Overview

Sample Manager is a KDXplore plugin that enables users to assign collected samples with barcodes to plate wells. These samples can then be uploaded to the DArT Online Ordering system for sample submissions. See the Workflow page if you want more information on how to use the plugin.

Note

Sample Manager is still under development. If you experience any issues or have feedback, please contact kdxplore@diversityarrays.com


Sample Data File Format

Sample data files must be a CSV file in a specific format so that Sample Manager can recognise it. If you do not already have a sample data file, follow the links below to download an example file (with example data) or a template file:


Sample Data File - Example: Download


Sample Data File - Template Download


See the table below for more information about the mandatory columns that must be present in a sample data file for Sample Manager to recognise the file:

Sample Data File Format

Column Name

Description

Barcode

Any barcode associated with the sample.

Genotype

Genotype of the sample.

Organism

Organism type of the sample e.g. wheat.

Tissue

Tissue collected from the sample e.g. leaf.

Comments

Any comment related to the sample.

Note

The example file above contains many non-mandatory columns that provide an example of the data that might be collected in actual use.


Main Window

The Sample Manager Main window displays all plates that have been created, as well as any well contents that have been assigned to them. There are also tools for the management of plates, samples, and associated files. See the image and table below for more information:


Sample Manager Main Window
Sample Manager Main Window (select to zoom)


UI Elements of the Sample Manager Main Window

UI Element

Description

circle1 Plates List panel

Lists all plates that have been created within Sample Manager. There are also options for viewing or deleting these plates.

circle2 Plates panel

Contains one or more Plate tab/s as well as options for managing these plates such as importing sample data and unassigning samples from wells.

circle3 Plate tab

Displays each opened plate as a tab with a 96 well plate.

remove_dna_plate_btn Delete Plate button

Deletes any plate from the local machine.

dna_plate_btn View Plate button

Opens the selected plate as Plate tab within the Plates panel.

add_dna_plate_btn Create New Plate button

Displays options for the creation of a new plate.

import_csv_btn Import button

Displays the Import Sample Data window for importing sample data and assigning samples to well.

save_plates_btn Save button

Saves any changes made to any of the plates in the Plates list.

export_btn Export button

Displays export options for the any plates that are opened in the Plates list (so that they can be used in Online Ordering).

unassign_btn Unassign Well button

Unassigns a sample from the selected well.

Auto-Select checkbox

Automatically selects the next well after assigning content to another.

Auto-Open checkbox

Automatically opens any exported file for viewing.

Resizing Radio buttons

These radio buttons allow the user to choose Auto_Resize_Off which turns automatica resizing of columns off, or All_Columns which automatically resizes all columns.

Locked checkbox

This can be checked or unchecked to allow/prevent editing of the selected plate.


Import Sample Data Window

The Import Sample Data window enables the user to add imported data to a newly created plate within Sample Manager. It can be accessed by selecting the import_csv_btn Import button in the Plates panel. The following image an table outline the main elements of the window:


Import Sample Data Window
Import Sample Data Window (select to zoom)


UI Elements of the Import Sample Data Window

UI Element

Description

circle1 Files panel

Displays any sample data files that have been imported. These files can be selected so that they are displayed in the Data panel.

circle2 Data panel

The sample data of any file selected in the Files panel will be displayed here. Each line can be assigned to a well that is also currently selected in the Plates panel of the Main window.

circle3 Barcode panel

Allows for the entering of a barcode that is associated with a collected sample.

circle4 Messages panel

Displays any errors or warnings when importing samples or assigning them to wells.

import_csv_btn Import button

Opens a window for selecting a samples file that is stored on the local machine.

assign_btn Assign Well button

Assigns the sample that is currently selected in the Data panel, to the well that is currently selected in the Plates panel of the Main window.

Show Filename checkbox

Displays/hides a file name column in the Data panel.

Sort by Plate/Well button

Sorts the listed samples by plateID or by well.