (reagent type) formats.
Sequence (column D): Provides examples of sequence properties of theIndex special type of the reagent type. Dual-indexes may be used, separated by a hyphen.
To complete your label list, add new rows between the opening and </LABEL ENTRIES> closing tags and enter reagent label information into these rows:
Group Name: (Required on upload) Enter the name of the label group (reagent category) into which you are adding labels.
Label ID: Leave this column empty. It is populated by the LIMS when you upload your completed label list.
Label Name: (Required on upload) Enter the names of the reagent labels (reagent types) you would like to add to the LIMS, using one of the example formats.
Sequence: (Optional on upload) Enter the index sequence of the Index special type of the reagent type, for example, "ATCACG." You may enter dual-indexes, separated by a hyphen.
Save your label list file.
Return to the Labels configuration screen, select Upload Label List and upload your completed labels list. If there are errors in the list, the upload does not complete. Refer to #label-list-upload-error.
In the Label Groups list, the label count shows the number of labels in the group.
When editing/deleting label groups, keep the following in mind:
The only item you can change directly in the LIMS is the label group name.
To make changes to the labels within the group, you must upload a modified label list. See #edit-and-delete-label.
Deleting a label group does not affect historical run data. This information is preserved in the LIMS.
When editing and deleting labels (reagent types), keep the following in mind:
Changes you make to a label are reflected on all future steps on which the label is applied.
Steps that have already been run are not affected by changes you make to labels. The labels are mapped to samples in the run and historical run data are preserved.
When uploading a label list, the following conditions result in an error:
One or more of the four headers (Group Name, Label ID, Label Name, Sequence) is missing or misspelled.
Attempting to rename a label to the same name as an existing label within any label group.
Attempting to rename a label to the same name as an existing label—even if you are also renaming the other label at the same time.
Adding a label with the same name as another label within any label group.
Attempting to edit a label without providing the Label ID.
Providing labels for the wrong group. That is, the Group Name column does not match the name of the label group into which you are uploading labels.
Providing a sequence for a reagent that does not have the 'Index' special type.
This section describes how to add and configure the control samples used in your lab, and enable them for use on specific master steps.
Controls behave like special samples that can be enabled at specific points in your workflows. However, unlike samples, controls do not need to belong to a project and do not have to be assigned to a workflow.
Add the control samples used in the lab to Clarity LIMS, and enable them for use on steps. When running a step on which control samples are enabled, the lab scientist can add those control samples to the Ice Bucket.
All users logged into the LIMS can access the Controls configuration screen. However, their user permissions determine what they are allowed to do in this screen.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.
There is no limit to the number of controls you can create or the number of steps on which you can enable a control. When adding a new control, you are not required to enable it on a step. You can do this action at any time.
Control sample/step configuration is bidirectional. Enable a control sample on a step in the following situations:
When adding control samples on the Controls configuration screen (described in this section).
When configuring a step (see #add-and-configure-master-steps-and-steps).
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Controls.
On the Controls configuration screen, select New Control.
Type a name for the control sample. This name displays in queues of steps on which controls are enabled. This field is the only required field.
[Optional] Enter additional details for the control sample:
Supplier—Enter the commercial vendor name. If this control sample was made in the lab, enter in-house.
Cat. #—Enter the catalog number.
Website—Enter the website of the commercial vendor. If it is an in-house control, enter the URL of the internal web page that contains details of the in-house control. When viewing details for the control sample, lab scientists can select the link to open the web page in a new browser window.
In the Control Use section, note the following defaults:
The status of the new control is set to Active.
The new control is not flagged as a single step only control.
Select Save.
The new control displays in the Control Samples list.
Enabling controls on steps makes them available for use in the lab.
To enable a control sample on a step, complete the following steps:
On the Controls configuration screen in the Control Samples list, select the control to enable on steps.
In the Control Use area, select the protocol that includes the step on which you want to enable the control. Type the first few letters of the protocol to filter the list.
In the adjacent list, select the step on which you want to enable the control.
Enable the control on additional steps, if necessary.
Select Save.
The Control Samples list now indicates that the control has been enabled on a step. Hovering over the 'On 1 step' label displays a popup that shows the protocol and step involved.
The status of a control may be Active or Archived.
Active controls are controls that are in use or available for use in the lab workflows.
Archived controls are controls that are not currently available for use in the lab workflows.
Lab users do not see archived controls when initiating steps.
Configuration details for archived controls are saved, so it is easy to reactivate them.
In the Control Samples list, archived controls are listed in their own group. Select the arrow to expand the list and view control details.
Single step only controls do not progress in workflows. When completing a step, lab users do not need to select a Next Step for these controls.
Use this option to represent single-use, disposable samples such as QC standards, molecular weight ladders, and blanks.
In the Control Samples list, select the control to archive.
On the Status of Control slider, select Archived.
Select Save.
In the Control Samples list, expand the archived control group and select the control to be activated.
On the Status of Control slider, select Active.
Select Save.
When deleting controls, keep the following details in mind:
You can only delete control samples that have not been used in a step.
If a control sample has been recorded in a step, or is currently being used in a step, you cannot delete it. The Delete button is not enabled.
On the Controls configuration screen in the Control Samples list, select the control to delete.
In the Control Sample Details area on the right, select Delete.
This section describes how to add and configure the containers used in your lab, and enable them for use on specific master steps.
Clarity LIMS is a container-based system requiring that samples reside in a container at every step of a workflow. Add the types of containers used in your lab to Local Analysis Software and enable them for use on specific steps.
When running a step in the LIMS, the lab scientist scans in the container barcode and proceeds to the Ice Bucket screen. In the Ice Bucket, the output container types that can be used in the step are listed.
To access the Containers configuration screen, the Configuration:update permission is required. Users who do not have this permission do not see the Containers option displayed under the Consumables tab.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see User Roles and Configured Role-Based Permissions.
When adding a new container to the LIMS, you are adding a container type (ie, a tube, a 96 well plate, a flow cell). When the container barcode is scanned, an instance of that container type is added.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Containers.
On the Containers configuration screen, select New Container.
In the Container Details area, enter the name of the container type you are adding. This is the only required field. When you have entered a name, the Save button becomes available.
[Optional] Specify the details of the rows and columns in the container:
In the Number fields, enter the number of rows and columns in the container.
Use the Naming toggle to specify whether the rows and columns have Alphabetic or Numeric labels.
For numeric rows and columns, use the Start at field to specify the number at which the row/column labels start.
[Optional] If you enter 1 in both row and column Number fields, an additional Yes/No toggle setting displays, asking "Do you want to skip the placement screen?".
Yes—The LIMS does not display the placement screen when the step is run. It automatically places the samples into the container.
No—The placement screen displays samples that need to be manually placed into the single well.
[Optional] List any unavailable wells (ie, wells in which samples must not be placed). Specify these in a comma-separated format, for example, A:1, A:2, A:3, A:4.
Note the following:
If you switch between Numeric and Alphabetic rows/columns, the list of unavailable wells updates to reflect the change.
If you change the Start at number for numeric rows/columns, the list of unavailable wells updates to reflect the change.
If you specify an invalid unavailable well, or change the dimensions of the container such that one or more of the specified unavailable wells becomes invalid, the List unavailable wells field turns red.
The Save button is only available when all specified unavailable wells are valid.
Select Save.
To prevent lab users from placing samples in specific wells of a container, list the unavailable wells in a comma-separated list. Each well must be listed individually. You cannot enter a range.
Wells that are marked as unavailable are shown with a dashed line border in the sample placement screen. If a sample is placed into an unavailable well, a Destination is unavailable error message displays.
On the Containers configuration screen, in the Containers list, select a container type.
The Container Details area displays the details for the selected container type.
Edit the details as required.
Select Save.
When editing container type details, keep the following in mind.
To view and edit container types, the Configuration:update permission is required.
Changes made to a container type are reflected on all future steps on which that container type is enabled.
Steps that have already been run are not affected by changes made to container type details.
When a container type has been used, its row, column, and unavailable wells settings are not editable.
On the Containers configuration screen, in the Containers list, select a container.
The container details display on the right.
Select Delete.
Confirm the deletion.The container is no longer be available for selection on steps.
When deleting container types, keep the following in mind:
To delete container types, the Configuration:update permission is required.
Container types cannot be deleted if an instance of that container type is in use, or has been used, in a step.
Consumables are the Instruments, Reagents, Containers, and other equipment used in the lab. Configure these items in Clarity LIMS and associate them with specific master steps. When the steps are run in the LIMS, the consumables used are recorded.
This section describes how to add and configure the reagent kits and lots used in your lab, and enable them for use on specific master steps.
Add the reagent kits and lots used in the lab to Clarity LIMS and enable them for use on specific steps. When lab scientists run samples through a step, they can record the reagent lots used.
All users logged into Clarity LIMS can access the Reagents configuration screen. However, their user permissions determine what they are allowed to do in this screen.
By default, only the Administrator role has the Configuration:update permission. For more on user roles and permissions, see and .
Enabling kits on steps makes them available for use in the lab. When running those steps, the reagent lots used are recorded
When a new reagent kit is added, it is not a requirement to enable it on a step. It can be enabled at any time.
Reagent kit/step configuration is bidirectional. Enable a reagent kit on a step in the following situations:
When adding reagents on the Reagents configuration screen (described in this section).
NOTE: The Configuration:update permission is required to add new reagent kits to Clarity LIMS.
On the main menu, select Configuration.
On the configuration screen, select the Consumables tab, then select Reagents.
On the Reagents configuration screen, select New Reagent Kit.
Type a name for the reagent kit. This name displays in queues of steps on which use of the reagent kit is enabled.
Enter details for the reagent kit to help with future reordering:
Supplier: Enter the commercial vendor name.
Cat. #: Enter the catalog number.
Website. Enter the website of the commercial vendor. When viewing details for the reagent kit, select the link to open the web page in a new browser window.
In the Reagent Kit Use section, the status of the new kit is set to Active. This status means that it is available to be used in the lab (after it is enabled on steps).
Select Save to add the new reagent kit.
The new kit displays in the Reagent Kits list.
On the Reagents configuration screen, in the Reagent Kits list, select the kit to enable on steps.
In the Reagent Kit Use area on the right, compete the following actions:
Select a protocol from the drop-down list. Type the first few letters of the protocol to filter the list.
In the adjacent list, select the step on which to enable the reagent kit.
Enable the control on additional steps, if necessary.
Select Save. The Reagent Kits list now indicates that the kit has been enabled on the selected steps.
On the Reagents configuration screen in the Reagent Kits list, select the kit for which you would like to add a new lot.
Below the Kit Details in the Lots area, select New Lot.
In the Lot Details area, enter the lot name.
[Optional] Enter additional details about the lot, such as the lot number and expiry date.
Specify a storage location and add notes about the reagent lot. For example, use this field to note why a lot is being archived).
Clarity LIMS automatically populates the LIMS ID and Created and Modified dates.
Select Save.
The new lot displays in the Reagent Kits list.
By default, when a new lot is added, the status is Pending. The Status of Reagent Lot slider at the bottom of the Lot Details area controls the lot status.
The status of a reagent kit may be Active or Archived. The status of a reagent lot may be Pending, Active, or Archived.
Note the following details about reagent kit status:
Active reagent kits are in use, or are available for use, in the lab workflows. By default, when a new kit is added, the status is saved as Active.
Archived reagent kits are kits that are not currently in use, or available for use, in the lab workflows. Configuration details for archived kits are saved, so reactivation is easy.
Archived kits are listed at the bottom of the main Reagent Kits list in the Archived Reagent Kits group.
Note the following details about reagent lot status:
Active reagent lots are in use, or are available for use, in the lab. Select the active reagent lots as they record work for a step.
Pending reagent lots have been ordered but not yet received in the lab. They are not available for selection by lab users running steps in Clarity LIMS. By default, when a new lot is added, the status is saved as Pending.
Archived reagent lots have typically expired or been used up. They are not available for selection by lab users. Note the following information:
When the expiry date for a lot has passed, Clarity LIMS automatically archives the lot.
Archived lots that have passed their expiry date cannot be reactivated.
Archived lots display in an Archived Reagent Lots group within the Reagent Kit details list.
In the Reagent Kits list, select the kit to be archived or reactivated.
In the Reagent Kit Use area on the right, select Archived / Active.
Select Save.
In the Reagent Kits list, select the kit containing the lot to be activated or archive
At the bottom of the Lot Details area on the Status of Reagent Lot slider, select Active / Archived.
Select Save.
In the Reagent Kits list, select the reagent kit or lot to delete.
In the Kit Details/Lot Details area on the right, select Delete.
When deleting reagent kits and lots, keep the following in mind:
Only reagent kits and lots that have not been used in a step can be deleted.
If a kit or lot has been recorded in a step, or is being used in a step, it cannot be deleted. The Delete button is not enabled.
On the Reagents configuration screen, select Upload Reagents Kit Lot.
In the Upload File dialog, select Choose File and browse to and open the reagent lot list file.
Select Upload File.
As part of the upload process, Clarity LIMS validates the file to make sure the reagent kits are already in the system. If the file contains invalid data, an error message displays.
When the upload process completes, the reagent lot display in the Reagent Kits list.
When configuring a master step or step. For details, see .
If a reagent lot list is not readily available, select the Download a reagent lot list template link to download a reagent lot list template. Open the template file in Excel, populate it with the reagent lot details, and save the file. For details, see .