Samples Accessioning
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
On the main menu bar, hover over Projects and Samples tab and select Add Samples when the option displays.
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.
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.
To upload sample files, select Upload File at the bottom of the Sample Details section.
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.
Repeat steps 3 to 5 as required.
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.
On the Project and Samples tab, select a project to add samples.
In the Submit Samples section, select Add Samples.
On the Sample Management screen, because the project has already been specified, the project details are automatically completed.
Follow steps 3 to 7 of the previous section to add the sample details.
Modify Samples
On the Project and Samples tab, select a project to add samples.
In the samples list, select the submitted samples to modify (derived samples cannot be modified).
Select Modify Samples.
Modify the sample and project details as required (the Project Name or Container Name fields cannot be modified).
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.
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.
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
Navigate to the Projects and Samples tab.
In the Projects list, select a project to add samples. The Project Details area updates to show the details for the selected project.
Select Upload Sample List.
In the Upload File dialog, select Choose File and browse to and open the sample list file.
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.
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
Navigate to the Projects and Samples tab.
In the Projects list, select the project containing the samples to modify.
Select Modify Samples.
Clarity LIMS generates a sample list containing all samples in the project and downloads it.
Open the file in Excel. It contains the Clarity LIMS IDs of all samples and all custom field data.
Update the sample information as required.
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.
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