Workflow

Whilst Sample Manager allows users to manage files for submission, there are also other integrated DArT applications that are involved in the entire process. This process might look something like:

  1. Collecting samples with KDSmart. This will produce a CSV sample data file that can be used in Sample Manager;

  2. Creating a new plate in Sample Manager;

  3. Importing a sample data file the CSV file that was created in KDSmart;

  4. Assigning samples to wells, along with any barcodes; and then

  5. Exporting a samples file for use in DArT Online Ordering.

  6. Importing the samples file into the DArT Online Ordering system.

Note

Steps 1 and 6 do not occur in the Sample Manager plugin. Please follow the respective links for more information.


Creating a New Plate

Before importing data into Sample Manager, there will need to be at least one plate created so that samples can be assigned to plate wells. Plates refer to the 96 well plates that are used when providing samples to DArT, and also the corresponding entity within Sample Manager.


Creating a New Plate
Creating a New Plate (select to zoom)


Creating a New Plate

Step

Action

1.

Select the Create New Plate button add_dna_plate_btn from the Plates panel. This will display the New Plate window as seen in the above image.

2.

Enter a name for the new plate within the text field.

3.

Select the Use button which confirms the name and creates the new plate. The new plate will now be listed in the Plates List panel.


Importing a Sample Data File

Samples data files contain information about samples that have been taken (possibly with KDSmart) and are in the CSV format. Once imported, these samples can be assigned to plate wells with Sample Manager. The instructions below provide information on how to import a sample data file:

Note

Before importing sample data, ensure that there are enough plates created to contain all of that data. 94 wells from each 96 well plate can contain samples we operate on a 94 sample per plate basis, file cannot contain information for wells G12 and H12.


Importing a Sample Data File
Importing a Sample Data File (select to zoom)


Importing a Sample Data File

Step

Action

1.

Select the Import button from the Main window (at circle1 in the above image). This will display the Import Sample Data window.

2.

Any previously imported samples files will be displayed in the Files panel. If there are no sample data files available, then select the Import button at circle2 in the Import Sample Data window. This will open a File Viewer window.

3.

Choose a file and select the Open button at circle3. This will populate the Import Sample Data window with the data from the selected file.

Note

After sample data is imported, it still needs to be assigned to wells. See the next section for more information on how to do this.


Assigning Samples

Samples that have been imported to Sample Manager can be assigned to wells of the any plate that has been created. See the below instructions for more information on how to assign samples to wells:


Assigning Samples 1/3
Assigning Samples 1/3 (select to zoom)


Assigning Samples 1/3

Step

Action

1.

From the Main window, navigate to the Plates list and open a plate by either double-clicking the plate in the list or selecting it and then selecting the View Plate button. This will ensure that the empty plate is available as a Plate tab as seen in the image above.

2.

Ensure that the first well you want to assign sample data to is selected. In the above image, it can be seen that well A1 (the first well) is selected.

3.

Also in the Main window, select the Import button to display the Import Sample Data window (as seen in the image below). If you have not yet imported a sample data file, then see the Importing a Sample Data File section above for more information.


Assigning Samples 2/3
Assigning Samples 2/3 (select to zoom)


Assigning Samples 2/3

Step

Action

4.

Select a row from the Data panel. Each row represents one sample.

5.

If you have a barcode to assign to the sample, it can be entered in the Barcodes panel.

6.

Select the Assign button to assign the sample selected in the Import Sample Data window to the well that is selected in the Plate tab located in the Main window. This will be updated live and any sample that is assigned to a well can immediately be seen in the Plate tab.

7.

If the Auto-Select checkbox is selected in the Main window, then each time a sample is assigned to a well, Sample Manager will automatically select the next well to have sample data assigned to it. If the option is not selected then after assigning a sample to a well, you must navigate to the Main window and select the next well.


Assigning Samples 3/3
Assigning Samples 3/3 (select to zoom)


Assigning Samples 3/3

Step

Action

8.

Continue assigning all required samples to wells. If there are more samples than wells, new plates can be created as needed. Each time a sample is assigned to a well, it will be disabled in the Import Sample Data window. This is so that the same sample can not be assigned twice.

9.

In the Main window, select the Save button to save the plate/s that have been assigned samples. Saving is not required for exporting, but ensures that changes will be recorded if Sample Manager is closed and opened again.

Note

See the Sample File Guidelines page for more information about sample files and how to assign them in the correct order.


Exporting a Samples File

After all sample data has been assigned to wells, it is ready to be included in an order in DArT’s Online Ordering system. This is done by creating a samples file from plates with assigned samples. The instructions below demonstrate how to create a sample file from the assigned sample data:


Exporting a Samples File
Exporting a Samples File (select to zoom)


Exporting a Samples File

Step

Action

1.

When all samples have been assigned to plates, ensure that any required plates are open and that all changes have been saved by selecting the Save button (at circle1) in the Main window. The samples file will include a tab for each plate that is exported and these tabs will be in the same order that plates are displayed in Sample Manager.

2.

Select the Export button (at circle2) when you are ready to export the file. This will open the Export window as seen at circle3.

3.

Choose a location from the dropdown menu at circle4. This will determine where the samples file is exported to.

4.

Name the file in the text field at circle5. The name of the file in the example is plates.csv.

5.

Select the Open button to complete the export. This will save the file and open it with your default spreadsheet application at the same time.

Note

The exporting of a samples file is the last step in the potential workflow (as described in the Workflow section) that can be completed in Sample Manager. The final step involves using the samples file in a order that is created with Online Ordering.


Deleting a Plate

Plates can be deleted from Sample Manager when they are no longer needed. When a plate is deleted, it and any samples are only deleted from the local machine and not from KDSmart or Online Ordering. The instructions below demonstrate how to delete plates:


Deleting a Plate
Deleting a Plate (select to zoom)


Deleting a Plate

Step

Action

1.

Select a plate to be deleted from the Plates List panel at circle1.

2.

Select the Delete Plate button remove_dna_plate_btn. This will display the Delete Plate window at circle2.

3.

Select the Yes button to confirm the deletion of the plate.

Note

Any plate that does not contain assigned content will be deleted immediately without a warning message.