Trial Management

Trial Manager Main Window

The initial Trial Manager window shows the Trials stored in the local KDXplore database along with Traits and Tags for the selected Trial.

The next three annotated examples show the Trial Manager with the Trials tab, Traits and Tags tabs selected highlighting the main window areas.

Trial Manager Home screen - Trials
Trials panel of the Trial Manager window (select to zoom)


The main sections of the Trial Manager window highlighted above are:

  • circle1 Trials tab which has been selected.
  • circle2 Trials panel which lists the Trials available within KDXplore’s database that can be selected.
  • circle3 Trial Details panel which displays Trial details for the Trial selected.
  • circle4 Uses Traits panel which lists the Traits associated with the selected Trial.
  • circle5 Measurements panel which lists the measurements in the trial by the source.

Selecting the Traits tab will display the following window:

Annotated Traits panel of the Trial Manager window
Traits Panel of the Trial Manager window (select to zoom)


The main sections of the Trial Manager window Traits tab highlighted above are:

  • circle1 Traits tab which has been selected.
  • circle2 Traits panel lists the Traits and Trait Bundles available in KDXplore/KDDart.
  • circle3 Used by Trials panel lists all of the trials that contain the selected trait.
  • circle4 Details panel lists the details of the currently selected trait.

Selecting the Tags tab will display the following window:

Annotated Tags panel of the Trial Manager window
Tags panel of the Trial Manager window (select to zoom)


The main sections of the Trial Manager window Tags tab highlighted above are:

  • circle1 Tags tab which has been selected.
  • circle2 Tags panel lists the Tags and Tag Bundles available in KDXplore/KDDart.
  • circle3 Details panel lists the details of the elected Tag.

The following illustration shows section A from above where Trials are displayed and selected.

Annotated Trial panel of the Trial Manager window
Trial Grouping and Filtering (select to zoom)

Trials that are imported into the KDXplore Trial Manager can be grouped by related characteristics. Grouping and filtering makes it easier to quickly locate the required Trial(s) when many Trials are in KDXplore, or when logged into a KDDart database. Trial groups can be displayed based on trial type, KDDart URL, organism, and planting year. To view a trial group, the user will need to:

Trial Grouping
Step Action
1 Select the Group By drop-down menu at circle1 which will display the available grouping options.
2 Select a grouping option e.g. Trial Planting Year. Once this is selected, the system will display the trial group that has been. It will always display All Trials by default.
3 Once a trial grouping is selected, it can be changed by repeating the steps above and choosing another trial grouping.
  • circle2 Demonstrates the selection of the 2018 trial year grouping which is opened and the All Trials group which is collapsed.
  • circle3 Is the filter option which displays a text field below the button for entry of desired Trial Name text.

Note

Functionality to create new types of trial groups will be added in future versions.


Manage Trials

In Trial Manager, the Trial tab is the default/home view which displays all the information regarding the Trials currently stored in KDXplore. All trials in KDXplore’s offline database are displayed here.

Trial Manager Window
Trial Manager Window (select to zoom)

Selecting a Trial in the top left Trials panel at circle1 will display Trial Details in area circle2, Uses Traits panel at circle3 and Measurements by Source at circle4:

  • Trial Details - All trials in KDXplore’s offline database are displayed here. This displays the information regarding the trial. To edit Trials, either select a Trial by double-clicking it or by selecting the Edit Current Trial button at circle5. By selecting either of the two buttons at the bottom of this panel at circle6, both plot attributes, and trial attributes can be visualised. To quickly edit in Trial Details, double-click in the values column to change values.
  • Uses Traits - This area displays the Traits that are currently active for the selected Trial. These Traits are ordered by the user for preference during scoring in KDSmart. Traits can added or removed from Trials by selecting the ‘+’ or ‘-‘ symbols at the top of this panel.
  • Measurements by Source - This area displays the phenotypic datasets for the selected Trial and how populated (in percent) each dataset is. Datasets can be created from this panel. Datasets can also be created for a list of specific Traits to send to KDSmart for scoring. The source of each set of measurements (e.g. phone 1) can be viewed from this panel also.


Import Trials from File

KDXplore can import CSV and Excel XLS or XLSX files easily using drag and drop. For information on file import formats please see the “KDSmart/KDXplore - CSV Import File Formats” help page. Although .CSV files can be easily imported given almost any column format.

Importing Trials
Importing Trials (select to zoom)

Trials can be imported from various sources and in different formats. One of the easiest ways is to import a .CSV file which is outlined below:

Importing a .CSV file
Step Action
1 Select the Add Trials button at circle1 and select the Load From CSV option. This will bring up the Import Trials window at circle2.
2 Either drag and drop a .CSV file into the window, or select the Browse button located at circle3.
3 Select the Add Device button at circle4 to link any connected devices to import data (this is optional).
4 Change the Trial Name and Operator if necessary. The Traits that are contained in this file will also be listed in the window. Selecting a Trait by right-clicking it will allow the user to choose import options for that particular Trait i.e. Don’t Import
5 Select the Import button at circle5 to save the preferences and import the trial.

Note

Whilst this covered the import of a .CSV file, the same process applies for a .XLS or .XLSX file except the user must choose the Load From XLS option after choosing to add Trial.

Once a Trial has been imported it will appear in the list in the Trial Details panel. Trials can also be imported from KDDart by selecting Load From Database and from connected KDSmart devices through the Load From Tablet Data option when selecting the Add Trials button.


Import Trials from KDDart

KDXplore can also import Trials from the KDDart Database. To be able to do this, you must first be logged into KDDart. To see how to log into KDDart, follow the next set of instructions. If you are already logged in, then skip to the next part.

Connecting to KDDart
Connecting to KDDart

Connecting to KDDart
Step Action
1. Select the File button at the circle1 and then choose the connect option.
2. The KDDart Login window will then appear as at circle2. Enter your username and password and then select the Login button to log into the KDDart Database.

Logging into KDDart allows the user to easily import Trials with the relevant Traits and Tags attached. The following instructions will demonstrate how to import a Trial from the Database:

Importing Trials from KDDart Database 1/2
Importing Trials from KDDart Database 1/2(select to zoom)


Importing a Trial from the Database
Step Action
1 Select the kdx_download icon at circle1 and choose the Load from Database option to open the Database Import window as seen in the image above.
2 Choose an attribute to search for such as the one at circle2. This example is a location attribute that will only display the Trials that take place at Roseworthy.
3 Select the Find Trials button to search for the Trials. If no attributes were selected, then all Trials in the Database are presented.
4 The search results will then be displayed (such as in the following image). Choose a Trial (or multiple Trials) such as the one in circle1 and then select the Download Trials button at circle2 to complete the import.

Importing Trials from KDDart Database 2/2
Importing Trials from KDDart Database 2/2 (select to zoom)

Below is an animation that demonstrates the above instructions:

Importing Trials


Export Trials

Trials can also be exported so that it can be used on other devices. The exported files can be either a zip file, .CSV, or can be exported through KDXchange. It can also include media such as photographs. The following image and instructions detail how to export a Trial in the .CSV format.

Exporting Trials
Exporting Trials (select to zoom)

To export a Trial, follow the steps below:

Exporting a Trial
Step Action
1 To export a Trial in KDXplore select a Trial such as the Trial at circle1.
2 In the Measurements by Source panel, select the column of the dataset for export such as the column at circle2.
3 By then selecting the Export Sampled or Traits for Trial button at circle3, a dialog will open asking details for export as in circle4.
4 Trial Manager will choose a file destination, but to change it, select the Browse button at circle5 and then choose a folder in which to export to.
5 Choose the Output Options which will determine the format of the export (KDX, Zip, or CSV).
6 Choosing the Include Media Files option will include any photos that were taken with the samples.
7 Select either the Close, Export, or Export and Close options to finish the export.


Manage Traits

The Trial Manager module has the function to manage Traits that are available to use within Trials.

Actions available include:

  • Adding new Traits;
  • Removing a Trait (that is not used by any Trial);
  • Editing Trait details;
  • Viewing Trait information, e.g. Trait validation rules; and
  • Organising them, e.g. using Trait Bundles.

Trait Manager Home Screen
Trait Manager Home Screen (select to zoom)

The instructions below demonstrate accessing Traits via the Traits tab and provide an explanation of the available information:

Selecting a Trait to Manage
Step Action
1 In the Trial Manager module, select the Traits tab at circle1 to display the Trait information panels.
2 Traits that are currently in KDXplore can be seen here. Selecting a trait such as the Trait at circle2 will display information about the selected Trait in the Details panel at circle4. All information about a Trait is shown here including: Trait Name, Datatype, Validation Rule and Barcode.
3 In the Used by Trials panel, the Trials that are in KDXplore that are currently using the selected Trait will appear. For the example, only one Trial is using that Trait and it displays the Name, Acronym, and Planting Date of the Trial.


Adding Traits

Users can add new Traits which can then be added to Trials. These new Traits provide users the flexibility the add Traits after a Trial has been created, e.g. adapting a previously used Trial for a new experiment.

The following image and instructions demonstrate how to add new Traits.

Adding Traits
Adding Traits (select to zoom)

New Traits can be added by:

Adding a New Trait
Step Action
1 Select the Add Traits button at circle1 to create a new Trait. This will bring up the Edit Trait Properties at circle2.
2 Within the Edit Trait Properties window are the key Trait fields. Enter the details of the Trait. More information on traits can be found below.
3 Select the Save button to save the new Trait and the Trait will be displayed in the Traits window.

In order to add a new Trait, all of the following details must be entered:

Trait Details
Attribute Description
Trait Name The name for the new Trait. Must be unique and short because it is displayed in the Scoring screen and there may be limited screen space on smaller devices.
Alias An alternative name for the Trait. This can be something shorter than the Trait name and is optional.
Level This will define the Trait as one that is relevant on the Plot or Sub-Plot level.
Description This is an optional longer explanation of the Trait to assist in data entry.
Unit The unit of measurement in which the Trait can be scored by e.g. centimetres so that a plant leaf can be measured
Data Type
This constrains the values permitted for scoring against the Trait. One of the following must be chosen:
  • CATEGORICAL,
  • DATE,
  • ELAPSED_DAYS,
  • INTEGER,
  • DECIMAL; or
  • TEXT;
Validation Rule The Validation rule optionally restricts the values being entered. The nature of the rule is dependent upon the selection of Data Type and can include a minimum and maximum value.
Add Traits to Bundle Checkboxes that allow the user to add the new Trait to existing Trait Bundles.


Creating Calc Traits

The Calc datatype for Trait’s will allow a Traits value to be derived from other Trait data that is available e.g. the user can create a Calc Trait called PLANT_AREA which is equal to PLANT_WIDTH x PLANT_HEIGHT.

Calc Trait Datatype
Calc Trait Datatype (select to zoom)

Creating a Calc Trait
Step Action
1 By selecting the Calc datatype from the drop-down menu at circle1, a second expression panel can be seen in area circle2.
2 Here an expression can be entered representing the derived value. Taking the example used previously, PLANT_AREA* would be: PLANT_WIDTH(asterisk)PLANT_HEIGHT. Traits can be typed, or selected from the Traits panel at circle3.
3 The new Calc Trait can also be added to bundles in circle4.

Once Traits have been added they will appear in the table in area circle1.


Editing Traits

Any details of a Trait can be edited if the user wants to change the characteristics of the Trait.

Editing Traits Button
Editing Traits Button (select to zoom)

To edit Traits, the user must unlock the option. This can be done by selecting the Editing Locked option at circle1 in the image above. Trait editing is automatically locked so that details of Traits that are in use by Trials are not changed.

Editing Traits
Editing Traits (select to zoom)

After Trait editing is unlocked, KDXplore will display that in circle1. To edit a Trait:

Editing a Trait
Step Action
1 Select a Trait by double-clicking it. This will bring up the Edit Trait Properties Window as shown at circle2.
2 Make the desired changes to the Trait and then select the Save option at circle3.

Tip

It is best practice to lock Trait editing when finished editing Traits.


Import Traits

The KDXplore Trial Manager module has the ability to import Traits from external sources. Traits can be imported from either KDDart or a CSV file.

Importing Traits
Importing Traits (select to zoom)

Once in the Traits tab of KDXplore, select the Import button at circle1 and then chose either Load from Database or Load from CSV.

For Trait and Trial file format information please refer to the “KDSmart/KDXplore - CSV Import File Formats” help page.


Trait Bundles

The Trial Manager module allows for the creation of Bundles which are groups of traits that share a common theme. Adding traits to a bundle allows for easier visibility and management of related traits and custom bundles can be created by the user.


Adding Trait Bundles

All traits will be automatically allocated to a bundle named All Traits. To create a new bundle, the user can:

Adding Trait Bundles
Adding Trait Bundles (select to zoom)

Adding a Trait Bundle 1/2
Step Action
1 Select the Add Trait button at circle1. It will give you the option of choosing to create a new Trait or bundle. Choose the Add Trait Bundle option.
2 The Add/Edit Trait Bundle window at circle2 will open and there will be a list of available traits. If a required Trait is not available, the bundle can still be created and then edited later. Choose the Trait required and select the Add Trait arrow at circle3 to add the selected trait to the new bundle. Multiple Traits can be selected at once by shift+clicking or ctrl+clicking (on Windows).

Filtering Traits
Filtering Traits (select to zoom)

Adding a Trait Bundle 2/2
Step Action
3 The Filter function at circle1 allows for Traits to be searched by Trait names and Traits can be added from the search results.
4 Pick a name for the bundle and enter it into the right panel circle2. After adding Traits and entering a name, the bundle can be saved.

Note

Traits can exist in more than one bundle


Editing Trait Bundles

Once a bundle has been created, it can also be edited to remove or add more traits, or to change the name of the bundle:

Editing Bundles
Editing Bundles (select to zoom)

Editing a Trait Bundle
Step Action
1 Select the bundle to be edited.
2 Select the Edit Bundle button at circle1 on the toolbar. This will open the Add/Edit Trait Bundle window and traits can be added as were previously done. If more traits were added to the trial then they will now appear in the left panel and can be selected.
3 To remove a trait, select the trait to be removed in the right panel and select the Remove From Bundle button at circle2.

Note

The All Traits bundle cannot be edited or removed.


Removing Trait Bundles

A bundle can also be removed from the list of bundles and deleted:

Removing Bundles
Removing Bundles (select to zoom)

Removing a Trait Bundle
Step Action
1 Select the bundle to be removed.
2 Then the Remove traits icon can be selected. If you have selected a bundle there will be the option to Delete Trait Bundle.
3 Once this option is selected, a window will open to confirm the removal of the selected bundle.

Note

Once a bundle is removed, it cannot be restored.


Manage Tags

In KDXplore Trial Manager, tags are short, coded descriptions that are used to represent information about a plot in a Trial. Tags available for use in scoring in Trials can be seen, along with definitions in the ‘Tags’ tab of KDXplore Trial Manager.

Annotated Tags panel of the Trial Manager window
Tags panel of the Trial Manager window (select to zoom)

To display the Tags that are currently available in Trial Manager:

Displaying Tags
Step Action
1 To navigate to the Tags tab select the Tags Tab towards the top of the window at circle1.
2 From here, tags can be selected from the list in area circle2.
3 This will display the tag details in the Tag Description Panel which will


Adding Tags

New Tags can be added by the user that can be used in Trials.

Adding a Tag
Adding a Tag (select to zoom)

To add a Tag:

Adding Tags
Step Action
1 Select the Add Tag/Tag Bundles button at the top of the panel at circle1 ad then choose the Add Tag option.
2 The Add Tags window will open (shown with circle2) which will allow the user to create a new tag by entering a New Tag Label and a Description. Tags must have a unique name in KDXplore, similarly to Traits. This example demonstrates the creation of a tag known as HD which is describes as Human Damage.
3 Choose a Tag Bundle with the checkbox at circle3. If there are no user-created bundles then there will only be the All Tags bundle to choose (Note: Creating Tag bundles will be examined later).
4 Once the tag name and details have been entered then select the Save button at circle4.

Once saved, the new tag will be added into the Tags Panel


Editing Tags

Previously created Tags can also be edited to better suit a Trial.

Editing a Tag
Editing a Tag (select to zoom)

Editing Tags
Step Action
1 To edit a tag, select the Description field by double-clicking in area circle1. Note that tag names cannot be edited following creation. To change the name of a tag, a new tag should be instead created.
2 Tags can be deleted by highlighting the tag and then selecting the Delete button at circle2.


Tag Bundles

The Trial Manager module also has the creation on Tag Bundles which, similar to the Traits Bundles, are Tags that share a common theme and allows for better visibility and management of related tags.


Adding Tag Bundles

The steps below are an example of how to add a new Tag Bundle:

Adding Tag Bundles
Adding Tag Bundles (select to zoom)

Adding a Tag Bundle 1/2
Step Action
1 Select the Add Tag button at circle1. It will give you the option of choosing to create a new tag or bundle. Choose the Add Tag Bundle option.
2 The Add/Edit Tag Bundle window at circle2 will open and there will be a list of available traits. If a required tag is not available, the bundle can still be created and then edited later. Choose the tag required and select the Add Tag arrow at circle3 to add the selected tag to the new bundle. Multiple tags can be selected at once by shift+clicking or ctrl+clicking (on Windows).

Filtering Tags
Filtering Tags (select to zoom)

Adding a Tag Bundle 2/2
Step Action
3 The Filter function at circle1 allows for tags to be searched by tag names, and tags can be added from the search results.
4 Pick a name for the bundle and enter it into the right panel circle2. After adding tags and entering a name, the bundle can be saved.

Note

Tags can exist in more than one bundle


Editing Tag Bundles

Similar to Trial Bundles, Tag Bundles can also be edited e.g. changing the name of the Bundle or adding Tags to the Bundle.

Editing Tag Bundles
Editing Tag Bundles (select to zoom)

Editing a Tag Bundle
Step Action
1 Select the bundle to be edited.
2 Select the Edit Bundle button at circle1 on the toolbar. This will open the Add/Edit Tag Bundle window and tags can be added as were previously done. If more tags were added to the bundle then they will now appear in the left panel and can be selected.
3 To remove a Tag, select the tag to be removed in the right panel and select the Remove From Bundle button at circle2.


Removing Tags and Tag Bundles

If a Tag Bundle is not needed, it can be removed with the following steps below:

Removing Tags and Tag Bundles
Removing Tags and Tag Bundles (select to zoom)

Removing a Tag Bundle
Step Action
1 Select the bundle to be removed.
2 Select the Remove tags icon. If you have selected a bundle there will be the option to Delete Tag Bundle.
3 Once this option is selected, a window will open to confirm the removal of the selected bundle.

Note

Once a bundle is removed, it cannot be restored.


KDXplore - KDSmart Data Exchange

Note

This is a common help topic for both KDXplore and KDSmart.

Introduction

There are several methods of moving data into and out of KDSmart which can be found on the Data - Import, Export, Backup page. This topic focuses on using KDXplore with KDSmart, which provides more time saving and productivity benefits for the user. Previously, inbuilt software called KDXchange was used to exchange data between KDXplore and KDSmart. Both applications have recently been updated to include integration with Google Drive which requires much less effort in setup and whilst an internet connection is required, both devices do not need to be on the same WiFi network. Google Drive is now the recommended method, however there may still be a need to use KDXchange so both methods are outlined here.
The following sections outline the steps required for exchanging data between KDSmart and KDXplore:

  • Setup - Connecting KDXplore to KDSmart Devices; and
  • Transfer - Moving data (Trials, Traits and Tags) between KDSmart and KDXplore.

Beforehand, a little background information is useful in understanding some of the technicalities before launching into the task.


What is KDSmart and KDXplore?

KDSmart and KDXplore are two flexible applications in the KDDart platform:

KDSmart is used on Android tablets or phones to collect phenotypic data in the field for Trials or Nurseries; and

KDXplore is a multiplatform desktop/laptop application which fullfils several roles including managing data on one or more KDSmart devices.

The following illustration depicts a simple trial data workflow for KDDart, however look to the centre to see KDSmart and KDXplore’s role in the workflow:

Example of the Trial Data Workflow (select to zoom)


Why Use KDXplore?

Whilst KDSmart can be used on its own using CSV files for data transfer there may be a need to upscale to multiple KDSmart devices and larger trials. Using KDXplore benefits the user by improving data management and handling.

Some of these benefits are:

  • Work more efficiently and productively with Trial and Nursery data offline (away from office networks or Internet) using laptop or workstation, not just small screens of tablets or phones;
  • Provides visualisation tools to assist with data exploration and review;
  • Provides broader toolset coverage of the breeding cycle;
  • Enables easier management and data exchange with multiple KDSmart devices;
  • Retains data from each individual KDSmart device “download” with TableName/Operator/When details;
  • Facilitates uploading data to a KDDart database when possible (i.e. when a connection to the office network/Internet is available);
  • Barcode production for printing to use with KDSmart barcode scoring;
  • Facilitates improved consistency amongst multiple KDSmart devices with Trait and Tag editing and distribution;
  • Viewing Traits used in different Trials; and
  • The ability to exchange data whilst on site so that data can be curated as efficiently as possible.

A few setup steps are required, however this has been made as easy as possible. The communication software between KDSmart and KDXplore is referred to as KDXchange.


Data Exchange - Google Drive Method

Google Drive is a quick and easy way of exchanging data between devices and requires little set up time. The example provided will take you from exporting a Scoring Set from KDXplore to Google Drive, importing it into KDSmart, exporting the Scored Data file to Google Drive, and then importing that file into KDXplore for curation.

The process of exchanging data will be described in the following steps:

  1. Connect to the Internet
  2. Google Drive Setup
  3. Transferring Files from KDXplore to Google Drive
  4. Transferring Files into KDSmart from Google Drive
  5. Transferring Files from KDSmart to Google Drive
  6. Transferring Files into KDXplore from Google Drive


Step 1 - Connect to the Internet

Google Drive transfers will only work when devices are connected to the internet but they do not have to be connected at the same time. For example, a user on KDXplore may export a Scoring Set to Google Drive which is uploaded to their personal folder, turn off their computer, and then go out into the field and import that Scoring Set into to KDSmart. For users who do not have mobile data on their KDSmart device or are in an area that does not have signal, it will still be necessary to connect to WiFi.

For further information on setting up WiFi please see the Step 1 - Using WiFi section below.


Step 2 - Google Drive Setup

As well as having an internet connection, you will need to have a Google account which gives you access to Google Drive. A free account will provide 15gb of space which is more than enough for using with KDXplore and KDSmart. To sign up or access Google Drive see Google Drive.

This link will be usable on KDXplore, Android devices should have a Google Drive application that would usually be already installed by default but can also be found in the Google Play Store.


Step 3 - Transferring Files from KDXplore to Google Drive

Once a Trial, Trait or Tag has been created, it needs to be transferred to a KDSmart device for use in the field. The following instructions demonstrate how to transfer Trials (or other data) from KDXplore to Google Drive so that they can be used in KDSmart.


Exporting a Scoring Set
Exporting a Scoring Set(select to zoom)


Transferring a Trial from KDX to Google Drive
Step Action
1. Ensure that Google Drive is opened in an internet browser and have KDXplore open to prepare for the transfer.
2. Choose a Scoring Set such as the one at circle1 and then select the export button at circle2.
3. The Export window will display (as at circle3) which provides export options. Selecting the Browse button will allow you to choose a location on the computer to save the Scoring Set to. Ensure that the radio button for KDX file is selected so that it is ready to be used in KDSmart.
4. Select either the Export or the Export & Close options within the Export window and the KDX file will be exported to your chosen location. A dialogue will open and ask whether you want to open the containing directory - do this is you want to transfer the file to Google Drive right away.
5.

Click+Drag the file into the web browser with Google Drive opened and drop it to complete the upload. The file should now appear in Google Drive and there will be a message which confirms that the upload has been completed.

Uploading Files to Google Drive
Uploading Files to Google Drive (select to zoom)


Step 4 - Transferring Files into KDSmart from Google Drive

Files that have been uploaded to Google Drive from KDXplore need to be imported into KDSmart. The following steps will demonstrate how to open Google Drive on your device and choose files to be imported into KDSmart.


Importing a Trial 1/3


Importing a Trial
Step Action
1. Navigate to the Trials screen and select the Import button at circle1.
2. Select an import option - for this tutorial choose the File KDX option at circle2. This will open Google Drive.
3.

Select the KDX file to be imported such as the one at circle2 in the below image. Then select the Open button at circle2 and the import will begin.

Importing a Trial 2/3

4.

A successful import will result in the following screen. The attachment message indicates that there are no attachments to the Trial.

Importing a Trial 3/3


Step 5 - Transferring Files from KDSmart to Google Drive

Once data is collected by scoring with KDSmart, the data will need to be transferred to KDXplore for curation. Step 5 will demonstrate how to transfer scored data for KDXplore using Google Drive.


Transferring a Trial 1/5


Transferring a Trial
Step Action
1. On the Trials screen in the above image, ensure that the Scored Trial that you want to transfer is selected and then choose the Options button at circle1 and then the Share option at circle2.
2.

The Choose Export Option window will then be displayed as seen in the image below. Select the Full Data for KDXplore option at circle1.

Transferring a Trial 2/5

3.

You will be presented with options for sharing the KDX file. Select the Save to Drive option at circle1 in the below image.

Transferring a Trial 3/5

4.

Choosing the Save to Drive option will display some options for saving the file as seen in the below image. Select the Save option at circle1 when you are ready to save the file to Google Drive.

Transferring a Trial 4/5

5.

Once the file has been saved, confirmation notifications will be displayed on the device as seen in the below image. This will indicate that the Scored Trials are now stored in Google Drive.

Transferring a Trial 5/5


Step 6 - Transferring Files into KDXplore from Google Drive

The final step is to load the Scored Trial from Google Drive into KDXplore. This will allow the user to curate and analysing the scored data.


Downloading a Trial from Google Drive
Downloading a Trial from Google Drive(select to zoom)


Loading a Trial from Google Drive
Step Action
1. Ensure that Google Drive is opened. If it is not, then there is a Google Drive button in KDXplore which will open it in a browser. This button is located at circle1 in the above image.
2. Choose any file such as the one located at circle2. Right-Click this file and then choose the Download option. This will download the file to the default location for your browser (e.g. The Downloads folder).
3.

Click+Drag the downloaded file (such as the one circle1 in the below image) to the Trials panel in KDXplore. This will display the Load Trial Data window at circle3. The Download button can also be selected to display the Load Trial Data window.

Loading Trial Data
Loading Trial Data (select to zoom)

4. Select/highlight the file you want to import, select a Source device, and then enter the Name of the Device User.
5.

Select the Import button at circle4 to complete the import.

Import Trial Data
Import Trial Data (select to zoom)


Data Exchange - KDXchange Method

Whilst the Google Drive method is now the recommended method for exchanging data between KDXplore and KDSmart, KDXchange is still provided as a backup method for exchanging data.


Setup - Connecting KDXplore to KDSmart Devices

Connecting Devices has three steps.


Step 1 - Using WiFi

KDXplore and KDSmart devices connect and synchronise data using a WiFi network.

The KDSmart device(s) and the KDXplore laptop/PC must be connected and visible to each other on the same network (i.e. same wifi connection). This is a networking requirement and not a limitation of KDSmart/KDXchange.

Note

Depending on the network configuration, there may be times when your PC/Laptop is connected to a wired network (not on WiFi) yet will be able to connect to KDSmart devices on WiFi.

Tip

Many organisational IT policies lock computer settings preventing the set up or activation of your own WiFi Hotspot without needing Administrator user access on the computer.
Before traveling to ‘the field’ we suggest you prepare, test and become familiarised with this means of connecting devices. Seek support in your organisation if needed.

KDSmart - WiFi Connection Warning Example

If the message above is displayed try the Connect Anyway button, however this may result in mixed success. Only a couple of tries is needed!


In the Field - Your Own WiFi Hotspot

When a WiFi network is unavailable at your location, a portable WiFi hotspot can be created on your Laptop (if it has that capability). The connection can then be shared with your other KDSmart devices using KDXchange (see the above tip).


The KDXchange Window

The KDXchange window can be found by opening KDXplore on a PC and then opening the Trial Manager module by selecting the trial_manager_btn icon. Once the module is open, select the KDXchange Server picture3 icon.

The following image displays a section of the KDXchange screen highlighted to show the following areas:

  • circle1 Connection panel is where the options to connect devices are located. This includes the IP Address where the KDXchange server will be created.
  • circle2 KDXplore panel links KDXplore from the user’s computer. This means that the list of Trials, Traits, and Tags that are on the user’s version of KDXplore are displayed. The user will need to choose between either the Trials, Traits or Tags to be selected.
  • circle3 KDSmart Devices is a list of all the KDSmart devices that are connected to KDXchange or are available for connection. The image demonstrates that a device named ‘Galaxy S8+’ from the user named ‘Tester’ is currently connected.
  • circle4 Device is a panel which displays data from the currently connected KDSmart device.

KDXchange Main Window (select to zoom)

Note

KDXchange server software in KDXplore and KDSmart enables them to communicate and needs to be kept running on the pc/laptop until any synchronisation tasks between the devices has completed. Also the devices should be kept in close proximity whilst connected. Once tasks have completed the KDXchange server can be stopped.


Step 2 - Prepare KDXplore/KDXchange

Step 2 involves preparing KDXplore on the laptop/pc to communicate with KDSmart devices. The following steps must be performed on the laptop/pc:

Confirm Network/IP Address and Port number

Step 2 - Starting the KDXchange server in KDXplore
Step Action
2.1 (KDX) On the Laptop/PC start KDXplore and select the Trial Manager trial_manager_btn icon.
2.2 (KDX) Select the KDXchange Server picture3 icon at top of the Trial Manager window to open KDXchange.
2.3 (KDX) Select the Start button ( or Shift Start to enter address and/or port number) which is located at circle1 on the above image.
2.4 (KDX) The Network/IP Address and the Port number need to be confirmed.
The selected Network/IP Address in this example is different to that of another computer. The IP address of the computer running KDXplore (suggested by default), is usually fine but can changed if required.
Select the OK button in the window at circle2 to confirm this IP Address.
The Port Number usually should be left at the default setting, however if it is changed, both KDSmart and KDXplore must have the same port number. Once OK has been selected, the window will disappear and the program will start listening for devices which means that it is scanning for available devices on the Wi-Fi network.
2.5 (KDX)

Once KDXplore is listening for devices, there will be a message displaying the IP address and port number at circle1 in the following image. By selecting the Stop button at circle2, the user can stop KDXplore listening for devices.

KDXchange connection to KDSmart devices (select to zoom)


Step 3 - Preparing KDSmart Devices For Upload/Download

Step 3 involves connecting one or more KDSmart devices via WiFi with KDXplore on the laptop/pc. These ‘connection’ steps are common to both Upload to KDXplore or Download from KDXplore and for Trials, Traits or Tags.

Step 3 - Connecting KDSmart devices to KDXplore’s KDXchange server
Step Action
3.1 (KDX) Ensure that the KDXchange server is listening for any KDSmart device(s) from the previous Part 2 steps (as demonstrated above).
3.2 (KDS)

From the home screen on each KDSmart device, select the appropriate Trials, Traits or Tags panel then select the Connect button as seen in circle1 then choose the KDXplore icon at circle2.

Starting a Connection (select to zoom)

3.3 (KDS)

A dialogue box asking whether to continue will appear. Choose the tick at circle1 to continue.

Accept a Connection (select to zoom)

3.4 (KDX)

Return to KDXplore on the PC/Laptop and at circle1, the KDSmart device will appear as Pending which means it is ready to connect. To connect the device, select the Allow button shown at circle2.

Allowing KDSmart devices (select to zoom)

3.5 (KDX)

A dialogue box will open which will ask for information about the device as seen in the following image:

Allowing KDSmart devices (select to zoom)

3.6 (KDX)

Once user information has been entered, the device connection is complete. The KDXplore will should look like the following image:

Allowing KDSmart devices (select to zoom)

The Device panel will display the device as Accepted and the data from both the connected computer and KDSmart device will appear in panels circle2 and circle3.


Transfer - Moving data (Trials, Traits and Tags) between KDSmart and KDXplore

Transferring KDSmart data to/from KDXplore requires KDXplore and the KDSmart device(s) to be connected and waiting to transfer files.

The steps in the previous section, Setup - Connecting KDXplore to KDSmart Devices must be performed first before proceeding here.

Battery - Power Saving

When a WiFi connection between KDSmart device(s) and KDXplore is established the power saving options on the device(s) may be overridden and the devices could remain on.
If needing to conserve battery power on the phone/tablet/laptop it may be advisable to stop the connection once data transfers have been completed.


From KDXplore to KDSmart

The following image and table show the steps required to perform a KDXplore to KDSmart File transfer.

Transfer Steps - KDXplore to KDSmart (Select to zoom)

Transferring data from KDXplore to KDSmart
Step Action
1 Select an item e.g. the Trial namesd ‘wheat-with-data’ that is shown at circle1 in the above image.
2 Once the item is highlighted, select the KDXchange Server picture3 icon at circle2 to start the transfer of data. Another method of choosing files to transfer is to click+drag an item such as a Trial to the KDSmart device. This method of transfer can work for single files, or for bundles of Trials, Traits, or Tags.
3 The Dataset Upload window will open and files that have been selected will appear in it. The purpose of this window is to confirm the upload of datasets. Select the checkbox as seen at circle3 and then select the OK button at circle4 to finalise the upload.


From KDSmart to KDXplore

The steps outlined in the following image and table describe how to transfer Trials, Traits, or Tags from KDSmart to KDXplore when they are connected using KDXchange.

Transfer Steps - KDSmart to KDXplore (Select to zoom)

Transferring data from KDSmart to KDXplore
Step Action
1 Select an item e.g. the Trial named ‘wheat-with-data’ that is shown at circle1 in the above image.
2 Once the item is highlighted, select the KDXchange Server picture3 icon at circle2 to start the transfer of data. As with the KDXplore to KDSmart transfer, files can be transferred by click+drag.
3 A Confirmation window will appear. Select the Collect button at circle3 which will confirm the transfer and the Trial will then be copied into KDXplore.


Finished - Disconnecting Devices

When a KDSmart device is connected any touches to the KDSmart window, accidental or otherwise, may cause the following warning to display:


Disconnection Warning (Select to zoom)


If disconnection is unintended, select the X button to dismiss the message and continue, otherwise select the tick to confirm.

Disconnection can also be achieved using the Stop button adjacent to the Run button in the below image. Either method will return KDSmart to normal operation and close the connection.


Disconnection Warning (Select to zoom)


Tip

After disconnection of KDSmart device(s) the KDXchange server will still be running on the PC/Laptop. Whilst this is still running reconnection of a device can be quickly achieved.

The KDXchange server can be stopped when data transfers is finished.

KDSmart/KDXplore - CSV Import File Formats

To find information on importing CSV file formats, follow the link to the following KDSmart Help topic CSV Import File Formats which will open in a new tab.

Curation

Curation is the aspect of Trial Manager that allows for exploration, visualisation and QC/QA checking of phenotypic data. Entering curation with a new dataset, the aim is to assess data and either accept values from a device as quality information, or to correct values potentially using another data source. This can also be done by editing values manually. The result of curation is phenotypic data that has been pushed to the offline database of KDXplore as known values for the selected Trial and for later export if wished. See below for how to access Curation.

Accessing Curation
Accessing Curation (select to zoom)

To access Curation:

Displaying the Curation Window
Step Action
1 Curation can be located by entering the Trial tab of Trial manager at circle1.
2 Select a Trial by clicking on it to display the Trial information.
3 Either double-click on the Trial, or select the Edit Current Trial button at circle2 to open the Curation window.

Curation Window
Curation Window (select to zoom)

  • circle1 Curation Messages panel which displays information and messages about events that are occurring in the Curation window.
  • circle2 Values panel displays information on selected sample values and allows for the editing of values.
  • circle3 Plot Info & Traits panel lists all Traits that are in the Trial and contains checkboxes that are used to select Traits that can be used in curation.
  • The Curation Samples panel displays all information on the selected Traits and samples within two tables:
    • circle4 Trait Instances table lists all selected Traits that are included in the Trial. There is a colour associated with each Trait Instance which remains consistent across visualisation tools and highlighting.
    • circle5 Curation Samples table displays all sample measurements from selected Traits.

Plot Info & Traits

The Plot Info & Traits panel lists all Traits that are included in the Trial that is being curated and plot information i.e. Plot numbers. The purpose of this panel is to select Traits and plot information that can be displayed in the Curation Sample panel. The checkboxes allow for quickly changing what is displayed to the user. Any changes to the items selected will be evident in the Curation Messages window. To select items, the user can:

Plot Info & Traits
Plot Info & Traits (select to zoom)

To display any information about plots and Traits:

Displaying the Plots and Traits Information
Step Action
1 Select a checkbox to an associated Trait or Plot Info as represented in circle1.
2 If it is desirable to choose all traits, then select the Check Traits button at circle2. Plot Info can also be selected by holding down the shift key before selecting the button. Holding down the ctrl key and then selecting the button will result in only Plot Info to be selected.
3 The Uncheck All Traits button at circle3 will uncheck all Traits that are currently chosen if it is selected. Plot Info will also be selected by holding shift and only Plot Info will be selected if holding ctrl
4 By selecting the Check Selected button at circle4 will only select Traits that are highlighted.
5 The selection of the Data Entry Mode checkbox will allow the user to choose Traits that they can use for the entering of new data.
6 Once The desired Traits have been selected, they will appear in the Curation Samples panel.

Sample Table

Once Traits have been chosen in the Plot Info & Traits panel, they will appear in the Curation Samples panel and are displayed in both the Trait Instances table and the Curation Samples tables.

Curated Values appear in the sample table as Bold.

Missing Values appear as an Empty cell.

The example below demonstrates how to open the Curation Samples panel and how to use different aspects of it:

Curation Samples
Curation Samples (select to zoom)

  • Each Trait that appears in the Trait Instances table (such as the EH_CM Trait in circle1) will correspond to a Trait that is in the Curation Samples panel (as seen in circle2).
  • To present information on a specific Trait in the Curation Samples panel, double-click any trait in the Trait Instances panel.
  • The options in area circle3 allow the user the choice for displaying sample information;
  • Hide Inactive Plots allows for hiding plots which have been marked as inactive.
  • Un-Curated will only include samples that have been curated.
  • Only Scored displays only samples that have so far been scored.
  • The Help button at circle4 has a help guide to the Curation Window.
  • Values that are in the database have a symbol represented by 3 blue bars (e.g. circle5). Values from devices are shown with a red corner (if no value has been selected). When there are multiple values from different sources a yellow caution triangle is visible in the top left corner of each cell.

Curation Samples
Curation Samples (select to zoom)

There are some options for Trait samples that are available to the user in the Curation Samples shown at circle1 that can be reached by selecting either singular or multiple values, and then right-clicking the values:

  • Accept/Supress Values will either accept values as being valid, or supress values that the user deems as invalid. If this option is chosen then a dialogue box requesting information on the reason why it has been either accepted or supressed will appear.
  • Activate Plot/Reactivate Plot will deactivate an entire plot e.g. column 6, row 1 at circle2. Note that a deactivated plot will be ‘crossed out’. Deactivated plots can be reactivated by choosing the Activate Plot option.
  • Heatmap/Scatter Plot/Box Plot creates a visualisation of the selected data. More will be explained about visualisation in the future.
  • Inspect Plot opens the Plot Inspection window.

Plot Inspection

The Plot Inspection window displays a visualisation of a comparison of selected Traits from selected plots. It is highly customisable, and can be saved as a .PNG file or printed directly from KDXplore. To access the Plot Inspection window, simply righ click a value or mulitple values, and choose the Inspect Plot option.

Plot Inspection
Plot Inspection (select to zoom)

Curating Measurements

One of the primary functions of the Trial Management module is to curate data that is collected from the field before it is uploaded to KDDart. Values can be curated in a number of different ways in KDXplore. Once a value is selected, typing a value will immediately fill the cells and this must be confirmed by pressing the Enter key. Values can only be curated to values included by their validation rules, E.g. for EH_CM with a validation rule of (30...200). KDXplore will not let the user choose values that are below 30 or above 200. Simple statistics can be displayed when there are multiple sample sources for the selected measurements. These statistics are displayed in the Trait Values panel.

Single-Selection Curation

The most simple way to curate Trial data is to curate a single value. The examples below demonstrates how to curate a single measurement.

Curation of a Single Sample
Curation of a Single Sample (select to zoom)

Curating a single measurement can be done by:

Single Selection Curation
Step Action
1 Select a single measurement such as the one at circle1. This will display the measurment information in the Values panel at circle2.
2 Enter the new value into the text-field at circle3. You will be able to see that as you type this value, the corresponding value in the Trait Instances panel will also change in real time.
3 It will not be set permanantly until you select the Set Value button at circle4.

All previous changes and edits are listed in the Values panel as seen below:

Changing a Curation Edit
Changing a Curation Edit (select to zoom)

If the user would like to make a change to a previous edit, then they can choose that particular section and edit that e.g. If a value is set to missing and then the curation is saves, there is no option to undo the changes in values. In this situation, the user can select the particular edit such as circle1, and then delete the change (at circle2) which will revert the sample value to its original value.

Multi-Selection Curation

The Value panel also has the functionality of displaying multiple samples at once. This allows for the selection of multiple samples to curate at once and can make curation of multiple samples easier and more efficient.

Curation of Multiple Samples
Curation of Multiple Samples (select to zoom)

In the above image, the user has selected multiple samples in circle1 and they are all displaying in the Values panel in circle2. Samples are curated the same as in Single-Selection Curation, however there are additional display options such as the ability to display/not display curated and un-curated values.

Trial-Wide Curation

Specific Trait instances can be curated across the entire Trial. The below example provides an example of how to access this function.

Curating All Values of Trait Instances
Curating All Values of Trait Instances (select to zoom)

Navigating to the Sample Data tab of the sample editor panel seen in area circle1, the dataset available for the trial can be seen. By Selecting a dataset that is not the database set such as in circle2, sample measurements for one, or multiple selected Trait instances can be curated for the entire trial. Select the Trait instance or option by using the drop down seen in area circle3.

Warning

If changes to samples are made, then they need to be saved which can be done when exiting the Curation window and or by choosing the Save button at the top of the window.

Accepting/ Supressing Measurements

A quick and simple way of curating measurements is by accepting or suppressing values. It will be necessary to accept values if there are measurements from multiple devices in the dataset. The accepting is the choice of one of the values as the correct one and supressing a value marks it as the incorrect value.

Accepting or Supressing Measurements
Accepting or Supressing Measurements (select to zoom)

This can be done by right-clicking on a sample as in circle1 and then either choosing Accept Values(s) like in circle2 or Suppress Values(s) as in circle3. This will open a dialog (as seen below) where the sample source can be accepted or supressed. This is where you select a device (or data source) from the drop-down menu.

Accepting a measurement

Accepting Sample Measurements From Curation Table
Accepting Sample Measurements From Curation Table (select to zoom)


Supressing a measurement

Supressing Sample Measurements From Curation Table
Supressing Sample Measurements From Curation Table (select to zoom)


Values can also be accepted from visualisation tools, as seen below. Specific visualisation tools are covered in the following sections.

Accepting Sample Measurements From Visualisation Tools
Accepting Sample Measurements From Visualisation Tools (select to zoom)

Note

if there is no sample source for values the curated values of cells will be changed to MISSING.

Saving Measurements

Any changes made to Trial data in the Curation window will need to be saved to take effect. When sample measurements are curated in KDXplore they do not become the “database” value for that plot until they are saved. Before exiting curation, if changes have been made a dialog will appear confirming exit-without-save. All device measurements will still remain once curation is complete.

Saving Sample Measurements
Saving Sample Measurements (select to zoom)

Select the Save button at circle2 to save the curated values into the KDXplore offline database. Measurements can also be saved by selecting the File option at circle1. The Curation window also displays the amount of changes that have been made in circle3 which can inform the user as to whether they need to save or not. The Undo/Redo buttons at circle4 allow changes to be undone or redone.

Curation Export

Data from Trials can be exported from KDXplore through the Curation Export function. This allows for data to be more easily curated in the Trial Management module and then exported as a file so that it can be shared with other devices. The image below provides an example of how data might be exported.

Exporting Sample Measurements
Exporting Sample Measurements (select to zoom)

Curated data can be exported by:

Exporting Curated Data
Step Action
1 Select the Export button seen in area circle1. This will open the Export Curated Data window as seen at circle2.
2 Either enter a desired file path into the text-field, or select the Choose button in circle3 Toto choose a location for the exported data.
3 Choose a name for both the X Axis and Y Axis in circle3. The default name for these axes are Column and Row, and by choosing the Use Names From Trial button will allow the user to set their own names for these axes to the exported data.
4

Determine the options for:

  • Plots - Whether to export all plots or only selected plots.
  • Inactive Plot Values - How the export will treat inactive plots.
  • Plot Attributes - Shows that all plot attributes will be exported.
  • Trait Instances - Whether to export only Trait instances with data, those that are selected, or all.
  • Operator Info - The choice to export the name of the Operator e.g. Tester
5 The area in circle5 allows for setting particular values when exporting. The Use/Show Defaults button will set the default value for each field e.g. the Missing Values field will be set to MISSING.

Show Outliers

The ability to display outliers in data measurement will enable the user to determine possibly incorrect or notable measurements. The example below demonstrates how to display outliers for a particular Trait.

Displaying Outliers
Displaying Outliers (select to zoom)

This can be done by:

Showing Outliers
Step Action
1 Right-clicking a trait in the Trait Instance table (i.e. circle1), the option to Show Outliers can be selected from the menu.
2 Selecting this will display the values of outliers in a dialogue that is opened at circle2. It will also highlight the outlier measurements in the Curation Samples table and visualisation tools at circle3.

Visualisation Tools

KDXplore’s Trial Management Module provides users with a variety of data visualisation options.

Curation Options
Curation Options (select to zoom)

Visualisations for Trait Instances can be generated from both Trait Instance tables, the Curation Sample table, or from the tool bar at the top of the Curation window. Simply right-click a Trait Instance in the Trait Instance table or a group of samples in the Curation Sample and select the intended action e.g. Heat map. The following examples will detail the steps for creating each type of visualisation.

Heat Map

The Trial Management Module can create a Heat-Map which is a representation of the experiment data that is displayed as varying colours.

Heat Map Generation
Heat Map Generation (select to zoom)

To generate a heat map:

Generating Heat Maps
Step Action
1 First select the Heat Map button at circle1. This will display the Heat Map window at circle2.
2 Select both the axes and a value to display. The axes are set to the X and Y axis (which in this case are the Column and Row) by default. Select a trait instance and then the Value button at circle3.
3 Once the desired values have been chosen, select the Create Heat Map button at circle4.
4 This will display the heat map in a separate window at circle5.

Scatter Plot

The Trial Management module also has the function of creating a Scatter Plot to represent experiment data.

Scatter Plot Generation
Scatter Plot Generation (select to zoom)

To begin creation of a scatter plot:

Generating Scatter Plots
Step Action
1 Select the Scatter Plot button at circle1. This will display the Scatter Plot window at circle2.
2 The first checked Trait Instance will be the X-value in the to-be-generated scatter plot. Multiple Trait Instances can be plotted to the same plot by selecting multiple value instances. In the example above, the value EH_CM was chosen first at circle3 so it was automatically defined a the X-axis. The next value to be chosen was the PH_CM at circle4.
3 Once the desired Traits have been chosen, select the Continue button at circle5. The scatter plot will be generated and displayed as in circle6.

Box Plot

Another graph that can be created is the Box Plot.

Box Plot Generation
Box Plot Generation (select to zoom)

To begin creation of a box plot:

Generating Box Plots
Step Action
1 Select the Box Plot button at circle1. This will display the Box Plot window at circle2.
2 The first checked Trait Instance will be the X-value in the to-be-generated box plot. Multiple Trait Instances can be plotted to the same plot by selecting multiple value instances. In the example above, the value EH_CM was chosen first at circle3 so it was automatically defined a the X-axis. The next value to be chosen was the PH_CM at circle4.
3 Once the desired Traits have been chosen, select the Continue button at circle5. The box plot will be generated and displayed as in circle6.
4 Outliers, mean and median can all be seen on plot and deactivated using the check boxes at the bottom of the Box Plot window.

Field View

The Field View allows the user to have a top-down view of a grid which represents the plots of the experiment. The following image details steps for opening Field View.

Field View
Field View (select to zoom)

To open the Field View window:

Opening the Field View Window
Step Action
1 Select the Field View button at circle1 and then choose the Field View option. This will open the window at circle2.
2 The user can select a Trait Instance to display at circle3.
3 By selecting specific plots as in the ones at circle4, the user will be displaying these plots in the Values panel and the Curation Samples table as seen at circle5.