Clarity LIMS uses projects as the basis for all work performed in the system. All samples must be added to an existing project.

A project stores the following information:

• The client and account associated with the project.

• The priority of the project (Low, Standard, High).

• The samples submitted to the project.

• Project status (Pending, Open, Closed).

• The date the project was opened and closed.

• Files associated with the project.

• Any configured custom fields.

Create Projects

Before adding samples to Clarity LIMS, create a project to store them.

1. On the Projects and Samples tab, select New Project.

2. On the Properties tab, in the Project Details section, complete the following tasks:

   • Type a descriptive name for the project.

   • If creating a new account, type the name directly into the field. Otherwise, select an existing account from the drop-down list.

   • If creating a new client, type the name directly into the field. Otherwise, select an existing client from the drop-down list.

   • By default, the project opened date is set to the current date. To change this date, select the Opened field and select a date from the calendar.

   • If necessary, edit the project priority. The default is Standard.

3. On the Custom Fields tab, complete the additional details for this project. Mandatory fields are indicated with yellow shading.

4. [Optional] To upload a file to the project:

   • Select the Files tab, then select Upload File.

   • Select Choose File, browse for and select the file, and select Upload.

5. Select Save. The new project displays in the Projects list. Samples can now be added.

View and Modify Projects

View, Modify and Delete a Project

To view, modify, or delete a project, complete the following steps:

1. Navigate to the Projects and Samples tab.

2. In the Projects list, select the project. The Project Details screen displays the details for the selected project.

3. To modify project details, select the field and edit as required (see Project Creation).

4. Select Save.

5. To delete the project, select Delete.

Before deleting a project, consider the following details:

• Deleting a project also deletes any samples it contains.

• By default, projects can be deleted provided no work has been recorded (or is in progress) on the samples. However, this role-based permission is configurable.

• If the samples contained in a project have recorded or in-progress protocol steps, the project cannot be deleted without special user permissions.

View and Modify Project Status

To view and update the project status, complete the following steps:

1. Navigate to the Projects and Samples tab.

2. In the Projects list, select a project.

   On the Properties tab in the Project Details area, the Status slider indicates the status of the project.

3. To move the slider and change the project status, select the desired status.

View and Modify Custom Fields

To view and modify custom fields, complete the following steps:

1. Navigate to the Projects and Samples tab.

2. In the Projects list, select a project.

3. In the Project Details area, navigate to the Custom Fields tab.

4. Select a field to modify and edit as required.

5. Select Save.

Download / Upload Files

To download, view, and upload project files, complete the following steps:

1. Navigate to the Projects and Samples tab.

2. In the Projects list, select a project.

3. In the Project Details area, navigate to the Files tab. Files currently associated with the project are displayed.

4. To download and view a project file, select the file.

5. To upload a file:

   a. Select Upload File.

   b. Select Choose File.

   c. Browse for the file, select it, and select Upload.

Project Automation

See #project-automation on how to configure Project Automation.

When you add samples to Clarity LIMS, you must add them to a project. Clarity LIMS uses projects as the basis for all work performed in the system.

There are two ways to add samples to projects:

• Add samples individually to one or more projects. See #add-samples-to-one-project-or-to-multiple-projects.

• Upload a sample list (Excel spreadsheet) to a project. See #upload-and-modify-samples.

Sample Management

The Sample Management screen allows for convenient sample accessioning. On this screen, add multiple samples to a single project or to multiple projects, and modify samples already added to the system.

There are two ways to access the Sample Management screen:

• The main menu bar, which allows for adding samples to one project or to multiple projects.

• The Project and Samples tab, which allows for adding samples to a project or modifying samples already added to a project.

Add samples to one project or to multiple projects

1. On the main menu bar, hover over Projects and Samples tab and select Add Samples when the option displays.

2. In the Sample Management screen, select a project from the Project Name drop-down list. This selection auto-populates the fields in the Project Details area.

   • Edit the project details if necessary.

   • To upload files to the project, select Upload File.

3. In the Sample Details area, provide the following information:

   • Enter the name of the sample.

   • Choose a container from the drop-down list.

   • Enter the container name.

   • Complete any other applicable fields (mandatory fields are marked with an asterisk).

   NOTE: LIMS ID (Submitted Sample), Date Submitted, and LIMS ID (Container) fields are automatically populated after the sample is saved.

4. To upload sample files, select Upload File at the bottom of the Sample Details section.

5. To add another sample, select Sample +. Add this sample to the same project or select a different project from the Project Name drop-down list.

6. Repeat steps 3 to 5 as required.

7. When all samples are added, select Submit Samples. Clarity LIMS validates, saves the samples, and returns to the Project and Samples tab.

On the Project and Samples tab, the projects with recently added samples are automatically selected.

While adding samples, note the following details:

• To view a subset of samples, remove selected samples from view. For details, see #remove-sample-from-view.

• Copy values across to adjacent samples by selecting the arrows to the left of the fields. Clarity LIMS automatically populates the Well field.

• If editing well information, make those changes last (before submitting the samples). Changes to Container, Container Name, LIMS ID (Container), and Sample Name may reorder the well locations.

• Use the paging buttons to scroll pages of samples.

Add Samples to a Selected Project

In this method, only add samples to the project selected. It is not possible to select a different project as described in the previous section of the documentation.

1. On the Project and Samples tab, select a project to add samples.

2. In the Submit Samples section, select Add Samples.

3. On the Sample Management screen, because the project has already been specified, the project details are automatically completed.

4. Follow steps 3 to 7 of the previous section to add the sample details.

Modify Samples

1. On the Project and Samples tab, select a project to add samples.

2. In the samples list, select the submitted samples to modify (derived samples cannot be modified).

3. Select Modify Samples.

4. Modify the sample and project details as required (the Project Name or Container Name fields cannot be modified).

5. To save the changes, select Submit Samples.

   NOTE: To avoid modifying or seeing all the samples selected, remove them from the view. See #remove-sample-from-view.

6. Clarity LIMS validates the modifications, saves the samples, and returns to the Project and Samples tab. On the Project and Samples tab, the projects containing the modified samples are automatically selected.

Remove Sample from View

On the Sample Management screen, hovering over a sample displays a small Remove from view (X) button in the upper-right corner.

The effects of selecting this button differ depending on the circumstances.

Upload and Modify Samples

If there are many samples to process, add them to the system by uploading a Microsoft Excel spreadsheet file (*.xls or *.xlsx). Use the same method to modify information for multiple samples.

By default, a maximum of 3456 samples can be uploaded from a single sample list file. To upload more than 3456 samples, divide the samples into multiple files.

In the sample list, specify container placement and include values for standard and user-defined options and fields (for details, see #create-a-sample-list).

Samples can be added individually in the Sample Management screen. For details, see #add-samples-to-one-project-or-to-multiple-projects.

Upload a Sample List

1. Navigate to the Projects and Samples tab.

2. In the Projects list, select a project to add samples. The Project Details area updates to show the details for the selected project.

3. Select Upload Sample List.

   If a sample list is not readily available, select the Download Example Sample List link to download a sample list template. Open the template file in Excel, populate it with the sample details, and save the file. For details, see #create-a-sample-list.

4. In the Upload File dialog, select Choose File and browse to and open the sample list file.

5. Select Upload File.

   As part of the upload process, Clarity LIMS validates the file to make sure the custom field data it contains meet the requirements, presets, and restrictions that apply to submitted samples. If the file contains invalid data, an error message displays.

6. When the upload process completes, the samples display in the Submitted Samples list for the project.

   The Submitted Samples list allows the following actions:

   • Hover over the Information icon for a sample to view the details associated with it.

   • Modify sample details.

   • Add samples to a workflow.

   • If samples have been created in error, delete them from the sample list and the project (provided no work has been done on them). To complete this action, select the samples and select Delete.

After uploading, the submitted samples can be assigned to a workflow. When they are assigned, the samples are available for lab scientists to work on.

Modify sample information

1. Navigate to the Projects and Samples tab.

2. In the Projects list, select the project containing the samples to modify.

3. Select Modify Samples.

   Clarity LIMS generates a sample list containing all samples in the project and downloads it.

4. Open the file in Excel. It contains the Clarity LIMS IDs of all samples and all custom field data.

5. Update the sample information as required.

6. Return to the LIMS and upload the modified sample list. Follow the steps outlined in #upload-a-sample-list.

Rules for modifying sample information

• A sample list can be uploaded/imported in which custom field values have been changed, removed, or added.

• While sample custom fields can only be updated, the sample list can contain other columns of data. The original data from the sample list does not have to be removed.

• If the system does not require the custom field, leave the cell blank or enter NULL.

  • A ‘blank’ value will leave existing data in the system intact.

  • A NULL value will clear any existing data in the system for that field.

• Clarity LIMS uses the information defined in the sample list (sample name, container type, and so on) and looks for matching samples in the project. If a matching sample is found, the system updates the sample with the values specified in the sample list.

Projects and Samples —Allows for project and sample management. Use this screen to create and manage Projects, Samples Accessioning, and Assign and Process Samples.

The Overview Dashboard displays summary information about the current activity in the lab. It provides lab managers with at-a-glance information about workflow, sample status, and alerts across projects. The dashboard is dynamic and updates automatically as changes occur in the lab.

By default, the system administrator and facility administrator roles have access to the Overview Dashboard. However, access is a configurable role-based permission. For details, see Configured Role-Based Permissions.

Overall Status Bar

The Overall Status bar provides a snapshot of lab activity.

• Projects—The number of open and pending projects currently in Clarity LIMS. This number does not include closed projects.

• Samples—The number of samples in open and pending projects.

• Workflows—The number of workflows in which the samples are currently being worked through in the lab.

• Alerts—The number of unresolved alerts in the system. To trigger alerts, select Request manager review as the next step for a sample (in the Assign Next Steps screen).

Workflows

This section shows information for the lab workflows that currently have samples uploaded to them. Workflows are listed in alphabetical order.

For each workflow, the following information is shown:

• Projects—The total number of projects containing samples that are currently in the workflow. This number includes samples that are in progress in the workflow and samples that have completed the workflow.

• In progress samples—The number of samples that are currently in progress in the workflow.

• Completed samples—The number of samples that have completed the workflow.

• Protocols—The names of the protocols that are included in the workflow.

• Samples—The number of samples in each protocol of that workflow.

Protocol Capacity

If configuring the sample capacity of a protocol (see #configure-protocols), Clarity LIMS uses color coding to indicate the percentage of the protocol capacity that is being used.

The percentage of capacity is calculated according to the total number of samples that are currently assigned to all occurrences of the protocol (ie, across all workflows).

• Blue indicates that the number of samples currently in the protocol is less than or equal to the configured capacity.

• Yellow indicates that the number of samples currently in the protocol is between 100% - 200% of the configured capacity.

• Orange indicates that the number of samples currently in the protocol is greater than 200% of the configured capacity.

While the protocol for a particular workflow may have few, or even zero, samples assigned to it, its capacity might still display in yellow or orange. This display would occur if the number of samples in other occurrences of the protocol exceeds its configured capacity.

Hover over a protocol to view more information about its configured capacity and the total number of samples assigned to it.

The Projects dashboard helps with managing projects and the day-to-day flow of samples through the lab. This dashboard provides a dynamic, project-centric view of current lab activity. It allows for the management of projects and the day-to-day flow of samples through the lab.

Overall Status Bar

The Overall Status bar provides a snapshot of current lab activity.

• Projects—The number of open and pending projects currently in Clarity LIMS. This number does not include closed projects.

• Samples—The number of samples in open and pending projects.

• Workflows—The number of workflows in which the samples are currently being worked through in the lab.

• Alerts—The number of unresolved alerts in the system. To trigger alerts, select Request manager review as the next step for a sample (in the Assign Next Steps screen).

Project, Sample, Workflow Snapshot

Additional information provides a snapshot summary of projects and samples, including the workflows to which samples are assigned.

No Workflow Assigned

• The number of projects containing samples that do not have a workflow assigned to them.

• The number of samples that do not have a workflow assigned to them.

In Progress

• The number of projects containing samples that are in progress and being worked on in the lab.

• The number of samples that are in progress and being worked on in the lab.

Workflow Complete

• The number of projects in which all samples have completed all workflows assigned to them.

• The number of samples that have completed all workflows assigned to them.

Projects Table

By default, all open projects display in the Projects table and are sorted by creation date (most recent first).

• Select any project in the table to view its details on the right.

• Projects that have unresolved alerts display an icon in the upper-right corner.

The Projects table allows filtering to display projects that meet certain criteria.

The drop-down list provides several filters. Consider filtering for the following use cases:

• Completed projects—Prepare data and invoices to be sent to clients.

• Projects containing samples that do not have a workflow assigned to them—Find the projects containing these samples, assign workflows to the samples, and start working on them in the lab.

• Projects assigned to a particular workflow or to a particular project—View and manage their progress in the lab. In this case, type the workflow/project name into the filter box and press the Enter key.

View Project Summary Information

Select a project to display summary information about the workflows and samples related to that project. The summary includes the following information:

• The number of samples in the project that have not been assigned a workflow.

• The workflows to which samples in the project are assigned. If needed, scroll to see all the workflows.

• The number of samples involved in each workflow.

• Any unresolved alerts in the project. Select the alert to view and resolve it.

• The project completion percentage.

View Project Workflow Details

Below the Projects table and summary, the workflows for the selected project are listed.

• Directly under each workflow name, the number of in-progress and completed samples currently in the workflow.

• Select In-progress samples to view all in-progress samples across all protocols in the Samples table.

• Select the Completed samples count to view those completed samples in the Samples table.

To view workflow details:

1. To the right of the workflow name, select the arrow.

   The expanded workflow details area shows the following information:

   • All protocols included in the workflow, and the number of samples in each of those protocols.

   • The percentage of project samples currently assigned to each protocol (represented by blue shading). Hover over the shading to see this percentage. The percentage is derived from the number of samples in the protocol divided by the total number of samples in the workflow.

2. Select a protocol to see the steps it includes and the samples assigned to those steps.

View Step and Sample Details

Select a protocol to see the following information display in the Samples table:

• The steps included in the protocol, and the submitted and derived samples that are in each of those steps.

• The sample name and the first three sample custom fields.

In the Samples table, the following features are available:

• Search for samples—Select a submitted or derived sample name to search for that sample (see also #search-for-samples).

• View Alerts—Select an alert to go to the step in which the manager review was requested.

Run Automations on Derived Samples

Run automations on derived samples directly from the Samples table.

1. Select one or more derived samples (Ctrl + click to select multiple).

2. In the upper-right corner of the Samples table, expand the drop-down list and select an automation.

3. If the automation requires input, a prompt to enter a value displays. Enter a value and select Continue.

   NOTE: If the parameter name is truncated, hover over it to view the full name.

4. As the automation runs, the status is shown in the samples list.

For details on configuring an automation, see #add-and-configure-automations.

When working on a step, you can create multiple aliquots of each sample, move one aliquot to the next step in the workflow, and store the others for later use.

Create Store Aliquots for later use

1. Add samples to the Ice Bucket.

2. In the Ice Bucket, create the required number of sample aliquots.

   • To create the same number of aliquots for all samples, select the number of derivatives to create and select Apply All. (The number adjacent to each sample updates automatically.)

   • To create a different number of aliquots for each individual sample, adjust the number adjacent to each sample.

   • In the Assign Next Steps screen, all the sample aliquots are listed.

3. To store an aliquot for later use, select Store for later from the next step drop-down list.

Resume workflow on stored aliquots

1. In the Search drop-down list, select Sample, type the sample name, and press the Enter key.

   In the search results, all the sample aliquots are listed.

2. Select a sample aliquot to expand the details.

   A prompt appears to confirm this step.

3. Select Confirm.

   After it is confirmed, the search results update and the sample are shown as queued for the next step in the workflow.

   In Lab View, the sample aliquot is now ready to be worked on.

Lab View shows the protocols and steps used in the lab, and the number of samples queued for each step. Use this screen to do the following:

• See recent lab activities.

• See in-progress steps and steps that are ready to be worked on.

• Start or continue working on samples.

• View and follow up on .

Ice Bucket

When users run a step in the LIMS, they typically select a destination container type from a preconfigured list in the Ice Bucket screen, and then proceed to the Record Details screen - where they scan the barcode of a new container to add it to the LIMS.

However, users may sometimes want to place samples into an existing container - that is, a container whose barcode has already been entered into the LIMS. This is easily achieved in the Ice Bucket screen.

Add samples to an existing container

1. In Lab View, open the step containing the samples you want to place into an existing container.

2. Select the samples and add them to the Ice Bucket.

3. In the Ice Bucket screen, in the Container Options panel:

   • In the Destination Container drop-down list, select the desired container type.

   • In the Find Existing Container field, type the name or Clarity LIMS ID of the container in which to place the samples. While typing, Clarity LIMS presents a filtered list of containers with matching names or Clarity LIMS IDs. Select the appropriate container from the list.

4. Click Begin Work to proceed to the Record Details screen.

Remove samples from a queue

Occasionally, you must remove samples from a workflow queue in Clarity LIMS. Only administrator users can perform this operation.

1. In Clarity LIMS, open the step containing the samples to remove.

2. Select one or more samples, expand the Options drop-down list and select Remove.

If necessary, complete the following actions:

1. Search for the samples in Clarity LIMS.

2. Requeue them for a previous step.

Manually Moving Samples to the Next Step

Usually, samples move through the system according to the sequence of protocols and steps defined in a workflow.

However, sometimes samples are moved into the next step manually.

Move samples to the next step

1. In Clarity LIMS, open the step containing the samples to move.

2. Select one or more samples, expand the Options drop-down list and select Move.

   The samples move into the subsequent step in the protocol.

Next Step Selection and Sample Routing

The following tables summarize the expected results when choosing next steps for these three output types.

Step output: Derived sample

Step output: Pool

Step output: Derivative

This topic provides guidelines and tips to help you compile a sample list, in Microsoft Excel format, for importing into BaseSpace Clarity LIMS.

• Import up 3456 samples from a single sample list file. To import more than 3456 samples, divide the samples into multiple files.

• If an error is detected in the spreadsheet, the import process aborts. No sample imports until the error condition is resolved. See .

Column headers

Legend

• An asterisk indicates a *mandatory field.

• Regular font, without an asterisk, indicates an optional field. See for details.

• Text enclosed in angle brackets indicates a placeholder custom field name to replace with a value.

• Italicized text indicates a group of fields that depend on each other. All headers in the group must be either all present or all absent.

The following column headers can be used in the sample list:

• *Sample/Name—Specify the name of the sample. If the system has the unique sample name option enabled and there are duplicate sample names in the spreadsheet, expect an error message. The message provides information on this error condition. No sample is imported until duplicate names are resolved.

• Sample/Volume—Specify the volume of the sample.

• Container/Type—Specify the name of the container type to use for this sample. When specifying a value for this column, verify it exists in the system already. For instance, you can specify 100 well MALDI plate as a value, provided this container type is configured in the system.

• Container/Name—Specify the name of the container to place this sample. If the name does not match a container already in the system, a new container by this name (and of the specified type) is created.

• Sample/Well Location—Specify the well location for the sample. Values for this column are formatted like the following examples: A:1, B:12, or 1:10.

  The import process validates this location against the container type specified. If the location is out of range, the process rejects it. If placing a sample into an existing container, the process checks if the well location is already occupied and rejects it if occupied.

• Sample/Reagent Label—Specify the reagent label name to use for this sample. Values for this column are optional. They can exist in the system or, if the reagent label is not found, a new one is created. Only one reagent label is supported per sample via batch sample import.

• Custom Field/<Name of Custom Field>—Add a custom field instance to the sample. The name of the custom field must exist in the system. If the custom field name specified is not in the system, an error message displays.

  You can specify a value for this custom field in the remaining cells of this column. For example, if there is a custom field by the name Clinical Source, you may have a column header Custom Field/Clinical Source and a value of hospital for the sample. See for details.

• Container/Custom Field/<Name of Custom Field>—Add a custom field instance to container. This field functions in a similar way to the sample custom field previously described, except the values must be defined on each row (per container). If not, an error message displays.

Optional fields

Take Custom Field as an example. Its optional nature in the spreadsheet is contingent on whether a particular field is defined as optional or required in Clarity LIMS.

If there is a required custom field for a sample, there must be a column in the spreadsheet for this field. A value must be specified for it, before any sample can be imported.

Custom field values are validated against their type defined in Clarity LIMS, as follows.

• Date type—For example, if there is a custom field type of Date and the name is Completion Date, the best practice method is to have a column header Custom Field/Completion Date. The remaining values for the cells in the file should be formatted using one of the Excel date formats.

• Numeric type with a range defined—The value is first validated as a number. Then, the number is validated against the range defined in Clarity LIMS.

  • If the validation fails, error messages display.

  • No sample is imported until the value is validated.

• Custom field with values defined in a group of defaults—If a custom field is configured to have one or more values defined in a group of defaults and is only allowed to have one of these defined values, Clarity LIMS validates the value entered against the defined values.

  • If the value in the spreadsheet does not match one of the default values, validation fails.

  • If the validation fails, an error message displays. No sample is imported.

Troubleshooting

If Clarity LIMS expects certain information to be provided and this information is not included in the sample list, the samples are not imported.

Consider the following examples:

• If an option or field is mandatory, the sample list must contain a column to capture that information. The sample list must use the appropriate column title.

• If the samples must contain unique names, the sample list must not contain duplicate names or the names of samples already recorded in Clarity LIMS.

• Containers types referenced in the sample list must already be defined in Clarity LIMS. For example, 96-well plate or tube.

• The sample list must not place a sample into a container well that is already populated with another sample.

• Any custom fields referenced in the sample list must be defined in Clarity LIMS.

To process many samples, add them to Clarity LIMS by importing a Microsoft Excel spreadsheet file (*.xls or *.xlsx). This method also applies to updating sample information.

Requirements

• The sample list must be in *.xls or *.xlsx format.

• The sample list's column header names must match the default fields in the LIMS.

• The following column header names cannot be changed: Sample/Name, Container/Name, and Sample/Well Location.

• The following columns must be populated: Sample/Name and any sample-level custom fields that the system administrator requires.

• By default, import up to a maximum of 3456 samples from a single sample list file. To import more than 3456 samples, divide the samples into multiple files.

Create a sample list

1. Download a sample list template from the Projects and Samples view in Clarity LIMS.

2. Open the sample list template.

   By default, the template contains the following information:

   • <TABLE HEADER> and <SAMPLE ENTRIES> tags (red/purple text).

     These identifying tags are required by the LIMS import process. Do not edit these tags.

   • Column headers (white text on blue background)

     These headers must reference the names of the fields containing the information to capture for a sample. If editing the column headers or creating additional headers, make corresponding changes to the fields in Clarity LIMS. See .

3. Populate the columns with the information associated with the samples. Enter the data into the rows between the <TABLE HEADER> and <SAMPLE ENTRIES> tags. Insert additional rows as needed.

4. Save the file and import it into a project (see ).

   If the sample list specifies a container name that does not exist in Clarity LIMS, the system creates the container.

Tips for data entry

• Enter dates using Excel date cell formatting.

• To preserve currency characters (e.g. $), currency is best entered as a string (rather than using the Excel currency category).

• Numbers can be entered either as numeric or string values.

• If there are drop-down lists of values in Clarity LIMS, enter these exact values in the sample list.

• Container well locations are always Row:Column. The actual dimensions depend on the container type configuration.

• Excel may sometimes automatically alter values, depending on the type of data being entered.

For example, for Boolean fields such as Stored On Site? below, numeric values of zero and false will evaluate to FALSE whereas non-zero numeric values and true will evaluate to TRUE. Other values will result in an error on import.

Configuring sample list spreadsheets for usability and speed

Spreadsheet programs like Microsoft Excel contain features for increasing usability and speed when entering data. For example, the following configurations are available:

• Add drop-down lists of options that correspond to options available in Clarity LIMS. Use the Named Range and Data Validation Excel features.

• Hide header columns required by the system but not required.

The Clarity LIMS support team can create custom, efficient sample list templates.

Samples must be assigned to an active workflow before they can be accessed and worked on from .

Assigning samples to workflows

1. On the main menu, navigate to the Projects and Samples tab.

2. In the Projects list, select the project containing the desired samples.

3. In the Samples and Workflow Assignment area, the Submitted Samples and Derived Samples tabs list all the samples included in the project. Select the tab that lists the desired samples. If no work has been performed on the samples, no derived samples are listed.

4. In the chosen samples list, select the samples to be assigned to a workflow. Use the following methods to select or deselect samples:

   • Select a group to select all samples in the group (the button label changes to Deselect Group).

   • Expand the group and select samples to add them individually. Use Shift + select to select multiple adjacent samples or Ctrl + select to select multiple nonadjacent samples.

   • To deselect samples, select them or select Deselect Group to deselect all samples in the group.

5. When finished selecting samples, select Assign To Workflow and select the desired workflow from the drop-down list.

   The list displays all the workflows that are currently active in the system.

6. In the samples list, a label displays showing the samples that are now assigned to a workflow. Select the X inside a label to remove that sample from the workflow.

   In the Workflows area on the right, the number of samples assigned to the workflow displays. Select the X in the upper-right corner to remove all samples from the workflow.

7. Repeat steps 3 to 6 to assign other samples to workflows, as required.

8. Assigned samples now display in Lab View, in the Available Work area, listed under the first protocol step of the selected workflow.

   To locate samples in the queue quickly, filter on the sample name.

To requeue and rework samples, specific role-based permissions are required. For details, see .

Requeueing samples for a Step

Occasionally, a sample must be rerun through a particular step. For example, there may have been a technical error in the lab. More sequencing may be needed at the end of a workflow if there are not enough samples.

To solve this problem, return samples to the queue and repeat the step.

There are several ways to requeue samples:

• Search for the step with samples to requeue, view all samples that have completed this step, and choose the ones to requeue. See

• Search for a specific sample to requeue. See

Reworking samples from a previous step

In addition to requeueing samples for the same step, you can also rework samples from a previous step. For example, an action is needed if there is an insufficient quantity of a particular sample to meet the required target concentration level.

—Provides summary information about lab activity. Use this dashboard to view workflow status, sample status, and alerts.

—Provides a dynamic view of current lab activity. Use this dashboard to help manage projects and the flow of samples through the lab.

Requirements

• 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.

Create and Import a Reagent Kit Lot List

1. Download the reagent kit lot list template from the Configuration > Reagents page in Clarity LIMS.

2. 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.

3. Populate the columns with the information associated with the reagent kit lot. Enter the data starting from row 5 onwards.

4. Save the file and import it to reagent kits.

   The import process aborts, if the reagent kit lot list contains one of the following

   1. specifies a reagent kit name that does not exist in Clarity LIMS

   2. specifies a reagent kit name that has more than one reagent kits with the same name in Clarity LIMS

Column headers

Legend

• 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 two tasks that Clarity LIMS administrators are often required to perform:

• Temporarily prevent a user from logging in by archiving the user.

• Email a link to a user that allows them to reset their Clarity LIMS password.

Archive a User

1. On the main menu, select Configuration.

2. Select User Management.

3. Select the Users tab to see a list of all current active and archived users in the system, categorized by role.

4. Select the user to archive.

   The details for the selected user display in the User Details area on the right. The Status slider displays the current status of the user.

5. Select Archived to temporarily archive the user.

6. Select Save.

By default, every new user created in Clarity LIMS is an active user and can sign in to Clarity LIMS with their username and password.

Reset a User Password

1. On the main menu, select Configuration.

2. Select User Management.

3. Select the Users tab to see a list of all current active and archived users in the system.

4. Select the user whose password is to be reset.

   The details for the selected user display in the User Details area on the right.

5. Select Login and Password and select Reset password.

   This sends the user a link that allows them to reset their password.

   NOTE: The new password must satisfy the following requirements:

   • Contain at least 12 characters

   • Contain at least one special character (# $ % ? ! @, etc.)

   • Contain at least one number

   • Contain at least one lowercase letter

   • Contain at least one uppercase letter

The Send login instructions option sends the user the following information:

• The URL for the login screen.

• Instructions on how to set their login password.

• This email is sent automatically when a new user is created, but you may occasionally need to resend it.

After signing into Clarity LIMS, you can update some of the details associated with your profile, including your password, email address, and profile photo.

Update User Profile

1. In Clarity LIMS, at the right of the menu bar, select your username and then select Profile.

2. The Profile page opens, displaying the details associated with your user profile.

3. On this page, you can:

   • Change your password.

   • Change your email address.

   • Upload an image to associate with your profile.

Reset a forgotten password

1. On the Sign In screen, click the Forgot your password link.

2. In the Reset Your Password screen, enter your username or email address and click Submit.

Configure Protocols

Clarity LIMS includes preconfigured protocols, each containing a series of steps through which a sample must pass. You can create custom protocols, adding steps that represent the steps that are run in your lab. You can then add the protocols to workflows so that lab users can work with them in Lab View.

Use the Lab Work configuration screen to view, add, and configure the protocols used in the lab. For an overview of this screen, see #lab-work-overview.

View Protocols

1. On the main menu, select Configuration.

2. Select the Lab Work tab.

   The Workflows, Protocols, Steps, and Master Steps navigation panel displays.

3. In the Protocols list, select a protocol to highlight it:

   • The Workflows list updates, highlighting the workflows that contain the selected protocol.

   • The Steps list updates, highlighting the steps included in the selected protocol.

   • The Master Steps list updates, highlighting the master steps on which the highlighted steps are based.

4. Below the main navigation panel, review the protocol configuration form.

   This displays the name of the protocol and its settings.

Protocol Settings

The Protocol Settings area captures important information about the protocol—the date it was created, the date it was last modified, and other settings that determine how the protocol is used in the lab. The following table summarizes these settings.

Add Protocols

When adding and configuring protocols, note the following details:

• When adding steps to a protocol, reordering steps, or removing steps from a protocol, changes are autosaved. You do not need to select Save after every modification.

• When #configure-next-steps, you must select Save to save your changes.

To add a protocol:

1. On the Lab Work configuration screen, in the upper-right corner of the Protocols list, select Add.

   Below the main navigation panel, the protocol configuration form displays.

2. To begin, type a name for the new protocol.

3. Select the settings for this protocol (For details, see #protocol-settings):

   • Select whether this is a QC or Non-QC protocol.

   • Select the Protocol Type:

     • If you are adding a QC protocol, this automatically is set to QC.

     • If you are adding a Non-QC protocol, select the type from the drop-down list.

     • In the Capacity field, enter the sample capacity of this protocol.

4. [Optional] To temporarily hide the protocol from Lab View, use the Show in Lab View? slider. Change the setting to No.

5. Select Save. The new protocol displays at the bottom of the Protocols list. You can move it to a different position in the list by dragging and dropping.

   To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.

Add Steps to Protocols

This section provides an overview of the step creation process. For detailed information on steps and master steps, and step-by-step instructions for configuring them, see #add-and-configure-master-steps-and-steps.

To add a step to a protocol:

1. In the Protocols list, select the protocol.

2. In the upper-right corner of the Steps list, select Add.

   Below the main navigation panel, the step configuration form displays.

3. Type a name for the new step.

4. In the adjacent Master Step list, select the master step upon which to base the new step.

5. Select Save (this button is not enabled until you have selected a master step).

6. In the Protocols list, select the protocol again.

   • The step you added displays at the top of the Step list.

   • If this is a non-QC protocol, a 1 is in front of the step name, indicating that this is the first step in the protocol.(QC steps are not numbered as they are typically not sequential.)

   • In the Master Step list, the master step upon which the step is based is also highlighted.

7. Repeat steps 1–5 to add more steps to the protocol.

   • To delete a step, select it and select the Delete.

   • To reorder steps within the protocol, simply drag and drop them.

   To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.

8. Select Save.

You can now configure the order in which the steps are run, and the method used to assign and run 'next steps.' See #configure-next-steps.

Configure Next Steps

When configuring non-QC protocols, the protocol configuration form includes a Next Steps table. This allows you to configure the sequence in which steps are run in the protocol. This table does not display for QC protocols, because the steps in a QC protocol are typically not sequential.

In the table:

• Each row represents a numbered step in the protocol.

• Each column represents a 'permitted next step' for each of the numbered steps.

• The cells at each row/column intersection indicate which steps are potential permitted next steps for the step represented in that row.

  • If there is an icon in the cell (an X or a checkmark), the step represented by that column may be selected or deselected as a permitted next step.

  • Previous and current steps cannot be selected as permitted next steps, and are shown as nonselectable cells.

• The bottom two rows determine whether the next steps are started and assigned manually or automatically. Manual is the default setting.

To configure next steps

1. In the Next Steps table, select a cell to select (or deselect) one or more permitted next steps.

2. In the Start Next Step and Assign Next Step rows, select a cell to switch between Manual and Automatic.

Configure QC Filters

When configuring QC protocols, the protocol configuration form includes a QC Filters section. This section lets you configure QC logic to make sure that only certain samples are queued for each QC step. Typically, QC protocols contain multiple nonsequential steps that culminate in a QC aggregation step.

QC filters are composed of two drop-down lists.

The first list refers to the QC flag assigned at run time:

• Passed means that a pass QC flag was assigned to the sample at run time.

• Failed means that a fail QC flag was assigned to the sample at run time.

• Did not pass means that the sample did not run, or received a fail QC flag, at run time.

• Did not fail means that the sample did not run, or received a pass QC flag, at run time.

The second list refers to the master steps from which the steps are derived:

• All master steps used in the protocol are included in the list. Together, these form a statement (for example, Failed Bioanalyzer).

• Each statement may be followed by an'AND', which allows you to create an additive statement.

• Statements are separated by an'OR', which allows you to create mutually exclusive statements.

• Together, these AND/OR statements create the QC filter logic for a given step.

For example:

You may want the NanoDrop QC queue to show samples that have not passed NanoDrop QC (ie, they did not run, or received a fail QC flag), and that have passedBioanalyzer QC.

• If the procedures dictate that all samples must have passed Bioanalyzer QC and NanoDrop QC, use an 'AND' statement to ensure samples are not queued for a QC aggregation step unless they have passed both of these steps.

• If your lab procedures dictate that all samples must have passed Bioanalyzer QC or NanoDrop QC, use an 'OR' statement to ensure samples are not queued for QC aggregation unless they have passed one of these steps.

Modify Protocols

You may want to rename a protocol, or add or reorder steps. Some modifications are only permitted if the protocol is not included in an active or archived workflow.

NOTE: We recommend that you do not modify or delete the preconfigured protocols without first consulting the Clarity LIMS Support team.

To modify a protocol:

1. In the Protocols list, select the protocol.

2. Make your changes and select Save.

Note the following details:

• You can rename protocols in pending, active, and archived workflows.

• For non-QC protocols, you can modify the protocol type. For example, you can change a Sample Prep protocol to a Library Prep protocol.

• You can choose to hide or show the protocol in Lab View.

• You cannot change a QC protocol to a non-QC protocol, and vice versa.

• You cannot add, reorder, or delete steps if the protocol is included in an active or archived workflow.

Delete Protocols

To delete a protocol:

1. In the Protocols list, select the protocol.

2. On the protocol configuration form, select Delete.

Note the following details:

• You cannot delete a protocol if it is included in an active or archived workflow. In this case, the Delete button is not enabled.

• If you delete a protocol, the steps it contains, and the master steps on which those steps were based are not deleted.

Copy Protocols

After you have added and configured a protocol, you can copy it and then modify the copy for use in other workflows. This is useful if you have multiple protocols with similar base configuration, as it saves you having to recreate each one from scratch.

When you copy a protocol, all of its steps are also copied—along with any step-level fields, automations, reagents, controls, and instruments configured on those steps.

You can also create copies of the master steps, or you can reuse the same master steps.

• Copying master steps does copy step-level fields.

• Reusing master steps does not copy step-level fields.

• If a copied master step has custom field default values that refer to other steps within the protocol, update those values to refer to the copied steps. See #update-custom-field-default-on-copied-master-steps.

Copy a Protocol and its Step

1. On the main menu, select Configuration.

2. On the LIMS configuration screen, select the Lab Work tab.

3. In the main navigation panel, in the Protocols list, select the protocol to copy.

4. Below the navigation panel, select Copy.

5. The Copy Protocol Options dialog opens. This dialog provides two options:

   • Append name with—This option lets you specify text to be appended to the protocol name (default is _copy). This text also is appended to the copied step names, and to the master step names if you also choose to copy those. Note: Copied step-level field names do not have the text appended.

   • Copy Master Steps?—This option lets you choose to reuse the same master steps (this is the default behavior), or create copies of the master steps.

   • Selected an option and then select Continue to copy the protocol and steps.

6. The copied protocol displays in the Protocols list, and is selected along with its related steps and master steps.

   Below the navigation panel, the protocol configuration form displays. You can work with the protocol and its steps just as you would with any other protocol/steps in the system.

Update Custom Field Default on Copied Master Steps

If you have configured a custom field default on the master step you are copying, and the default value refers to the name of another step within the protocol, you must update that default value on the copied master step, so that it refers to the appropriate step in the copied protocol. The default values are not automatically updated to refer to the copied step names.

Similarly, if you have configured a script or logic that uses custom field defaults that refer to another step within the protocol, you must update those default values on the copied master step.

For example, in a QC protocol:

• The Aggregate QC step has various 'Copy Task' UDFs defined - eg, Copy Task 1 - Source Step and Copy Task 2 - Source Step.

• The values of these fields are determined by other QC steps within the protocol.

• The script that is configured on the QC Aggregate step references those QC step names, locates the specified custom field values from the steps, and uses them to determine QC results.

If the QC protocol is copied, the copy of the master step on which the Aggregate QC step is based must be updated so that the custom field default values refer to the appropriate steps within the protocol.

Configure Workflows

After protocols are created and configured, add them to workflows that represent how samples move through your lab.

In Clarity LIMS, use the Lab Work configuration screen to view, add, and configure the workflows used in the lab. For an overview of this screen, see #lab-work-overview.

View Workflows

The Lab Work screen provides an at-a-glance view of all workflows configured in the LIMS, along with the protocols and steps they contain. You can quickly see which workflows are active, which are archived, and which do not yet have protocols assigned to them.

To view workflow details:

1. On the main menu, select Configuration.

2. Select the Lab Work tab.

3. In the Workflows list, select a workflow to highlight it.

   • The Protocols list updates to show all protocols included in the workflow. These are highlighted and displayed sequentially at the top of the list. A dashed line separates these workflow protocols from the comprehensive list of all protocols in the system.

   • The Steps list updates, highlighting the steps included in the highlighted protocols.

   • The Master Steps list updates, highlighting the master steps on which the highlighted steps are based.

     Note: You can also select a protocol, step, or master step to view the related workflows.

4. Below the main navigation panel, review the workflow configuration form. This displays the name of the workflow and its status.

Workflow Status

The status of a workflow may be Pending, Active, or Archived. The following table provides an overview of each status setting and describes the implications of each.

Add Workflows

The following section shows how to add a workflow to the LIMS and add protocols to it. When configuring workflows, keep the following in mind:

• You are not required to add protocols immediately. If you prefer, you can create empty Pending workflows and assign protocols to them later.

• You can only activate a Pending workflow if it contains at least one protocol.

• When adding protocols to a workflow, reordering protocols within a workflow, or removing protocols from a workflow, your changes are autosaved. You do not have to select Save after every modification.

• You cannot add empty protocols to a workflow. The protocol must include steps.

Add a new workflow

1. On the Lab Work configuration screen, in the upper-right corner of the Workflow list, select Add.

2. Below the main navigation panel, the workflow configuration form displays.

3. To begin, type a name for your new workflow.

4. Select Save.

   The workflow is saved in a Pending state, and displays in the Workflow list of the main navigation panel.

Add protocols to a workflow

1. In the Workflow list, select the workflow.

2. In the Protocol list, locate the first protocol to include and select Add.

   The protocol is added to the workflow and displays at the top of the Protocol list. The 1 indicates that this is the first protocol in the workflow.

3. Repeat step 2 until you have added all required protocols to the workflow.

   • To remove a protocol from the workflow, select its Remove button.

   • Drag and drop to reorder protocols within the workflow.

     • To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.

   • To view or modify a protocol, select the protocol to display its configuration form below the main navigation pane.

4. You can now save the workflow as a Pending workflow.

   - or -

   Select Activate to use this workflow immediately.

   NOTE: After you activate a workflow, you cannot modify or delete it.

Modify and Activate Pending workflow

1. On the Lab Work configuration screen, in the Workflow list, select the Pending workflow to modify or activate.

2. Make your changes and select Save to save the workflow as a Pending workflow.

   -or-

   Select Activate to change the workflow status to Active and begin using the workflow.

When modifying or activating workflows, keep the following in mind:

• You cannot activate empty workflows.

• You can only modify a workflow while it remains in the Pending state. That is:

  • You cannot add a protocol to an Active or Archived workflow.

  • You cannot remove a protocol from an Active or Archived workflow.

  • You cannot rename or reorder protocols in an Active or Archived workflow.

  • You cannot delete protocols included in Active or Archived workflows.

Archive and Reactivate Workflows

While you cannot delete workflows after they have been activated, you can archive them. This makes them temporarily unavailable for use in the lab. You can reactivate an Archived workflow at any time.

To archive a workflow:

1. On the Lab Work configuration screen, in the Workflow list, select the Active workflow to archive.

2. In the Workflow Settings area, select Archive. Select Save.

To reactivate an archived workflow:

1. On the Lab Work configuration screen, in the Workflow list, select the Archived workflow to reactivate.

2. In the Workflow Settings area, select Activate. Select Save.

Delete Workflows

1. On the Lab Work configuration screen, in the Workflow list, select the pending workflow to delete.

2. On the workflow configuration form, select Delete.

3. Confirm the workflow deletion:

   • To proceed with the deletion, select Delete.

   • To cancel the deletion, select Cancel.

You can only delete a workflow while the workflow remains in the Pending state. You cannot delete Active or Archived workflows.

Lab Work Overview

To access the Lab Work configuration screen, the Configuration:update permission is required. Without this permission, the Lab Work tab is not visible.

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.

To view and configure lab work components:

1. On the main menu, select Configuration.

2. Select the Lab Work tab.

   The main navigation panel lists the Workflows, Protocols, Steps and Master Steps configured in Clarity LIMS. From here, complete the following actions as needed:

   • View the relationships between workflows, protocols, steps, and master steps.

   • View workflow, protocol, step, and master step configuration in the form beneath the navigation panel.

   • See the status of workflows (pending, active, or archived).

   • Add and modify workflows, protocols, steps, and master steps.

3. Select a workflow, protocol, step, or master step to view related configuration items in the other lists.

   Selecting a protocol highlights the following items:

   • All workflows that include the selected protocol are highlighted.

   • All steps in the selected protocol are highlighted.

   • All master steps from which the steps are derived are highlighted.

   Selecting a workflow highlights the following items:

   • All protocols in the workflow, which display sequentially at the top of the Protocols list.

   • All steps in those highlighted protocols.

   • All master steps from which the highlighted steps are derived.

   Zoom out in the browser to maximize the number of items visible in the lists. Drag the lower edge of the panel to see more list items.

Best Practice for Lab Work Configuration

The best practice method for creating and configuring lab work components in Clarity LIMS is as follows.

1. Create and configure master steps.

2. Create and configure protocols.

3. Create and configure steps, adding them to the appropriate protocols, and using the master steps Create and configure workflows, adding required protocols.

4. Create and configure workflows, adding required protocols.

Lab Work, Custom Fields and Automations Configuration Restrictions

When working with workflows, protocols, steps, and master steps, there are some restrictions you should be aware of. These restrictions are summarized below, and are also described in the articles that discuss the configuration details of each component.

The following section also lists the restrictions associated with custom fields and automations.

• Custom fields are configured on the Custom Fields configuration screen. Refer to Custom Fields.

• Step automations are configured on the Automations configuration screen. Refer to Automations.

Overview of Steps and Master Steps

In Clarity LIMS, steps and master steps are techniques or procedures that are performed on a sample. They are the building blocks of the lab work.

Think of master steps as starting points to create the individual steps that are run in the lab.

• The master step <--> step relationship is one to many:

  • Each step is derived from a master step.

  • A master step may be used as the foundation for multiple steps.

• All steps are derived from a master step and inherit any properties configured on the master step.

• If you configure properties at the step level, those properties only apply to that particular step.

To understand how properties set on the master step propagate down to the step level, see#rules-for-propagation-of-master-step-properties.

Rules for Propagation of Master Step Properties

In Clarity LIMS, all steps are derived from a master step and inherit any properties configured on the master step.

The rules for how properties set on the master step propagate down to the step level apply to all properties. Those configured on the Master Step Settings configuration form and those configured on the #step-milestones.

• By default, master step properties are not set (values are null). Therefore, by default, the property settings do not propagate down to the derived steps. This means that you can set, or not set, the property freely at the step level.

• If you set a property on the master step, that property is locked (a Locked icon displays) at the step level, and cannot be modified.

In some situations, you can add to or reorder a locked property at the step level, but you can never remove the property. For example, on the Step Settings form:

• You can add and reorder the column headers that display in the Sample table, even if some of those column headers are set on the master step.

• You cannot remove column headers that are set on the master step.

Master Step Property Propagation Rules

When you add a master step property setting, the setting is also added to all steps derived from that master step.

When you update a master step property setting, the setting is also updated on all steps derived from that master step. This overrides any previous values that had been applied at the Protocol Step level.

When you remove a master step property setting, the setting is also removed from all steps derived from that master step. There are a few exceptions to this rule where appropriate defaults must be applied to keep the step in a valid, workable state.

The following table summarizes what happens at the step level when a property setting is removed from the master step.

For details on configuring step and master step property settings, see #add-and-configure-master-steps-and-steps.

To configure each milestone, milestone, see #step-milestones.

About Step Types and Outputs

In Clarity LIMS, steps are categorized by type, where each type is based on the requirements and goals of the step, and the outputs generated by the step. Some step types have unique interfaces and properties designed to perform specific tasks, such as adding reagent labels or pooling samples.

The step type is set on the Master Step Settings configuration form, and all steps inherit the step type of the master step on which they are based. (To understand the relationship between master steps and steps, see Steps and Master Steps.)

The step type is also displayed on the Step Settings configuration form, but as a read-only property.

Step Inputs and Outputs

All step types must have a submitted sample or derived sample input, and may generate either derived sample outputs, measurement outputs, or no outputs.

Keep in mind that only one output type is permitted. A step cannot generate both a derived sample and a measurement output. The type of step you choose determines which output generation options display. For example:

• Selecting the Standard step type only displays settings for derived sample generation.

• Selecting the Standard QC step type only displays settings for measurement generation.

• Selecting the No Outputs step type only displays settings for no output generation.

Downstream Functionality

The type of step you choose also enables or disables certain functionality downstream. For example:

• Selecting the Pooling step type displays the Pooling screen when the step is run, allowing the ability to create pools of samples. Choosing this step type allows you to configure the number of aliquots used to generate the pools.

• Selecting the Add Labels step type displays the Add Labels screen when the step is run, allowing the ability to configure reagent label format options.

Rules and Constraints

• When creating a master step, you must choose a step type.

• When you have saved a master step configuration:

  • Step type cannot be changed.

  • The number of outputs generated can be adjusted, or switch from a fixed number to a variable number (Standard, Standard QC, Add Labels, Pooling, Analysis step types).

Step Types

The following step types are available in Clarity LIMS:

Standard

Standard steps can have a fixed or variable ratio of samples entering the step to derived samples being generated from the step. After saving, you can switch between fixed and variable.

Default step output: By default, this step type generates one derived sample for every sample tracked in the step.

Downstream functionality: Choosing this step type disables the Pooling and Add Labels screens. Derived sample outputs require placement.

Example steps of this type: Library Normalization, Fragment DNA

Standard QC

Standard QC steps may be included in QC protocols, and may also be included as inline QC steps in other protocol types.

Standard QC steps generate sample measurements, which can have a Fixed or Variable ratio of samples entering the step to measurements being generated.

Default step output: By default, this step type generates one measurement for every sample tracked in the step.

Downstream functionality: Choosing this step type disables the Pooling and Add Labels screens. You may configure a QC step to display or not display the Placement screen.

Example steps of this type: Bioanalyzer QC, NanoDrop QC, Qubit QC

No Outputs

The No Outputs step type does not generate any outputs. You can use this step type for sorting steps or for aggregate QC steps.

Default step output: This step type does not generate any outputs. (This is not configurable.)

QC aggregation is the final step in a QC protocol. This step aggregates the data from the previous Standard QC steps to determine the overall quality of the samples. At the end of the step, samples either pass QC and proceed to the next protocol, or fail QC and are rerun or removed from the workflow.

• At least one aggregate QC step is required in QC protocols.

• At a minimum, one Standard QC step must be run before QC aggregation can occur.

To use a No Outputs step type for QC aggregation, enable QC flags on the Record Details milestone. See #configure-record-details-milestone.

Downstream functionality: Choosing this step type disables the Pooling, Placement, and Add Labels screens.

Example steps of this type: Aggregate QC (DNA), Aggregate QC (RNA), Aggregate QC (Library Validation)

Add Labels

This step type is used to apply a reagent label (or molecular barcode) to each sample entering the step. It may be run on multiple tubes and on multiple plates. Running an Add Labels step allows for a permanent reagent label to be added to each sample. The label data appears while running the step, in a new column in the Sample Data table on the Record Details screen.

Add Labels steps generate derived samples, which can have a Fixed or Variable ratio of samples entering the step to derived samples being generated.

Default step output: By default, this step type generates one labeled derived sample for every sample that enters the step.

Downstream functionality: Choosing this step type disables the Pooling screen and enables the Add Labels screen.

Example steps of this type: Add Multiple Reagents, Adenylate Ends and Ligate Adapters, PCR Amplification.

Pooling

This step type allows for multiple samples to be pooled into a single sample/container for sequencing efficiency. The number of pools is determined while running the step. Samples typically have a label, which is used to differentiate each sample at the demultiplexing stage.

Pooling steps generate pools that are created from a Fixed or Variable number of aliquots.

Default step output: By default, for every sample that enters the step, one aliquot is used to generate pools.

Downstream functionality: Choosing this step type disables the Add Labels screen and enables the Pooling screen.

• The number of pools is determined on the Pooling screen.

• By default, users are prevented from pooling samples without labels or with identical labels. You can modify this on the Pooling Settings configuration screen.

Example steps of this type: Pool Samples

Analysis

Analysis steps allow data to be manipulated by scripts, for example, they may be used to trigger secondary analysis or import data post analysis.

Analysis steps behave similarly to Standard QC steps and generate sample measurements. They can have a Fixed or Variable ratio of samples entering the step to measurements being generated.

Default step output: By default, this step type generates one measurement for every sample that enters the step.

Downstream functionality: Choosing this step type disables the Pooling, Placement, and Add Labels screens.

Example steps of this type: Sample History Report, Process Summary Report

Demultiplexing

This is essentially an Analysis step that deals specifically with labeled samples. It separates pools of samples based on the label assigned to those samples.

Demultiplexing steps have a Fixed ratio of samples entering the step to measurements being generated.

Default step output: By default, this step type generates one measurement for every sample that enters the step.

Downstream functionality: Because samples are placed automatically by a script configured on the step, choosing this step type disables the Placement screen. Choosing this step type also disables the Pooling and Add Labels screens.

Example steps of this type: BCL Conversion and Demultiplexing.

Add and Configure Master Steps and Steps

Clarity LIMS includes preconfigured steps and master steps designed to support established lab processes. You can create additional steps and master steps to represent the procedures that are specific to your lab. There are two approaches:

• Create steps based on the preconfigured master steps. The steps you create inherit the properties of the configured master steps, and you can then set additional properties on the steps themselves.

• Create master steps, and then use them as the foundations on which to create your steps.

You can add the steps to protocols and workflows so that lab scientists can work with them in Lab View.

To access the Lab Work tab and configure steps and master steps, the Configuration:update permission is required. By default, only the Administrator role has this permission. For details, see User Roles and Configured Role-Based Permissions.

View Master Steps and Steps

The Lab Work screen provides an at-a-glance view of all steps and master steps configured in the LIMS, along with the protocols and workflows in which they are included.

1. On the main menu, select Configuration.

2. On the LIMS configuration screen, select the Lab Work tab.

   The Workflow, Protocol, Step, and Master Step navigation panel displays. This lists the workflows, protocols, steps, and master steps configured in the LIMS.

3. In the Master Steps list, select a master step to highlight it:

   • The Steps list updates, highlighting the steps derived from the selected master step.

   If multiple steps are derived from the same master step, the Master Steps list includes duplicate rows, each mapping to a different step, and each representing the same master step. All of these rows are highlighted.

   • The Protocols list updates, highlighting all the protocols that contain the highlighted steps.

   • The Workflows list updates, highlighting all workflows that include the highlighted protocols.

4. In the Steps list, select a step to highlight it: The Master Steps list updates, highlighting the master step on which the selected step is based. If multiple steps are derived from the same master step, the Master Steps list includes duplicate rows, each mapping to a different step, and each representing the same master step. All of these rows are highlighted.

   • The Protocols list updates, highlighting the protocol that contains the selected step.

   • The Workflows list updates, highlighting all of the workflows that include the highlighted protocols.

   Below the main navigation panel, the step and master step configuration forms display.

5. Select these tabs to switch between the forms and see which settings are configured on the step and which are configured on the underlying master step.

Master Step and Step Configuration Settings

Table 1 shows which settings must be configured on the master step and which may be configured on the master step or on the step.

Settings configured on the master step are locked at the step level. On the step configuration form, these settings display with a Locked icon.

Table 1: Master Step and Step Settings

Add a Master Step

1. On the Lab Work configuration screen, in the upper-right corner of the Master Steps list, select Add.

2. Below the main navigation panel, the master step configuration form displays.

3. To begin, type a name for your new master step.

4. Configure the settings for this master step - see #configure-a-master-step, below.

5. Select Save to save your master step configuration.

When adding a master step, keep the following in mind:

• Each step is created from a master step. You can create multiple steps from the same master step.

• Any settings you configure on the master step are inherited by all steps derived from that master step.

To understand how properties set on the master step propagate down to the step level, see #rules-for-propagation-of-master-step-properties.

Configure a Master Step

The following sections describe the settings available when configuring a master step. Note the following:

• Any settings saved as part of the master step configuration cannot be configured at step level. On the step configuration form, these settings display with a Locked icon.

• Some settings may be configured at the step level, as indicated in Table 1.

• The master step configuration form does not show the default setting values (this includes toggle switches).

Step Type

Step types are configured on master steps.

Steps are categorized by step type, where each type is based on the requirements and goals of the step, and the output generated by the step (derived samples, measurements, or aliquots).

The step type is set on the master step, and all steps inherit the step type of the master step on which they are based. After you have chosen a step type and have saved it as part of a master step configuration, you cannot change it.

• If you are not sure which step type to choose, review #about-step-types-and-outputs.

• To understand the relationship between master steps and steps, see Steps and Master Steps.

The step type you choose determines which step milestones are available for configuration.

Output Generation

Configured on master step.

A step may generate a derived sample output, a measurement output, an aliquot output, or no output.

The type of step you choose determines which output generation options are available. Usually, you may choose to keep the default setting or modify the output generation configuration.

For details on the output generation options available for each step type, see #about-step-types-and-outputs.

Output Naming Convention

Configured on master step.

By default, the name of the outputs generated by a step follows the naming pattern of the inputs to the step.

You can use tokens to configure the naming convention so that it resolves to other unique attributes of the output. These tokens function as placeholders that are replaced with actual values at run time. For example, for the Standard step type, the default naming convention resolves to the value of the {InputItemName} token.

The following table lists the default naming conventions for each of the step types.

Table 2: Default Naming Conventions for Step Types

The Tokens list provides a list of tokens you can use to configure the naming convention. For descriptions and examples, see Derived Sample Naming Convention Tokens.

To add a token:

1. Copy the token you want to use from the Tokens list and paste it into the Naming Convention field. If using multiple tokens, add a space between each entry.

2. Below the Naming Convention field, you can see a preview of how one or more tokens resolve. Some runtime-specific items, such as dates and times, do not preview exactly as they resolve at run time.

Automation

Automations are enabled on master step. Automation triggers may be set on master step or step.

A master step can be configured to update sample fields, assign QC flags, generate files, and submit files and command-line parameters to third-party programs, using automations and the Rapid Scripting API.

When you have configured an automation, you can enable it on one or more master steps and set its trigger location and style.

You can enable automations on master steps in two configuration areas of the LIMS:

• On the Automations tab, when adding/configuring an automation.

• On the master step configuration form.

After it is enabled on a master step, the automation becomes available for use on all steps derived from that master step.

You can set the trigger location and trigger style for an automation on the master step, or on the steps derived from that master step:

• On the master step—In this case, all steps derived from the master step inherit the automation and the trigger settings.

• On the steps derived from the master step—In this case, all steps inherit the automation from the master step, but you can configure different trigger settings for each step, if necessary.

To enable an automation on a master step, you must have first configured the automation on the Automation tab. For details, see #add-and-configure-automations.

To enable an automation on a master step:

1. In the Automation section, click the Automation configuration screen link. The Automation configuration screen opens, with the Step Automation tab active.

2. In the Automation Use section, select inside the Enable on the Master Steps field and select the master step on which to enable the automation. (If you make a mistake, select the X button to remove a master step from the field.)

3. Select Save.

4. Return to the master step configuration form. The automations are listed alphanumerically by name.

To set an automation trigger on a master step (or step):

1. In the Trigger Location drop-down list, select the stage of the step at which to enable the automation.

   • The list displays all available stages of the step from which the automation can be triggered.

   • Only valid options for the step are displayed, for example, the Pooling option only displays on Pooling steps, the Step Setup option only displays for steps on which the Step Setup screen is enabled.

   • To ensure sequence of execution, only one automation can be associated with each trigger location.

2. In the Trigger Style drop-down list, select how to initiate the automation. For example, automatically on entry to or exit from the screen or manually when a button is selected on the screen.

   The trigger location and style are saved with the automation configuration.

3. Repeat steps 1 and 2 to configure triggers for each automation added.

4. Save the automation configuration.

Instrument Types

Configured on master step or step.

You can specify the instrument/equipment types that may be used in a step. You can do this on the master step or at the step level. At run time, on the Record Details screen, the lab scientist selects from a list of instruments/equipment of that type.

To enable an instrument/equipment type on a master step or step, you must have first added the instrument type to the system. See #add-and-configure-instruments.

Note also that instrument type/master step configuration is bidirectional - when adding an instrument type, you can select master steps to associate with that instrument type.

To enable an instrument type on a master step (or step):

1. In the Instrument Types section, select Add.

2. At the right of the screen, a list of instrument/equipment types displays. Select one or more instrument/equipment types and select the checkmark button.

   The instrument/equipment types are added to the master step/step configuration.

   • If necessary, you can remove an instrument type by clicking the X button.

   • Step configuration form only: You can reorder instrument types by dragging and dropping them. The order is reflected on the step Record Details screen, in the Instrument selection drop-down list.

3. Save the master step/step.

Reagent Kits

Configured on master step or step.

You can specify the reagent kits that may be used in a step. You can do this on the master step or at the step level.

Configuring reagent kits on the step/master step enables reagent lot tracking on the Record Details screen at run time.

To enable a reagent kit on a master step or step, you must have first added the reagent kit to the system. See #add-and-configure-reagent-kits-and-lots.

Note also that reagent kit/master step configuration is bidirectional—when adding a reagent kit, you can select master steps to associate with that kit.

To enable a reagent kit on a master step (or step):

1. In the Reagent Kits section, select Add.

2. The reagent kits are added to the master step/step configuration.

   If necessary, you can remove a reagent kit by clicking the X button.

3. Save the master step/step.

Control Types

Configured on step.

You can specify the control types that may be used in a step. This is done at the step level.

Selected controls are then available to add to the Ice Bucket when running the step.

To enable a control type on a step, you must have first added the control type to the system. For details, see #add-and-configure-controls.

Note also that control type/step configuration is bidirectional—when adding a control type, you can select the steps to be associated with it.

To enable a control type on a step:

1. In the Control Types section, select Add.

2. At the right of the screen, a list of control types displays. Select one or more control types and select the checkmark. The control types are added to the step configuration.

3. Remove a control type by clicking the X button.

4. Save the step.

Step Milestones

Configured on master step or step.

When running samples through steps in the LIMS, each screen displayed represents a specific stage, or 'milestone' of the step.

Some screens display on all steps, while others only display on certain step types.

For more on milestones, and instructions on configuring milestone settings, see #step-milestones.

Add a Step

When adding steps to the LIMS, first select a protocol to include the new step, and a master step on which to base it. The new step inherits all settings configured on the master step.

To add a new step:

1. On the Lab Work configuration screen, in the Protocols list, select the protocol in which to add the new step.

2. In the upper-right corner of the Steps list, select Add.

   Below the main navigation panel, the step configuration form displays.

3. Type a name for the new step.

4. In the adjacent Master Steps list, select the master step upon which to base the new step.

   If creating a step within a QC protocol, the Master Steps list only displays master steps that are Standard QC and Aggregate QC step types.

5. Select Save (this button is not enabled until a master step is selected).

6. In the Protocols list, select the protocol again.

7. The step added displays at the top of the Steps list.

   • The '1' indicates that this is the first step in the protocol. (QC protocol steps are not numbered as they are typically not sequential.)

   • In the Master Steps list, the master step upon which the step is based is also highlighted.

8. Repeat steps 1–5 to add more steps to the protocol.

   • To delete a step, select it and select Delete.

   • To reorder steps within the protocol, drag and drop them.

9. Select Save.

   To drag and drop on a mobile or touch-screen device, touch and hold the item you wish to drag. After a moment, the item appears to lift off the page and its color changes to white. You can then drag the item and drop it into its new position.

Configure a Step

On the step configuration form:

• Any settings that were configured on the master step are locked. On the step configuration form, these settings display with a Locked icon.

• You can configure settings that were not configured on the master step. These settings only apply to the step.

• Settings not configured on the master step typically use the default value at the step level, unless those settings are configured on the step.

If not locked on the master step, the following settings can be configured at the step level.

• Automation triggers

• Instrument types

• Reagent kits

• Control types

• Step Milestones

Modify Master Steps and Steps

1. In the Master Steps list, select the master step you would like to modify.

2. Make your changes and select Save.

When modifying master steps and steps, keep the following in mind:

• You can change the master step on which a step is based, providing the new master step is of the same step type. The list of master steps is filtered to show valid options.

• If you remove configured settings from a master step, those settings on the derived steps revert to their default values, except if this would leave the step in an unworkable state. For example, you cannot remove the last container from a step. Exceptions to this revert to default rule are noted where applicable.

• If you rename a step, the Recent Activities list in Lab View continues to display the name of the step as it was when the step was run. This is because the step name in this case is derived from the activity record.

Delete Master Steps and Steps

1. In the Master Steps list, select the master step to delete.

2. On the master step configuration form, select Delete.

When deleting master steps and steps, keep the following in mind:

• You cannot delete a step if it is included in an active or archived workflow.

• You cannot delete a master step if it is used to generate a step that is in an active or archived workflow.

• You cannot delete a master step if it has already been used to create one or more steps. First delete the step, and then delete the master step.

To modify the information captured on the Record Details screen of a completed step, the CanEditCompletedSteps permission is required. This functionality allows for modifications to correct errors and/or bad data.

The CanEditCompletedSteps permission is not assigned to any user roles by default. A Clarity LIMS administrator must explicitly assign the permission to each user who requires it. See the User Roles and Configured Role-Based Permissions sections for details.

NOTE: Signature is not enforced again when editing completed steps. For recommended best practice, the role with CanEditCompletedSteps permission should be the same role that electronically signs off on steps. See #rules-and-constraints for details.

Users who have been assigned the CanEditCompletedSteps permission see an Edit button on the Assign Next Steps screen of completed steps. Selecting this button takes them to the Record Details screen, where they may modify certain step details.

Editable details

The following table lists and describes the step details that can be modified:

Rules and Constraints

To ensure the integrity of data, the following rules and constraints are in place when editing a completed step:

• Only steps that were completed in Clarity LIMS v5.1 and later are editable. If the system is upgraded to Clarity LIMS v5.1 or later, steps that were completed in a previous version cannot be edited.

• Steps that were executed using the API cannot be edited.

• If the configuration of a completed step changes after the step was run, it cannot be modified. This constraint includes any changes made to the protocol or workflow in which the step is included.

  • The automations enabled on the step.

  • The automation triggers configured on the step.

• An automation cannot be rerun on a completed step. The details of the automation command line cannot be viewed.

• Manager review/escalation comments on completed steps cannot be edited.

• The eSignature is not enforced again when editing completed steps. The eSignature from the original step execution is retained. There is not a prompt for a new signature when editing the step.

Modify a Completed Step

1. On the Assign Next Steps screen of the completed step, select Edit (upper-right corner).

   A prompt displays to confirm the desire to proceed and edit the step details.

2. Select Yes to confirm.

   The Record Details screen displays.

3. Modify the step details as required.

4. Review your changes and select Save.

By default, the name of the outputs generated by a step in the LIMS follows the naming convention of the inputs to the step.

When configuring a master step, you can use tokens to configure the naming convention so that it resolves to other unique attributes of the output. These tokens function as placeholders that are replaced with actual values at runtime. For example, for the Standard step type, the default naming convention resolves to the value of the {InputItemName} token (shown below).

The Tokens list provides a list of tokens you can use. You can copy and paste these directly into the Naming Convention text box.

• If using multiple tokens, add a space between each entry.

• Below the Naming Convention field, you will see a preview of how the token(s) will resolve.

• Note that some runtime-specific items, such as dates and times, will not preview exactly as they will resolve at runtime.

NOTE:

• Output names are limited to 100 characters. If a name exceeds this limit, the LIMS automatically removes characters from the middle of the name.

• To pad a resolved value, add a colon (:) and a whole number to indicate the desired number of digits. For example, if {OutputItemNumber} resolves to 23, {OutputItemNumber:4} will resolve to 0023.

Simple Tokens

You can use simple tokens that will resolve to system-specified results, such as container location and LIMS ID of an output. These tokens are replaced with the appropriate value of the specified item at runtime. Tokens are case sensitive.

{InputItemName}

The name of the input used to generate the output.

{InputItemNameNoSpaces}

The name of the input used to generate the output, but with spaces removed.

{InputWellLocation}

The location or name of the well where the input resides.

To get a sub-string of the location or name of the well, add a colon (:), and one or two whole numbers to indicate the start index (zero-based, i.e. starts with 0. Inclusive) and end index (Exclusive). {InputWellLocation:<startIndex>,<endIndex>}

Example

If {InputWellLocation} has the value of A:3, the following examples show the derived values with the new format:

• Lane {InputWellLocation} -> Lane A:3

• Lane {InputWellLocation:0,1} -> Lane A

• Lane {InputWellLocation:1,3} -> Lane :3

• Lane {InputWellLocation:1} -> Lane :3

{InputContainerIdentifier}

The container identifier in which the input resides.

{InputItemNumber}

The number of the input used to generate the output, such as 7 of 20. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.

{InputItemTotal}

The total number of inputs used to generate the outputs. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.

{OutputItemLIMSID}

The LIMS ID of the output.

{OutputItemNumber}

The current output's absolute position within the order of all outputs, such as 9 of 40. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.

{OutputItemTotal}

The total number of outputs generated. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.

{OutputItemSubsetNumber}

The current output's relative position within its relative set, such as 1 of 2. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.

{OutputItemSubsetTotal}

The fixed count of relative outputs per input. You can pad the resolved value to a certain number of digits, and the LIMS will prefix the number with zeros. See note above.

{AppliedReagentLabels}

The type of reagent label applied to the input.

{SubmittedSampleName}

The name of the sample’s related submitted sample - the original parent sample that was submitted to the LIMS.

{ProjectName}

The name of the project that contains the inputs to the step.

{ProcessLIMSID}

The LIMS ID of the step that created the outputs.

{ProcessTechnicianFullName}

The name of the lab scientist who runs the step.

{ProcessTechnicianFirstName}

The first name of the lab scientist who runs the step.

{ProcessTechnicianLastName}

The last name of the lab scientist who runs the step.

{ProcessTechnicianInitials}

The initials of the lab scientist who runs the step.

{DATE:MMM d, yyyy}

The date the step was run, according to the computer's clock.

{LIST:a,b,c}

With this variable, you can specify a comma-delimited list of words that will be used when generating output names. Clarity LIMS will cycle through the words from left to right, applying one word to each output name. When the last word has been used and there are further outputs that require names, Clarity LIMS will restart at the beginning of the list.

Complex Tokens

Complex tokens provide further flexibility with the use of parameters.

• You can combine any alpha-numeric text with simple and complex tokens for highly specialized and unique output names.

• When using complex tokens, you must specify parameters that will be used when the token is resolved.

• You can only use one LIST and one DATE token per output string, but you can use any combination of parameters within those tokens.

• With the DATE token, if you would like to include a word between parameters, enclose the word in single quotes (‘x‘).

• Times and dates resolve to the time and date the process was run, according to the computer's clock.

• Tokens and parameters are case sensitive.

As lab scientists work with samples in the lab, they may request a manager to review a sample at a certain step in the workflow. When a request for review occurs, an alert notification displays in Lab View, in the Recent Activities area.

1. In Lab View, in the Recent Activities area, select an alert to go directly to the step containing the sample to be reviewed.

2. Review the sample, add a comment, and select Finish Review.

   NOTE: You can also view and resolve alerts from .

Consumables are the , , , 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.

Controls Configuration Screen

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 and .

Add and Configure Controls

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).

Add a New Controls

1. On the main menu, select Configuration.

2. On the configuration screen, select the Consumables tab, then select Controls.

3. On the Controls configuration screen, select New Control.

4. 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.

5. [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.

6. 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.

7. Select Save.

   The new control displays in the Control Samples list.

Enable controls on a step

Enabling controls on steps makes them available for use in the lab.

To enable a control sample on a step, complete the following steps:

1. On the Controls configuration screen in the Control Samples list, select the control to enable on steps.

2. 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.

3. In the adjacent list, select the step on which you want to enable the control.

4. Enable the control on additional steps, if necessary.

5. 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.

Control Use Settings

Control Status

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

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.

Archived and Reactivate Controls

Archived Controls

1. In the Control Samples list, select the control to archive.

2. On the Status of Control slider, select Archived.

3. Select Save.

Reactivate and Archived Controls

1. In the Control Samples list, expand the archived control group and select the control to be activated.

2. On the Status of Control slider, select Active.

3. Select Save.

Delete Controls

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.

To delete a control:

1. On the Controls configuration screen in the Control Samples list, select the control to delete.

2. In the Control Sample Details area on the right, select Delete.

The Instruments Configuration Screen

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 and .

Add and Configure Instruments

When adding instruments to Clarity LIMS, there are two main steps involved:

1. Add a new instrument type (Configuration:update permission required).

2. 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.

Add a New Instrument Type

1. On the main menu, select Configuration.

2. On the configuration screen, select the Consumables tab, then select Instruments.

3. On the Instruments configuration screen, select New Instrument Type.

4. 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.

5. 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.

Add a New Instrument

1. On the Instruments configuration screen, in the Instrument Types area, select the appropriate instrument type.

2. Select New Instrument.

3. 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.

   • Software Name: Enter the name of the instrument software.

   • Software Version: Enter the instrument software version number.

4. Select Save.

   In the Instrument Types area, the new instrument is nested under its instrument type.

5. 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.

Instrument Status

The instrument Status toggles between Active and Archived. By default, when adding a new instrument, its status is Active.

Active instruments:

• 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.

Archived 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.

Edit in Instrument Types and Instruments

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.

Delete Instrument Types and 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.

Reactivate an Archived instrument

1. In the Instrument Types area, expand the Archived Instruments section and select the instrument to reactivate.

2. If the instrument has not expired, select Activate.

3. If the instrument has expired, reset the expiry date to a date in the future, and then select Activate.

4. Select Save.

   In the Instrument Types area, the reactivated instrument displays under its instrument type. The instrument may now be selected when running steps.

Reagents Configuration Screen

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 .

Add and Configure Reagent Kits and Lots

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.

Add a New Reagent Kit

1. On the main menu, select Configuration.

2. On the configuration screen, select the Consumables tab, then select Reagents.

3. On the Reagents configuration screen, select New Reagent Kit.

4. Type a name for the reagent kit. This name displays in queues of steps on which use of the reagent kit is enabled.

5. 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).

6. Select Save to add the new reagent kit.

   The new kit displays in the Reagent Kits list.

Enable a Reagent Kit on a Step

1. On the Reagents configuration screen, in the Reagent Kits list, select the kit to enable on steps.

2. 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.

3. Select Save. The Reagent Kits list now indicates that the kit has been enabled on the selected steps.

Add a Reagent Lot

1. On the Reagents configuration screen in the Reagent Kits list, select the kit for which you would like to add a new lot.

2. Below the Kit Details in the Lots area, select New Lot.

3. In the Lot Details area, enter the lot name.

4. [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.

5. 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.

Reagent Kit and 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.

Activate and Archive Reagent Kits and Lots

Activate and Achieve Reagent Kits

1. In the Reagent Kits list, select the kit to be archived or reactivated.

2. In the Reagent Kit Use area on the right, select Archived / Active.

3. Select Save.

Activate and Archive Reagent Lots

1. In the Reagent Kits list, select the kit containing the lot to be activated or archive

2. At the bottom of the Lot Details area on the Status of Reagent Lot slider, select Active / Archived.

3. Select Save.

Delete Reagent Kits and Lots

1. In the Reagent Kits list, select the reagent kit or lot to delete.

2. 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.

Upload Reagent Lot List

1. On the Reagents configuration screen, select Upload Reagents Kit Lot.
2. In the Upload File dialog, select Choose File and browse to and open the reagent lot list file.

3. 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.

4. When the upload process completes, the reagent lot display in the Reagent Kits list.

Milestones are the various stages of a step that are presented to lab users as they run samples through steps in Clarity LIMS.

Milestones and Step Types

Some screens (such as the Queue, Ice Bucket, and Record Details screens) display on all steps, while others only display on certain step types.

For example, the Pooling milestone only displays on steps of the Pooling type and the Add Labels screen only displays on steps of the Add Labels type. On all other step types, those milestones are disabled on both the master step and step configuration forms.

The following table shows the milestones that are available for display for each step type. For more information on step types, see .

Milestones Displayed for Step Types

*While the Step Setup screen is available for display on all step types, it is optional and does not display by default. To enable the Step Setup screen, you must first add file placeholders on the master step. For details, see .

Configuring Milestones

You can configure milestone settings on the master step and step configuration forms.

When switching between the step and master step configuration forms while viewing or editing a milestone, you are returned to the parent step/master step form. You need to select the milestone name again to open its settings form.

Similarly, if you wish to return to the step or master step settings form, select the parent master step or step tab.

To configure a milestone:

• Select it to open its settings form.

When configuring milestones on master steps and steps, consider the following details:

• If you configure a list of items at the master step level—for example, expanded view fields, instrument types, reagent kits—the order in which they are listed on the master step is overwritten by the order set at the step level. Set the order of any list at the step level. This includes the order of the Sample table column headers.

• If you remove configured settings from a master step, those settings on the related steps revert to their default values. The exception is if this would leave the step in an unworkable state. For example, you cannot remove the last container from a step. Exceptions to this 'revert to default' rule are noted where applicable.

• Settings configured at the step level only apply to that particular step.

Configure Queue Milestone

When running samples through a step, the first screen that displays is the Queue screen. This screen provides a sample table to select samples to be placed into the Ice Bucket, reserving them for use.

The following components of the Queue Sample table are configurable on the Queue Settings form:

• The Sample table column headers

• The Sample table expanded view fields

• Default grouping and well sort order of Sample table

Configure Sample Table Column Headers

On the Queue Settings form, configure the column headers that display in the Sample table, and the order in which they display.

Note the following:

• No default column headers are configured at the master step level.

• When configuring column headers on a new step, several default column headers will display. You can remove these, but the table must have at least one field remaining (this may be set on either the master step or the step).

Configure Sample Table Expanded View Fields

Expanded view fields are hidden by default in the Sample table. These fields contain additional details about the samples in the queue. At run time, choose to display these details by clicking the Show/Hide Details button.

On the Queue Settings form, in the Expanded View Fields section, you can select additional fields to add to the body of the Sample table.

Note the following:

• No default expanded view fields are configured at the master step or the step level.

• If expanded view fields are configured at the master step level, they display as locked at the step level and cannot be removed. You can modify the order in which the locked fields display.

• Expanded view fields are available for display in multiple milestone screens. The configuration options set in each milestone are specific to that milestone. You may choose to configure the expanded view fields differently in other milestones.

Configure Sample Table Defaults

On the Queue screen, samples are grouped by Container and sorted by well Row by default.

On the Queue Settings form, in the Defaults section, you can modify these settings if necessary.

Configure Ice Bucket Milestone

Samples move from the Queue into the Ice Bucket, where they are reserved for use for 30 minutes. The Ice Bucket screen displays for all step types. It comprises a Sample table that displays information about the samples entering the step.

The following components of the Ice Bucket screen are configurable on the Ice BucketSettings form:

• The Sample table column headers

• The Sample table expanded view fields

• Default grouping and well sort order of Sample table

Configure Sample Table Column Header

On the Ice Bucket Settings form, configure the column headers that display in the Sample table, and the order in which they display.

Note the following:

• No default column headers are configured at the master step level.

• When configuring column headers on a new step, several default column headers will display. You can remove these, but the table must have at least one field remaining (this may be set on either the master step or the step).

Configure Sample Table Expanded View Fields

Expanded view fields are hidden by default in the Sample table. These fields contain additional details about the samples in the Ice Bucket. At run time, choose to display these details by clicking the Show/Hide Details button.

On the Ice Bucket Settings form, in the Expanded View Fields section, you can select additional fields to add to the body of the Sample table.

Note the following:

• No default expanded view fields are configured at the master step or the step level.

• If expanded view fields are configured at the master step level, they display as locked at the step level and cannot be removed. However, you can modify the order in which the locked fields display.

• Expanded view fields are available for display in multiple milestone screens. However, the configuration options set in each milestone are specific to that milestone; you may choose to configure the expanded view fields differently in other milestones.

Configure Sample Table Defaults

By default in the Ice Bucket screen, samples are grouped by Container and sorted by well Row.

On the Ice BucketSettings form, in the Defaults section, you can modify these settings if necessary.

Configure Step Setup Milestone

The Step Setup screen is an optional screen. By default, it does not display at run time.

This screen lets you provide the lab scientist running the step—and provide Clarity LIMS—with access to files before samples are placed. You can then configure step automations that parse these files and use the information to place samples into destination containers, based on the result file specifications.

If you enable the display of the Step Setup screen (you can enable it on any step type), it displays immediately after the Ice Bucket screen.

The Step Setup Settings screen allows you to do the following:

• Add file placeholders that will be populated at run time. Configure these on the master step.

• After you have added file placeholders, you can then enable the display of the Step Setup Settings screen at run time. You can configure this on the master step or the step. However, as with all master step settings, if you enable the screen on the master step, it displays on all steps derived from that master step.

• Configure the attachment method for each file added—manual or automatic. You may configure this on the master step or the step.

To enable the Step Setup screen, you must first configure one or more file placeholders on the master step.

Add a File Placeholder

1. On the Lab Work tab, in the Master Steps list, select the master step on which you would like to configure the file placeholders.

2. Select the Step Setup milestone.

3. In the File Placeholders section, select Add.

4. Type a name for the file placeholder.

6. Enter instructional text.

Set the Attachment Method

To set the attachment method, select the Attachment toggle switch to set the file attachment method.

Remove a File Placeholder

To remove a file placeholder, select the X button.

Enable the Step Setup Screen

1. On the Lab Work tab, in the Master Steps or Steps list, select the master step or step on which you would like to configure Step Setup file placeholders.

2. Select the Step Setup milestone.

3. At the top of the Step Setup Settings screen, select the toggle switch to enable the Step Setup screen. The screen now displays at run time.

   When the Step Setup screen is enabled, it becomes available for selection as an automation trigger location. If you configure an automation trigger location on the Step Setup screen, the Step Setup screen cannot be disabled.

Configure Pooling Milestone

When you create a step and choose the Pooling step type, the Pooling milestone is enabled. When running the step, the Pooling screen allows the lab scientist to create pools of samples.

The following components of the Pooling screen are configurable on the Pooling Settings form.

• Enable and disable label uniqueness to control whether samples with the same labels, or no labels, may be pooled together. This must be configured on the master step.

• Configure defaults for sample grouping and well sort order. You can configure these settings at the master step or step level.

Configure Label Uniqueness

1. Select the Label Uniqueness toggle switch to turn label uniqueness on and off.

   • When Label Uniqueness is On (default setting), samples with the same labels cannot be pooled together.

   • When Label Uniqueness is Off, samples with the same label or no labels may be pooled together.

2. Save your changes.