Experiment Menu

The following items of the Experiment menu illustrate the order of dependency:

  1. Site
  2. Design Type
  3. Breeding Method
  4. Trials.
  5. Nurseries.

Site

Sites are high level groupings of Trials which may equate to places where breeding / variety evaluation occurs (e.g. breeding station). Geographic coordinates can be assigned to enable illustration on a map. A ‘Site’ may consist of a whole farm, breeding station or other general environmentally homogeneous area, where planting occurs.

The Add Site window:

Add Site window (location map not shown) (select to zoom)


This table describes the fields for the above illustration which allows adding a Site:

Field Mandatory Description
Site Name M A name to identify the site.
Site Type M Selection from defined or ‘classified’ Site Types. Site Types must have already been created using the Add Site function.
Site Acronym M Abbreviated site name, (e.g. may conform to the Trial naming convention)
Site Manager M An existing Contact - a person currently managing the site (not necessarily a user of this system).
Start Date M Date the site commenced operation (Format YYYY-MM-DD).
End Date M Date the site stopped operation (Format YYYY-MM-DD).
Site Geometry M This field contains the geographic coordinates of the site. It is populated by the selection of the site on the displayed map.

Design Type

Design Type defines how a Trial or experiment is to be conducted.

The fields capture the layout/method that will be used to plant the genotypes, the number of replicates, etc. The data entered here is used as input for external software, such as DiGGer, which may be used to create the design.

KDCompute has the ability to generate a Trial layout using DiGGer which will consume the data entered here.

Note

Whilst an external application can be used to construct the Trial design it is not mandatory.

The Add Trial Design Type window:

Add a Trial design type window (select to zoom)

This table describes the fields for the above illustration which allows adding a Design Type:

Field Mandatory Description
Name of Design M A name to identify the Design Type.
Name of Software M The software used for preparing the design. For example, DiGGer could be used to create a randomised block design.
Template File M Defines how the parameters need to be inserted in the input file for the design software.
Genotype Format M Format in which the Genotype Name and Genotype Id will be exported into the Trial design input file. The DesignGenotypeFormat must be GenotypeName | GenotypeId (eg VENTURA|41 ) to satisfy DiGGer requirements.
Factor Alias Prefix M Prefix used to find the factor for the Trial Design Parameter while importing Trial design from the output file generated by the Trial design software.

Breeding Method

Breeding method is an additional descriptor of specimen which complements pedigree information and caters for a controlled vocabulary.

Field Mandatory Description
Name of Breeding Method M Name of the breeding methodology.
Note M A short description of the breeding methodology.

Note

Where it is not important to specify a Breeding Method use the ‘Default’ Breeding Method.

The Add Breeding Method window:

Add Breeding Method window (select to zoom)

Trials

Trials are the equivalent to ‘field’ or ‘nursery’ experiments that are performed within a Site.

Selecting Trial from the menu displays the list of defined Trials which the user/group has permission to view as shown in the following illustration.

Trial window showing loaded trials (select to zoom)

In the illustration above the Trial window shows several Trial records. The Actions cell has been highlighted on the second row to illustrate the range of buttons representing the Actions that can be performed for that Trial.

The following table describes the contents of the Trial window:

Field Description
ID A unique ‘system’ identifier of the Trial
Trial Name The user provided name of the Trial
Trial Type The selected Trial Type (user defined ‘types’ for a trial)
Site The site of the Trial
Manager The manager assigned to the Trial (defined in Contacts although they are not necessarily a system user)
Start Date The date the Trial commenced (Format YYYY-MM-DD)
End Date The date the Trial ended (Format YYYY-MM-DD)
Action The actions that can be performed for the Trial which are described in the following Trial Actions section.

Trial Actions

The following table lists all the actions that can be performed for the selected Trial in KDManage.

Note

The presence of action types is dependent upon the Trial state - not all action types will be available for all Trials.

Trial Actions
Button Action Description
KDMan-add-Btn Add Trait Add a Trait to the Trial
KDMan-download-Btn Download Download the Trial data
KDMan-edit-Btn Edit Edit the Trial
KDMan-export-Btn Export Export the CSV template for the Trial
KDMan-list-Btn List List the Traits for the selected Trial
KDMan-upload-Btn Import Import a data file from KDSmart for the Trial
KDMan-view-Btn View Display the Trial units/layout for the selected Trial
upload_icon Upload files Uploads files to this trial.
folder_icon List files List all files that have been uploaded to this trial
delete-btn Delete Trial Delete this trial. Note: This can only be done if there are is no trial data uploaded to this group and this trial is not part of an existing Trial Group. Users can also choose to clear the trial of trial units and trial traits if they wish.

Three of the actions are relevant to KDSmart. These are:

  • Download - produces a CSV file for importing into KDSmart which contains a Trial’s Trait results
  • Export Template - produces a CSV file for importing into KDSmart without any of a Trial Trait’s results
  • Import - loads data back into KDDart from scoring in KDSmart.

Adding Trials

Prerequisite: Before a Trial can be added, the Site to be used must exist. When defining the Trial Location, the Trial must be contained within the boundaries defined for the Site.

To add a Trial select the Add Trial button to display the Add Trial window.

The following illustration shows the Add Trial window, displaying the description fields:

Add a Trial window (select to zoom)

The fields for Add Trial window are described in the following table:

Field Mandatory Description
Trial Name M The name of the Trial. A naming convention is suggested (e.g. a concatenation of site, type, date, number).
Trial Number M The Number of the Trial, which could be sequentially assigned.
Trial Type M Select from the list of Trial Types (A general type as opposed to design type which is a Trial specific definition).
Site M Select from the list of sites to specify where the Trial is to occur.
Trial Acronym M An alternative abbreviated name for the trial
Design Type M Select a Design Type that identifies the Trial design.
Trial Manager M Someone currently managing the Trial and defined in Contacts although they are not necessarily a system user.
Start Date M The date the Trial commenced (Format YYYY-MM-DD).
End Date M The date the Trial has/will end (Format YYYY-MM-DD).
Note M Descriptive notes for the Trial.
Access Fields M Access Settings and Permissions

After entry of the Trial description, select the Add button to add this Trial.

Add Traits to a Trial

Selecting the Add a Trait button KDMan-add-Btn adjacent to the selected Trial will display the following Add Trial Trait window. The Trait is selected from a list of predefined Traits (refer to the Traits topic).

When the Compulsory field is set to ‘yes’ the capturing of the trait will become mandatory when recording Trial data.

Add Trait to a Trial window (select to zoom)

Download Trial Data

To download Trial data in CSV format, select the Download button KDMan-download-Btn for the required Trial.

For the selected Trial the downloaded file will contain the previous results of scoring already performed using KDSmart.

The following download window will display. Complete the required fields then select the Download button KDMan-download-Btn to download a file. The File can be downloaded in one of three formats: KDManage format, KDSmart Format or Direct DAL format.

Download Trial data window (select to zoom)

Edit Trial

To edit an existing Trial select the Edit button KDMan-edit-Btn in the Action column to display the update window.

This window is the same as appears on the Trial Description tab.

Deleting Trials

Trials will not be able to be deleted if any of the conditions apply: - Trials that have uploaded trial data/sample measurements - Trials that are part of a Trial Group

Trials may be deleted if they contain trial units, trial traits and uploaded multimedia. However, they will be removed and will not be retrievable.

Users may also wish to delete trial units and trial traits from a trial. This effectively resets the trial for use. This is only possible if there is no Trial Data/Sample Measurements in Trial.

List Traits

To display the Traits for the Trial select the List Trait KDMan-list-Btn button. This will display the following List of Traits in Trial window:

List traits window (select to zoom)

Trial Data CSV Format

KDManage can accept trial data (or sample measurements) in the following three formats:

KDManage CSV Format

This is the standard format where each row points to either Trial Data for the plot or specific specimens in the plot (i.e. subplot data). Multiple instances of traits are separated in different columns and can be paired with the proceeding column for the date.

For Trait column headers, different instances are identified by “__” (dobule underscore). For example, YIELD__3 indicates the third instance point of trait YIELD of the line. If date columns are used, the date columns match to the trait columns before it (i.e. if YIELD__1 is column 3, column 4 will be used as DATE-YIELD__1).

Note

KDManage conforms to KDDArT Specimen Number specifications which means that numbering starts at zero (0).

KDSmart CSV Format

This is the standard format for KDSmart Android Application. Each row corresponds to a single plot with each instance of each specific specimen or subplot data is identified by separate columns. Dates can be paired with the proceeding column.

Each trait column header names must be in the following format [TRAITNAME]:[INSTANCENUMBER]#[SPECIMENNUMBER] for sub plot data and [TRAITNAME]:[INSTANCENUMBER] for plot data. Dates are formatted by Date-[TRAITNAME]:[INSTANCENUMBER]#[SPECIMENNUMBER] for subplot data and Date-[TRAITNAME]:[INSTANCENUMBER] for plot data.

For example: PlANT_HEIGHT:3#4 will correspond to the third instance of PLANT_YIELD of Specimen 4 (which is stored as 0 in DAL). YIELD:3 will correspond to the third instance of YIELD of the plot.

Note

While KDDArRT stores Specimen numbers beginning at zero (0), KDSmart begins at 1. KDManage will automatically adjust Specimen numbers (e.g. #1 will point to SpecimenNumber 0 through DAL).

Direct DAL CSV Format

This is also called Sample Measurement format. This is the format that uses the Database ID identities (including TrialUnitId, TrialUnitSpecimenId and TraitId) to directly upload data to the database. This is only recommended for advanced users as it requires a good understanding of the KDDArT Database schema.

For best examples, use the following feature to download a scoring template for a correctly formatted CSV.

Export CSV Template

The Export template action KDMan-export-Btn produces two CSV files from the selected Trial that can be loaded into the KDSmart application for scoring Trials or standalone.

The download requires entry of the unit position for the row and column and for each Trait, the number of repetitions to be entered (default is one). When a Trait is not required zero should be entered to suppress the trait from the download file.

Download Trial template

For KDManage format, users will be given the choice to add Date/Time columns per Trait instance per plot/subplot row.

Once the export has completed the number of Trial Units and Trait Columns in the file are displayed as shown in the following illustration.

The download Trial template window (select to zoom)

To download the template file to the workstation/laptop select the displayed link (illustrated above).

Note

The Trial template file contains empty Trait columns, without results.

Import CSV Data (KDManage Format)

To import Trial data from a CSV file, select the import button KDMan-upload-Btn in the Actions column for required the Trial or select the Import Trial data button in the Trial map tab in the Trial View Page. In the table view of trials, this interface will accept CSV in KDManage Format.

The import data for Trial window is displayed as shown and requires input as described in the following table.

Import Trial data window with KDManage format (select to zoom)

Note

For referencing the CSV file contents, column numbering commences with zero.

Field Description
Data File Browse to locate and select the appropriate CSV file for import.
Data Start Column The first column in the CSV file containing data for import.
Data End Column The last column in the CSV file containing data for import.
X Column The column that contains the X position of the plot.
Y Column The column that contains the Y position of the plot.
Z Column The column that contains the Z/Block position of the plot.
Barcode Column The column that contains the Barcode of the plot.
Specimen Number Column The column that contains the Specimen Number of the plot. For rows that that correspond to plot data, the number can be empty or “PLOT”
Sample Type The type of Sample, as defined in Type definitions.
Individual Date per Data Point? Whether if the trial data has individual columns for dates per Trait Instance. If trial data does not contain individual date columns, the uploaded sample measurements will use the current Date/Time as measured date/time.

Import CSV Data (KDSmart Format)

Import Trial data window with KDManage format (select to zoom)

Note

For referencing the CSV file contents, column numbering commences with zero.

Field Description
Data File Browse to locate and select the appropriate CSV file for import.
Data Start Column The first column in the CSV file containing data for import.
Data End Column The last column in the CSV file containing data for import.
X Column The column that contains the X position of the plot.
Y Column The column that contains the Y position of the plot.
Z Column The column that contains the Z/Block position of the plot.
Sample Type The type of Sample, as defined in Type definitions.

Import Sample Measurements

To import sample measurements from a CSV file, select the import sample measurements button in the Trial data tab in the Trial View Page

The import sample measurements for Trial window is displayed as shown and requires input as described in the following table.

Import Trial sample measurements window (select to zoom)

Note

For referencing the CSV file contents, column numbering commences with zero.

Field Mandatory Description
Data File M Browse to locate and select the appropriate CSV file for import.
Trial Unit Id Column M The column in the CSV that contains Trial Unit Ids of each sample measurement
Sample type Id M The column in the CSV that contains Sample type Ids of each sample measurement
Trait Id M The column in the CSV that contains Trait Ids Note: these traits must be included in the Trial as Trial Traits (see List Traits )
Operator Id M The column in the CSV that contains the User Ids of each sample measurement
Measure date/time column M The column in the CSV that contains Date/Time of each sample measurement
Instance number M The column in the CSV that contains Instance of each sample measurement
Trait value M The column in the CSV that contains Trait Value (or measured value of trait) of each sample measurements
Trial unit specimen   The column in the CSV that contains Trial Unit Specimen id of each sample measurement, if applicable

If required, sample measurements can also be uploaded and added to a new sample measurement group.

Field Mandatory Description
Sample Measurement Group Name M Name for new sample group measurement. Note: new sample measurements cannot be added to existing groups so these names must be unique.
Sample Measurement Group Status   Status for Sample Measurement Group
Sample Measurement Group Note   Note for Sample Measurement Group

List Sample Measurements Group

To list all sample measurement groups in a trial, select the list sample measurement group button in the Trial data tab in the Trial View Page

List Trial sample measurement groups window (select to zoom)

The following table lists all the actions that can be performed for the selected Sample Measurement Groups in KDManage.

Trial Actions
Button Action Description
KDMan-edit-Btn Edit Sample Measurement Group details Edit name, note and/or status of the Sample Measurement Group
delete-btn Delete Delete Sample Measurement Group and all Sample Measurements in the group

Note

Deleting Sample Measurement Groups is irreversible.

Display Trial Units-Layout

To display the Trial units button select the KDMan-list-Btn button in the Action column to display the update window.

Upload a File to a Trial

To add a file to a Trial, click on upload_icon in the Action column to display Upload file window.

File types are defined in the Types page.

List Trial sample measurement groups window (select to zoom)

To view all files that have been uploaded, click on folder_icon in the Action column to display list file window

List files for Trial (select to zoom)

Add Trial Event

To add a Trial event to a Trial select the + symbol and then Add Trial Event in the Trial data tab in the Trial View Page

Add Trial event window (select to zoom)
Field Mandatory Description
Unit M Unit of Trial Event
Event Type M The type of event, as defined in Type definitions.
Trial event value M Value of Trial event
Trial event date M Date of Trial event
Trial event nite   Note of Trial event

Trial Location

Once a Trial has been added within a site, a geographic location can be added to a trial. A Google map will be displayed. Drag the map to the appropriate location then double click repeatedly to drill down to the required location to define the site.

Add Trial window - Location tab (select to zoom)

When the map displays with sufficient detail to draw the Trial area, define the Trial area by selecting the ‘draw new object’ polygon button KDMan-DrawNewObjectIcon and select on the boundary corners of the required area.

In the following image the Trial location has been defined and is highlighted in a darker yellow.

Add Trial window - Location tab with selection made (select to zoom)

The text box which appears above the map will contain the coordinates for the area that has been selected for the Trial location as illustrated next.

The buttons at top left are to: ‘Draw a new object’ - to define the perimeter of the Trial ‘Select and Modify’ - To move the drawn object (using the centre button) or to change shape by selecting the edge buttons. ‘Select info’ to display the identification label for the area.

Location field data example (select to zoom)

Trial Unit Layout

This screen caters for adding the layout for Trial Units or plots.

Adding Trial Unit Layouts

There are two ways to add Trial unit layouts: via CSV format and via KDCompute method (if configured).

The Add Trial Unit Layout via CSV window:

Field Mandatory Description
Plant Date M Date the specimen was planted in the Trial unit. (Format YYYY-MM-DD)
Trial Unit Layout File M Browse and select the CSV import file.
Auto Column Mapping   When a file is chosen this box will be selected if ‘Specimen’ is found in the header. This can be deselected if it is not the desired column.
Specimen Column M The Specimen name column in the input file. It may be automatically provided using the Auto Column Mapping feature or manually entered.
Number of Specimens per Unit M Define the number of copies of the same Specimen that will be added per Trial Unit.
Unit Position Start Column M The Unit Position start column in the input file, numbered from zero.
Unit Position End Column M The Unit Position end column in the input file, numbered from zero.
Trial Unit X M Define the column that reflects X coordinates for Trial Unit Layout. This column must fall within the Unit Position Start and End Column ranges.
Trial Unit Y M Define the column that reflects Y coordinates for Trial Unit Layout. This column must fall within the Unit Position Start and End Column ranges.
Trial Unit Z M Define the column that reflects Z coordinates for Trial Unit Layout. This column must fall within the Unit Position Start and End Column ranges.
Trial Unit EntryId M Define the column that reflects the EntryId for Trial Unit Layout. This column must fall within the Unit Position Start and End Column ranges.

Note

X, Y, Z and EntryId columns must all be unique columns.

Add Trial Unit Layout via CSV window (select to zoom)

The Add Trial Unit Layout via KDCompute window:

Add Trial Unit Layout via KDCompute window (select to zoom)

Note

KDCompute method requires a working installation of KDCompute attached to your KDManage and specific set up for trial design plugins.

Add Keyword to a Trial Unit

Keywords tag_icon can be added or assigned to Trial Units.

To add a Keyword to a Trial Unit perform the following:

Step Action
From the Trial window, at the required Trial, select the Display Trial Layout Action button KDMan-view-Btn.
At the required Trial Unit select the Keyword button tag_icon.
Select the Keyword from the dropdown List.
Note: Multiple Keywords can be assigned. If the required Keyword is not appearing, new Keywords can be added via the Administrative Settings menu , top right.

Trial View Page

This page will display all the details of a trial. The actions described above are organised in boxes and tabs.

Trial View Page - Trial Details tab (select to zoom)

Important Trial information will be displayed in the each of the tabs.

To edit Trial details select Edit Trial details, below the Trial title and ID on the top of the window.

To add a Trial Event, select the plus symbol followed by “Add Trial event”

Trial Units can be added and viewed on the Trial Unit tab. Newly created trials can have Trial unit layouts added via csv or KDCompute method (see Adding Trial Unit Layouts).

Trial View Page - Trial Units tab (select to zoom)


After a trial unit layout is added, users may view the table of trial units.

Users can then also download a trial field map in SVG format by clicking on KDMan-triallayout-fieldmaps-Btn (Download Field Maps) and download the set of printable barcodes by clicking on KDMan-triallayout-barcodes-Btn (Download Barcodes).

Trial traits can be added and viewed on the Trial trait tab. Trial traits can be added individually or in Trait Groups

Trial View Page - Trial Group tab (select to zoom)

Trial location can be updated and viewed on the Trial location tab (see Trial Location)

Trial View Page - Trial Location tab (select to zoom)

Trial multimedia can be updated and viewed on the Trial multimedia tab (see Upload a File to a Trial)

Trial View Page - Trial Multimedia tab (select to zoom)

Trial data can be uploaded, viewed and downloaded in the Trial data tab and the Trial map tab. Importing Trial data is performed differently in both tabs but will result in the same outcome. The method depends on preferred Trial data import template.

The differences are listed below:

Import Sample Measurements Import Trial Data
Template use Trial Unit Ids to identify sample measurements Template uses Trial Unit positions to identify sample measurement
Able to add to Sample Measurement groups Unable to add to Sample Measurement Groups
Template incompatible with KDSmart Template compatible with KDSmart
Template compatible with multiple Trial Unit Specimens in single Trial Unit Template incompatible with multiple Trial Unit Specimens in single Trial Unit

Once Trial data has been uploaded, Trial data can be viewed and downloaded on the Trial data tab. Trial data can also be viewed as a “heat map” in the Trial map tab.

Tip

Currently only numerical trait values will be visualised.

Trial data graph options (select to zoom)
Trial data graphed as a scatter graph with two different trait values compared against each other (select to zoom)
Trial data map options (select to zoom)
Trial data map in a heat map based on Trial unit dimensions. Red specifies higher values while blue specifies lower values (select to zoom)

Exisiting Trial Data can be curated and imported as a seperate Instance in the Curate Data tab.

Curate Trial Data (select to zoom)

Tip

Curated data will not always be imported as the same Instance. Instances are determined on a per trait basis.

Nurseries

Nurseries can be defined and set up to allow for new crossings to be added.

Selecting Nursery from the menu displays the list of defined Nurseries which the user/group has permission to view as shown in the following illustration.

In the illustration above the Nursery window shows several Nursery records. The Actions cell has been highlighted on the second row to illustrate the range of buttons representing the Actions that can be performed for that Nursery.

Nursery table (select to zoom)

The following table describes the contents of the Nursery window:

Field Description
ID A unique ‘system’ identifier of the Nursery
Trial Name The user provided name of the Nursery
Nursery Type The selected Nursery Type (user defined specific trial ‘types’ to be nursery types )
Site The site of the Nursery
Manager The manager assigned to the Nursery (defined in Contacts although they are not necessarily a system user)
Start Date The date the Nursery commenced (Format YYYY-MM-DD)
End Date The date the Nursery ended (Format YYYY-MM-DD)
Action The actions that can be performed for the Nursery which are described in the following Nursery Actions section.

Nursery Actions

The following table lists all the actions that can be performed for the selected Nursery in KDManage.

Note

The presence of action types is dependent upon the Nursery state - not all action types will be available for all Nurseries.

Nursery Actions
Button Action Description
KDMan-plots-Btn Generate layout and crossing Automatically generate layout and crossing, if required, from two Specimen lists. See Generate layout and crossing.
KDMan-import-Btn Add Nursery Layout Import a nursery layout for nursery. See Trial Unit Layout.
KDMan-view-Btn Display nursery layout for nursery Display the nursery layout for nursery. See Trial Unit Layout.
print-btn Print Nursery Unit Barcode for nursery Export barcodes for nursery trials for printing.
KDMan-list-Btn List Crossing for Nursery List crossing for nursery.
KDMan-specimen-Btn Harvest Crossing If layout and crossing are present in nursery, harvest crossing. See Harvest Crossing.

Import Crossing

Crossing can be imported into nurseries, which can later be harvested to create new Genotype and Specimen entries.

Note

Dialog window will match column names once users select file for import.

Note

Entries for Male and Female parent Ids must be Trial Unit Specimen Ids used inside the Nursery.

Import Crossing
Field Mandatory Description
Crossing File M Select the input file for the import.
Trial Id Column M Column number for Trial Id. Note: Nurseries use Trial Id.
Breeding Method Id Column M Column number for Breeding Method
Male Parent Id Column M Column number for Male Parent Id (Use trial Unit Specimen Id)
Female Parent Id Column M Column number for Female Parent Id (Use Trial Unit Specimen Id)
Crossing Date/Time Column   Column number for Date/Time
User id Column   Column number for User Id
Crossing Note Column   Column number for Crossing Note

Generate layout and crossing

A layout and crossing can be automatically generated from two specimen lists.

Note

Additional crossing and algorithm algorithms can only be added by advanced users.

Import Crossing
Field Mandatory Description
Male Specimen Group (list) M List of specimens that will be the Male in a crossing
Female Specimen Group (list) M List of specimens that will be the Female in a crossing
Algorithm name M A choice of algorithm which the layout and crossing will be generated with
Make Crossing M An option whether the crossing will be generated following the layout
Breeding Method   If a crossing will be generated, then a breeding method must be defined for crossings.
Replicates M Number of replicates for crossings

Harvest Crossing

Once a nursery has a layout and a crossing set up, users can harvest from crossing and create new Genotype and Specimens, with appropriate pedigree entries.

Harvest crossing interface (select to zoom)

The following table is a small nursery with a basic crossing. Each row refers to a single cross where a new genotype and specimen may be created.

Note

In cases where two specimens have previously been crossed, no genotype will be created and the new specimen will take on the Female Genotype.

Harvest Crossing
Field Mandatory Description
Genotype Prefix M The prefix for the newly created Genotype. A unique number will be generated and appended to the prefix.
Specimen Prefix M The prefix for the newly created Specimen. A unique number will be generated and appended to the prefix.
Selected   If un-ticked, the corresponding crossing will skipped.
Create New Genotype   If un-ticked, the corresponding crossing will not have a new genotype created.