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The Configuration tab is only available to LabLink administrators. This tab consists of the following sections:
If there are any configuration errors, a red dot appears on the Configuration tab and the section that requires attention.
In LabLink, there are two types of resource materials:
Sample submission templates
Supplementary documents
The administrator can manage these resource materials to assist end users of the lab during the sample submission process. LabLink allows the admin to upload up to 20 resource materials.
To add new templates or documents, a LabLink administrator can use the following steps:
Select Create.
Provide a name and description for the document.
Select the resource type.
Upload the resource file.
By selecting the resource type, the document is added to the appropriate location on the Resource Material tab.
The Custom Fields section of the Configuration tab displays all custom fields that have been configured in Clarity LIMS for projects and submitted samples.
A LabLink administrator can choose to display custom fields by selecting the checkbox next to the custom field.
The project custom fields display during the sample submission process.
The sample custom fields display on the Samples tab.
The client custom fields display during the create new user and request a new user ID processes.
The Disclaimer section allows the LabLink administrator to manage the disclaimers that display for the following processes:
Requesting a new user ID
Creating a project for sample submission
Select Edit to modify the disclaimer text. The character limit is 4096 for each disclaimer.
The Contact Us section allows the LabLink administrator to manage the contact us information that displays for the end users of the lab. Select Edit to modify the contact us information.
The Resource Materials tab provides LabLink users with resource materials from the lab. The lab can upload different types of resources from the Configuration tab. There are two types of resource materials:
Sample Submission Templates—Templates that can be used to submit samples. Each template contains headers and custom fields that are required for each sample.
Supplementary Materials—Documents that can be used as part of the sample submission process.
The Contact Us tab provides LabLink users with information on how to contact the lab. The lab can update this information through the Configuration tab.
Project notes are made through the Project Overview tab. Sample notes are made through the project Sample tab.
When this feature is active, LabLink sends an email notification if a new project note or sample note is created.
The email notification is sent to the owner of the project/sample or to the distribution list configured in properties (lablink.admin.email), depending on who saved the note.
Notes saved by the project/sample owner produce email notifications sent to the distribution list.
Notes saved by anyone other than the project/sample owner produce email notifications sent to the project/sample owner.
Project note email notifications contain a link to the project details Project Overview page. Sample note email notifications contain a link to the project details Sample page.
NOTE: This feature is not active by default. To receive email notifications for notes, send a request to the Support team.
LabLink is a sample submission portal that is part of Clarity LIMS. LabLink allows end users of the lab (ie, principal investigators, clinicians, external labs) to submit samples to the lab for processing. By allowing end users to submit samples through LabLink, the lab benefits in the following ways:
Save time and avoid manual errors during sample accessioning by automatically receiving submitted sample information in Clarity LIMS.
Easily configure LabLink to include sample submission templates and supplementary materials (ie, shipping instructions). End users of the lab use these materials during the sample submission process.
Provide progress updates and publish files to end users of the lab.
To sign in to LabLink, open the LabLink URL associated with the Clarity LIMS instance for the lab.
On the Sign In screen, the following actions are available:
Sign in to LabLink with a user ID and password.
Request a user ID by selecting Request for a User ID.
Request to reset a password by selecting Forgot Password?.
Reset a password after multiple failed sign-in attempts.
The lab carrying out the processing/assaying of the samples can publish the following, and make them available to collaborators:
Files that are attached to steps and derived samples.
Examples include the following use cases:
Publishing an image of an electropherogram for a sample that failed Bioanalyzer QC.
Publishing small files such as AB1 files that result from Capillary Electrophoresis sequencing.
NOTE: It is not recommended to publish large NGS or microarray derived data (such as FASTQ or VCF files) through LabLink. Although technically possible, BaseSpace Sequence Hub works much better for these large files.
Custom fields that are defined and populated on samples in Clarity LIMS. For example, a field that tracks the progress of the samples.
The only way to publish a file is by using the Clarity LIMS API. To publish documents to LabLink, run a custom script in Clarity LIMS at the end of a step.
For example, at the end of a Bioanalyzer QC step, if individual electropherogram images are available, they may be published and made available immediately in LabLink. See the API & Database documentation for an example script that publishes files to LabLink.
Files published to LabLink are available under the Results and Documents tab of a LabLink project, in the Sample Results and Documents section.
The Sample Results and Documents section of the page has three elements for each row:
Document Name—The name of the file that has been stored in Clarity LIMS and published.
Sample Name—The name of the sample associated with the published file.
Download Link—Select this link to download a copy of the file from LabLink.
For example, if all samples in a project participate in a step, publishing a file associated with that step causes the file to also be associated with all samples in that step.
Publishing a step-level file may have undesired consequences. Imagine a single step that was run on samples from two separate LabLink projects. If that step includes a step-level file that is published, it is available to both LabLink projects.
Depending on the contents of the file, publishing might lead to one collaborator seeing sample data that relates to another collaborator.
NOTE: Only publish step-level files if they are associated with samples in a single LabLink project.
The lab can publish custom fields that are defined and populated on samples in Clarity LIMS. Collaborators in LabLink can then see these custom fields.
This functionality depends on how Clarity LIMS is configured. For example, assume that the sample-level custom field called Progress should be visible in Clarity LIMS.
Define the Progress custom field in Clarity LIMS, including field type, field options, and additional options.
Make the Progress custom field visible in LabLink.
Navigate to the Custom Fields screen from the Configuration menu.
Select the Progress checkbox for the field to be visible in LabLink.
When samples are first submitted to LabLink, the Progress field is empty.
When the lab receives the samples, they may set the Progress field to have the Awaiting QC value for all samples in the project.
When the samples have completed the QC steps, the lab may update the Progress field with different values depending on the success or failure of QC.
As the samples move through the workflow, lab technicians update the Progress field as required. These updates provide the collaborator with insight into what is happening in the lab, on a per-sample basis. You can configure a script that automatically updates the Progress field, eliminating the need for manual updates by lab technicians. For example, configure the following automation command line that uses Clarity LIMS Lab Logic Toolkit to update the Progress field.
bash -l -c "/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-
extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression - t
true -h false -exp '\
submittedSample.::Progress:: = ::Awaiting QC::; \
' -log {compoundOutputFileLuid0}"
If the value of the Progress field is long, it may be truncated in LabLink. However, the full value can be obtained by hovering the mouse over the truncated value.
NOTE: Widening the browser window may show more of the field, but truncation may still occur.
The Projects tab is the landing page that displays after signing in to LabLink. The view of the Projects tab differs between administrators and collaborators:
LabLink administrators—the Projects tab displays all projects submitted to the lab.
Collaborators—the Projects tab displays only the projects submitted to the lab by the current collaborator.
To create a project and submit sample, go to the Projects tab and select Create.
The Create A New Project guided sample submission form displays. This form includes the following steps:
Enter general information for the project, as follows:
Enter the project name.
[Optional] Enter project notes for the lab
Select Continue
By default, the Project Name and Project Notes fields are always shown. Other project fields can display, depending on the configuration of custom fields by the lab.
In this step, upload a sample submission document containing sample information for the lab.
Download a sample submission document template from the Resource Materials tab (the lab administrator uploads the templates). Populate the template with the sample information.
Select Browse Document and locate the sample submission document. Select Open to upload the document.
After the document has been added, LabLink validates the headers and fields. If the headers and fields are not valid, error messages display.
After successfully uploading a document, a list of fields populated with sample information displays for review.
If the sample information is incorrect, replace the existing document by selecting Replace.
If the sample information is correct, select Continue.
In this step, upload additional documents to share with the lab regarding this project. Skip this step if additional documents are not needed.
[Optional] Select Browse Documents and locate the document to be shared with this project submission. Select Open to upload the document.
Upload additional documents or select Continue.
In this step, review a summary of the project and uploaded documents before submitting the project and samples to the lab.
If the lab has configured a disclaimer for sample submission, the disclaimer is available for review.
After reviewing, select all required checkboxes.
The Submit Project button becomes available.
Select Submit Project.
After the project has been successfully created and submitted to the lab, a confirmation message displays.
[Optional] Select View Confirmation to print an overview of the submitted samples.
The Project Submission Confirmation page opens in a new tab. The page includes an overview of project information, lines for a signature and date of signature, and a list of all samples submitted.
This page can be printed and shipped to the lab with the submitted samples.
Once submitted, all projects are associated with one of the three following status types:
Pending—The lab has not started processing the samples (or samples have not been received).
Open—The lab has received the samples and the samples are being processed.
Closed—The lab has completed processing the samples (or the lab has decided to close the project).
These three status types correlate to the status shown in Clarity LIMS. By changing the status of the project in Clarity LIMS, the status automatically changes in LabLink.
After samples are submitted to the lab, the project is listed with a Pending status until the lab changes the status in Clarity LIMS.
To search for projects or samples in LabLink, enter a term in the search box and select one of the following criteria:
Projects—The search is performed on all projects.
Sample—The search is performed on all samples.
To view a single project, select a project in the project list.
The Users tab is only available for LabLink admins. This tab displays a list of pending requests and all users. If there are any pending requests, a red dot appears on the Users tab.
In the All Users section, only approved users display. The account status for each user shows as Active or Deactivated.
Pending requests require a LabLink admin to approve or deny the request. To approve or deny the request, complete the following steps:
Select the name of the pending request.
A Review User Request window displays with the option to approve or deny.
Approve or deny the pending request.
To approve, update any of the prepopulated fields and provide a user ID. When all fields are correct, select Approve and an email is sent to the requester stating that the request has been approved.
To deny, select Deny and provide the reason for the denial. After entering in the reason, select Deny and an email is sent to the requester with the reason for denial.
To deactivate a user, edit the user information as follows:
Select the name of a user.
The User Information screen displays.
Select Edit.
Deselect the Active checkbox (under Account Status) to deactivate the user.
Save changes.
Create a new user from the Users tab:
Select Create.
The Create A New User screen displays.
Define the user information, which includes the following fields:
First Name
Last Name
Title [optional]
Phone Number
Email Address
User ID
Role
Submitting Lab Name (Account).
Select Create.
LabLink offers the following two roles:
An admin role grants access to all submitted projects and samples, resources materials, users, configuration, and the Contact Us tab. The LabLink admin role is equivalent to a system administration role.
A collaborator role grants access to the submitted projects and samples from that user, available resource materials, and the Contact Us tab. The collaborator role in LabLink does not grant access to Clarity LIMS.
All users with a collaborator role in Clarity LIMS appear in the LabLink All Users list.