Experiment Menu¶

The Experiment Menu contains various pages with tools that can be used to create and manage the entities in KDDart that represent experiments and methods.

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

Site
Design Type
Breeding Method
Trials
Nurseries

This order of dependency means that a site must first be created before a design type can be added to it.

Site¶

Sites are high-level groupings of trials which may equate to places where breeding/variety evaluation occurs such as a breeding station. Geographic coordinates can be assigned to enable illustration on a map. A site may consist of a whole farm, breeding station or any other general environmentally homogeneous area, where planting occurs.

Sites can be added by selecting the Add Site Button which will display the Add Site Window which provides options for creating a new site. An image of the Add Site Window and a table describing it’s fields can be found below:

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

Design Type¶

A 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 can 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.

New design types can be added by selecting the Add Design Type Button which will open the Add Design Type Window. The window and a table which explains the relevant fields can be found below:

Field	Mandatory?	Description
Name of Design	Mandatory	A name to identify the design type.
Name of Software	Mandatory	The software used for preparing the design. For example, DiGGer could be used to create a randomised block design.
Template File	Mandatory	Defines how the parameters need to be inserted in the input file for the design software.
Genotype Format	Mandatory	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	Mandatory	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¶

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

A new breeding method can be added by selecting the Add Breeding Method Button which will display the Add Breeding Method Window. The window, along with a table explaining its fields can be found below:

Add Breeding Method Window (select to zoom)

Field	Mandatory?	Description
Name of Breeding Method	Mandatory	Name of the breeding methodology.
Breeding Method Type	Mandatory	Type of breeding method. A new breeding method type can be created by selecting the Add Button.
Acronym	Acronym for the name of the breeding method.
Symbol	Symbol to represent the breeding method.
Note		A short description of the breeding methodology.

Note

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

Trials¶

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

The Trials Page displays the list of defined trials which the user/group has permission to view as shown in the following image:

In the image above, the Trials Page shows several trial records. Each record contains a trial’s ID in KDDart as well as its name and available actions.

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.

Action	Description	Parent Button
Add Trait to Trial	Add a trait to the trial.	Edit Trial
Download	Download trial data.	Download CSV Template
Edit Trial	Edit the trial.
Download CSV Template	Down the CSV template for the trial.
List Trait for Trial	List the traits for the selected trial.	View Trial
Import CSV Scoring Data	Import a data file for trial	Download CSV Template
Display Trial Unit for Trial	Display the trial units/layout for the selected trial.	View Trial
Upload File	Uploads files to this trial.	View Trial
List files for Trial	List all files that have been uploaded to this trial	View Trial
Delete Trial	Delete this trial. This can only be done if there 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 Trial Data - produces a CSV file for importing into KDSmart which contains a trial’s trait results.
Download CSV Template - produces a CSV file for importing into KDSmart without any of a trial trait’s results.
Import CSV Scoring Data - loads data back into KDDart from scoring in KDSmart.

Adding Trials¶

New trials can also be created in KDManage. To add a new trial, select the Add Trial Button which will display the Add Trial Window. The window, along with a table that explains the relevant fields can be found below:

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

Note

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.

Trial Design¶

The trial design page allows data visualisation (e.g specimens) with XYZ dimensions.

To add the data to map, select from the search results and click on the button Add Specimens to Design. Data added will show in the Layout List and can be removed by clicking Remove Specimen.

The map will be displayed in the New Layout Visualised section using XYZ dimensions. Each unit comes with the drag and drop function and can be adjusted with the following settings:

Trial Design Map Settings¶
Field	Description
Max X	Maximum units show in a row.
Max Y	Maximum rows show in a block.
Max Z	Maximum blocks show in the map.
Map Size	Size of the map (e.g. 10x10, 20x20, 50x50, 100x100).
Orientation	View Direction either from top left, top right, bottom right and bottom left.
Zoom In	Enlarge the size of the map/ specific zone of the map.
Zoom Out	Reduce the size of the map.

There are also list of actions that can be performed to the map including:

Save Trial - Save the current arrangement of the map for future use.
Reset Trial - Start over again from initial stage of trial design page.
Randomise - Shuffle the arrangement of layout.
Recolour - Colour the units based on the frequency of a specimen has been used.
Rotate - Change the view direction of the map.

Trial Super Import¶

Prerequisite: Before the Trial Super Import can be used, a .csv file containing the relevant data must be prepared. This .csv should contain the columns listed within the Trial Super Import form.

This function allows the user to upload trial units for multiple trials with a single .csv file.

Where a trial already exists, it will update the existing trial. Otherwise, a new trial will be created with the given information within the csv. Similarly, existing trial units will be updated or created as necessary.

There are also flags that can be set in this super import function that will prevent certain actions:

Allow creation of Specimens/Genotypes - determines whether specimens and genotypes that don’t exist should be created.
Update existing Trial Information - determines whether an existing trial should be updated with given information.
Update existing Trial Units/Plots - determines whether existing trial units/plots should be updated with given information.

Generally, it is useful to prevent these actions where it is certain that the data is uploaded exclusively for updating existing trials/ trial units. This way, spelling and other administrative errors will be caught instead of automatically added as a new trial/trial unit/ specimen/ genotype.

To use the Trial Super Import, select the Trial Super Import button to display the Trial Super Import window.

The following illustration shows the Trial Super Import window, displaying the fields which represent the columns required for the super import to run. There are in total 4 steps:

Step 1: Trial Information

Field	Mandatory	Description
Trial Data File	M	The prepared .csv file containing the columns below.
Trial Name Column	M	The column that contains the trial names.
Site Column		The column that contains the sites for each trial.
Trial Start Date Column		The column that contains the Trial Start Date for each trial.
Trial Manager Name Column		The column that contains the manager for each trial.
Trial Type	M	The column that contains the Trial Type for each trial.
Update existing Trial Information	M	Flag to determine whether the super import should update existing trial information with given data.

Step 2: Trial Unit Dimensions

Field	Mandatory	Description
X Column	(!)	One of the trial dimension columns as part of XYZ which will be added to new trials, to create new trial units and to identify existing trial units.
Y Column	(!)	One of the trial dimension columns as part of XYZ which will be added to new trials, to create new trial units and to identify existing trial units.
Z Column	(!)	One of the trial dimension columns as part of XYZ which will be added to new trials, to create new trial units and to identify existing trial units.
EntryId Column	(!)	One of the trial dimension columns which will be added to new trials, to create new trial units and to identify existing trial units.
Position Column	(!)	(NOT CURRENTLY IN USE) One of the trial dimension columns which will be added to new trials, to create new trial units and to identify existing trial units.
Replicate Number Column	M	The column where the replicate number is listed for the Trial Unit.
Barcode Column	(!)	One of the trial dimension columns which will be added to new trials, to create new trial units and to identify existing trial units.

Step 3: Specimen & Genotype & Trial Unit

Field	Mandatory	Description
Specimen Name Column	M	The column where the specimen names within each trial unit are listed. For existing trial units, these will just be used to validate the correctness of the .csv file. The specimen number column is the primary identification of specimens within trial units.
Genotype Name Column		The column where the specimen’s genotype is defined and will be added to the specimen. For new genotypes, they will be created automatically.
Specimen Number Column	M	The column where a specimen’s number within a trial unit is defined. For existing trial units, these values will be used as the primary identification of specimens within trial units.
Treatment Column		The column where an existing treatment name is listed for the Trial Unit.
Notes Column		The column where descriptive notes for the Trial Unit are given.
TUS Label Column		The column where label for the Trial Unit Specimen are given.
Source Trial Unit Barcode		The column where the source trial unit’s barcode is listed for the Trial Unit.
Allow creation of Specimens and Genotypes	M	Flag to determine whether the super import should automatically create new specimens and genotypes.
Update existing Trial Units/Plots	M	Flag to determine whether the super import should update existing trial units with given data.

Step 4: Item Information

Field	Mandatory	Description
Item Type		The column that contains the Item Type for each item. Also, a flag to determine whether ths super import should create new items and add to specimen.
Item Unit		The column that contains the Item Unit for each item.
Amount Column		The column that contains the Item Amount for each item.
Storage Barcode		The column that contains the Storage Barcode for each item.
Item Barcode		The column that contains the Item Barcode for each item.

Note

(!) in the mandatory column denotes that at least one of these fields must be given.

Once the .csv file has been uploaded under Trial Data File, an additional view will be generated in the window that contains all the columns of the .csv file.

Now, the remaining fields can be selected using the dropdowns to match the requisite columns to the columns that exist within the uploaded file.

The existing columns on the right will turn green when they have been selected once, and turn red if they have been incorrectly selected more than once.

Once all the needed columns have been selected, select the Import button to run the super import. When the super import completes, a prompt should be shown with some statistics on the super import.

The general statistics are displayed at the top, while all the warnings will are printed in yellow below.

Add Traits to a Trial¶

Selecting Add a Trait to Trial (under dropdown) 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.

Trials need traits added to them before they can be measured in the field. To add traits to a trial, select the Add Button (adjacent to the relevant trial) which will display the Add Trial Trait Window which can be seen in the image below:

The trait is selected from a list of predefined traits (refer to the Traits topic).

When the Compulsory Checkbox is set to yes, the capturing of the trait will become mandatory when recording trial data.

More traits can be added by selecting “Add Trait to trial” (under dropdown) from the Action Column.

Downloading Trial Data¶

To download trial data in CSV format, select “Download Trial Data” (under dropdown) for the required trial. This will display the Download Trial Data Window (seen below) which provides some options for data to download. 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)

Editing Trials¶

To edit an existing trial select the Edit Button to display the Update Trial Window as seen in the image below:

Note

This window is the same as the Add Trial Window so the fields are described in the Adding Trials section.

Deleting Trials¶

KDManage can be used to delete trials from a KDDart database by selecting the ||kdmanage-button-deletetrial|| Delete Button for the relevant trial.

Trials will not be able to be deleted if any of the conditions apply: - Trials that contain trial data/sample measurements; - Trials that are part of a trial group.

Trials may be deleted if they contain trial units, traits, and uploaded multimedia. However, these 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 in the trial.

If any of the above criteria is not met, the selection of the Delete Button will display a warning message such as the one pictured below:

List Traits¶

To display the traits for a trial, select the “List Trait in Trial” (under dropdown). This will display the following list of traits in the Trait List Window:

Trial Data CSV Format¶

KDManage can accept trial data (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. sub-plot 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 a ‘:’(colon). For example, YIELD:3 indicates the third instance point of the 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).

KDSmart CSV Format

This is the standard format for the 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 name must be in the following formats:

Plot data: [TRAITNAME]:[INSTANCENUMBER]
Sub-plot data: [TRAITNAME]:[INSTANCENUMBER]#[SPECIMENNUMBER]

Dates are formatted by :

Plot data: Date-[TRAITNAME]:[INSTANCENUMBER]
Sub-plot data: Date-[TRAITNAME]:[INSTANCENUMBER]#[SPECIMENNUMBER]

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

The instance divider can also be set to “__” (double underscore) in import.

Direct DAL CSV Format

This is also called the sample measurement format and 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.

Exporting a CSV Template¶

A CSV template can be used to enter data into so that it can be imported into KDSmart and KDManage. The Export Template Button will open a window that provides options for exporting either a KDManage CSV template or a KDSmart CSV template (both options seen in the images below). The KDSmart format can be loaded into the KDSmart application for scoring trials in the field.

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.

Exporting a KDManage CSV Format Template (select to zoom)

Exporting a KDSmart CSV Format Template (select to zoom)

For the KDManage format, users will be given the choice to add date/time columns per trait instance per plot/sub-plot row.

For KDSmart format, users will be given the option to offset the specimen number. This should normally set to 0 unless legacy trials have specimen number 0.

Once the export has completed the number of trial units and trait columns in the file are displayed as (shown in the following image). Select one of the links to download the template.

CSV Template Download Window (select to zoom)

Note

The trial template file contains empty trait columns, without results.

Importing CSV Data¶

To import trial data from a CSV file, select “Import CSV Scoring Data” (under dropdown) in the Action Column for required trial (or select the Import Trial Data Button in the Trial Map Tab in the Trial View Page) and then choose the format of the CSV file that you want to import. See the section below for more information on each format.

Choose Trial Data Format Window (select to zoom)

Importing CSV Data - KDManage Format¶

When selecting the Upload with KDManage Format option from the Choose Trial Data Format Window, the Import Trial Data Window will look like the image below.

Import Trial Data Window - KDManage Format (select to zoom)

The table below outlines the fields that are present in this version of the Import Trial Data Window:

Import KDManage Trial Data Format Fields¶
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.
Instance Divider	Choose the character set that identifies the instance number of scored data

Note

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

Importing CSV Data - KDSmart Format¶

When selecting the Upload with KDSmart Format option from the Choose Trial Data Format Window, the Import Trial Data Window will look like the image below.

Import Trial Data Window - KDSmart Format (select to zoom)

The table below outlines the fields that are present in this version of the Import Trial Data Window:

Import KDSmart Trial Data Format Fields¶
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.
Plot Measure Date	If used, all measurements will use a single date defined in the Plot Measure Date Column.
Sample Type	The type of sample, as defined in type definitions.
Instance Divider	The character on how different instances are marked out in the trait columns
Remove Outliers	Option to remove outliers with given method.
Specimen Number Offset	Use if KDSmart and KDDart specimen numbers are misaligned. This will add the offset from KDSmart CSV to match KDDart specimen number.

Note

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

Importing 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. This will display the Import Sample Measurements Window which can be seen in the image below along with a table that describes the related fields:

Import Trial Sample Measurements Window (select to zoom)

Note

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

Import Trial Sample Measurement Fields¶
Field	Mandatory	Description
Data File	Mandatory	Browse to locate and select the appropriate CSV file for import.
Trial Unit ID Column	Mandatory	The column in the CSV that contains trial unit IDs of each sample measurement.
Sample Type ID	Mandatory	The column in the CSV that contains sample type IDs of each sample measurement.
Trait ID	Mandatory	The column in the CSV that contains trait IDs. These traits must be included in the trial as trial traits (see List Traits )
Operator ID	Mandatory	The column in the CSV that contains the user IDs of each sample measurement.
Measure Date/Time Column	Mandatory	The column in the CSV that contains date/time of each sample measurement.
Instance Number	Mandatory	The column in the CSV that contains an instance of each sample measurement.
Trait Value	Mandatory	The column in the CSV that contains a trait value (or measured value of trait) of each sample measurements
Trial Unit Specimen		The column in the CSV that contains the 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.

Sample Measurement Group Fields¶
Field	Mandatory	Description
Sample Measurement Group Name	Mandatory	Name for new sample group measurement. 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 mroup

Listing Sample Measurements Groups¶

To list all sample measurement groups in a trial, select the List Sample Measurement Groups Button in the Trial Data Tab of the Trial View Page. This will display the Sample Measurement Groups List Window which can be seen in the image below:

Sample Measurement Groups List(select to zoom)

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

Sample Measurement Group Actions¶
Action	Description	Parent Button
Update SM Group	Edit name, note and/or status of the sample measurement group.
Delete SM Group	Delete sample measurement group and all sample measurements in the group.

Note

Deleting sample measurement groups is irreversible.

Displaying Trial Unit Layouts¶

To view the trial units of a trial, select “Display Trial Layout for Trial” (under dropdown) in the Action Column to display the List of Trial Units Window:

Uploading a File to a Trial¶

To add a file to a trial, select “Upload file” (under dropdown)in the Action Column to display the Upload File Window (below image). File types are defined in the Types page.

To view all files that have been uploaded, select “List files for Trial” (under dropdown) which will display the List of Files Window as seen in the image below:

Adding a Trial Event¶

To add a trial event to a trial, select the + Button and then Add Trial Event in the Trial Data Tab of the Trial View Page.

Add Trial Event Fields¶
Field	Mandatory	Description
Unit	Mandatory	Unit of trial event.
Event Type	Mandatory	The type of event, as defined in type definitions.
Trial Event Value	Mandatory	Value of trial event.
Trial Event Date	Mandatory	Date of trial event.
Trial Event Note		Note of trial event.

Adding a Trial Location¶

Once a trial has been added within a site, a geographic location can be added to the trial. A Google map will be displayed in the Trial Location Tab of the Trial View Page. Drag the map to the appropriate location then double click repeatedly to zoom to the required location to define the site.

Add Trial Location Window (select to zoom)

When the map shows the required are, define the trial area by selecting the Create New Polygon Button and select on the boundary corners of the area. In the following image, the trial location has been defined and is highlighted in a darker yellow:

Add Trial Location Window - Area Selected (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 shown next.

The location field data is also listed in the text area below the map as seen in the image below:

Adding Trial Unit Layouts¶

A trial unit layout can be added to a trial by There are two ways to add trial unit layouts:

via CSV format; and
via KDCompute method (if configured).

Adding Trial Units Layouts via CSV Format¶

A trial unit layout can be added to the trial with the CSV method by selecting the Add Trial Unit Layout Button which will open the Add Trial Layout Window. The window, along with a table that outlines its fields can be seen below:

Adding Trial Unit Layouts Window (select to zoom)

Add Trial Unit Layout Fields¶
Field	Mandatory	Description
Plant Date	Mandatory	Date the specimen was planted in the trial unit (YYYY-MM-DD format).
Trial Unit Layout File	Mandatory	Browse and select the CSV import file.
Specimen Column	Mandatory	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	Mandatory	Define the number of copies of the same specimen that will be added per trial unit.
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.
Barcode Column		Barcode column in the input file. If this is left blank and a barcode configuration has been created for trial units, a barcode will be automatically generated.
Automatically Assign Repeat for Specimen		Automatically assign repetition number based on reoccurrence of specimen name.
Treatment Column		Treatment column in the input file.
Trial Unit Note Column		Trial unit note column in the input file.
Unit Position System		Type of position label of trial unit to be used.
Unit Position Start Column	Mandatory	The unit position start column in the input file, numbered from zero.
Unit Position End Column	Mandatory	The unit position end column in the input file, numbered from zero.
Trial Unit X	Mandatory	Define the column that reflects X coordinates for a trial unit layout. This column must fall within the unit position start and end column ranges.
Trial Unit Y	Mandatory	Define the column that reflects Y coordinates for a trial unit layout. This column must fall within the unit position start and end column ranges.
Trial Unit Z	Mandatory	Define the column that reflects Z coordinates for a trial unit layout. This column must fall within the unit position start and end column ranges.
Trial Unit EntryID	Mandatory	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.

Adding Trial Unit Layouts via KDCompute¶

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.

Adding a Keyword to a Trial Unit¶

Keywords can be added or assigned to trial units.

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

Step	Action
1.	From the Trial window, at the required Trial, select the Display Trial Layout Action button .
2.	At the required Trial Unit select the “Add keyword”
3.	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¶

When a trial is selected from the Trials Page, it will be displayed in a Trial View Page (see the image below). The Trial View Page provides all details and data of the selected trial including trial units, trial location, traits, etc. There are also tools available such as data curation.

A Trial Workflow Panel and a Trial Events Panel will always be visible on the Trial View Page, regardless of the selected tab.

The following sections will outline each of the tabs.

Trial Details Tab¶

The Trial Details Tab is the default tab of the Trial View Page (see the image in the above section) which shows details about the selected trial.

To edit trial details select the Edit Trial Details Button, below the trial title and ID on the top of the page. This will open the Update Trial Window which is pictured below:

Trial Units Tab¶

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 methods (see Adding Trial Unit Layouts).

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 selecting the Download Field Maps Button and or a set of printable barcodes by selecting the Download Barcodes Button.

Traits Tab¶

Trial traits can be added and viewed on the Trial Trait Tab.

Trial traits can be added individually or in the Trait Groups page.

Trial Location Tab¶

The trial location can be updated and viewed on the Trial Location Tab (see the Adding a Trial Location page).

Multimedia Tab¶

Trial multimedia can be updated and viewed on the Trial Multimedia Tab (see Uploading a File to a Trial).

Trial Data Tab¶

Trial data can be uploaded, viewed and downloaded in the Trial Data Tab.

Trial data can be viewed in a graph which shows selected traits and value:

A trial data map is a heat map based on trial unit dimensions. Red specifies higher values while blue specifies lower values:

Curate Data Tab¶

The Curate Data Tab provides options for curating data that has been collected.

Existing trial data can be curated and imported as a separate instance in the Curate Data Tab.

Tip

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

.. _lab-Nursery:

Nurseries¶

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

The Nurseries Page lists defined nurseries which the user/group has permission to view, as shown in the following image:

The following table describes the contents of the list in the Nursery Page:

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 (YYYY-MM-DD format).
End Date	The date the nursery ended (YYYY-MM-DD format).
Action	The actions that can be performed for the nursery. This is described in the following section.

Nursery Actions¶

The following table lists all the actions that can be performed for the selected nursery in KDManage:

Nursery Actions¶
Action	Description	Parent Button
Generate Layout and Crossing	Automatically generate layout and crossing, if required, from two specimen lists. See Generating Layouts and Crossings.
Add Nursery Layout	Import a nursery layout for the nursery. See Displaying Trial Unit Layouts.
Display Nursery Layout	Display the nursery layout for the nursery. See Displaying Trial Unit Layouts.
Print Nursery Unit Barcode	Export barcodes for nursery trials for printing.
List Crossings	List Crossing.	Display Nursery Layout
Harvest Crossing	If layout and crossing are present in the nursery, harvest crossing. See Harvest Crossing.	Display Nursery Layout

Note

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

Importing Crossings¶

Crossings can be imported (with a CSV file) into nurseries, which can later be harvested to create new genotype and specimen entries. To start importing crossings, select the Import Crossing Button which will open the Import Crossing Window. The window, along with a table that describes the relevant fields can be found below:

Import Crossings Window (select to zoom)

Note

The Import Crossing Window will match column names once users select a file to import.

Import Crossing Fields¶
Field	Mandatory	Description
Crossing File	Mandatory	Select the input file for the import.
Trial ID Column	Mandatory	Column number for trial ID (nurseries use a trial ID).
Breeding Method ID Column	Mandatory	Column number for breeding method.
Male Parent ID Column	Mandatory	Column number for male parent ID (Use trial Unit Specimen Id)
Female Parent ID Column	Mandatory	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

Note

Entries for male and female parent IDs must be trial unit specimen IDs used inside the nursery.

Generating Layouts and Crossings¶

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 Fields¶
Field	Mandatory	Description
Male Specimen Group (list)	Mandatory	List of specimens that will be the male in a crossing.
Female Specimen Group (list)	Mandatory	List of specimens that will be the female in a crossing.
Algorithm Name	Mandatory	A choice of algorithm which the layout and crossing will be generated with.
Make Crossing	Mandatory	An option of 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	Mandatory	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. To create a harvest crossing, select “Harvest Crossing” (under dropdown) from the Action Column of the relevant nursery. This will bring up the Harvest Crossing Window which can be seen in the image below, along with a table that outlines the fields relevant to harvest 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 Fields¶
Field	Mandatory	Description
Genotype Prefix	Mandatory	The prefix for the newly created genotype. A unique number will be generated and appended to the prefix.
Specimen Prefix	Mandatory	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 be skipped.
Create New Genotype		If un-ticked, the corresponding crossing will not have a new genotype created.