Marker Menu

When markers are available for the KDDart implementation and configuration being used, KDManage will display the Marker Menu as seen below:


Marker Menu (select to zoom)


The topics in this section are as follows:

  1. Genotyping Marker Process
  2. DNA Management
  3. Marker Data Management
  4. Marker Maps


Genotyping Marker Process

The steps for preparing, ordering and storing genotypic analysis data in KDDart are described in the following table:

Note

Bold items within the Action Column represent menu/selection text.

Genotyping Marker Process
Step Activity Action
1. Define a group of samples for genotyping. Select KDManage > Marker > Marker Data Management > Add Marker Data Management.
2. Download file (equivalent to the sample tracking file for the Online Ordering) Select the export_btn Download Button.
3. Submit the sample tracking file for the order in the Online Ordering system. Optional genotyping service (i.e. DArT)
4. Prepare specification, submit file, sign, pack and ship DNA.
5. Genotyping service performs DNA analysis
6. Genotyping service notification that results are ready

There are three choices to download marker datasets, depending on the KDDart configuration:

Genotyping Marker Process - KDManage
Step Activity Action
1. Import via KDManage. Select KDManage -> Marker -> Marker Data Management -> Upload dataset file for Marker Data Management 9
Genotyping Marker Process - KDCompute
Step Activity Action
1. Log into the Online Ordering and download the result file to a local/network location.
2. Use KDCompute to upload the result file to the KDCompute server for processing Select KDCompute -> File Manager -> Upload Files -> Select file and upload
3. Use KDCompute to import the data into KDDart Select KDCompute -> Submit a Job - > Import/Export Marker Data -> Import Marker Data -> Complete the form and submit the job
4. Check job status for successful import Select KDCompute -> File Manager -> submitted_jobs -> select job number -> download and view file(s)
Genotyping Marker Process - KDManage Collect Order via BrAPI
Step Activity Action
1. Retrieve Authentication Token and Order ID from vendors. This step may vary depending on choice of vendor.
2. Use Collect Order to import dataset. Select KDManage -> Marker -> Marker Data Management -> Collect Order

Note

DArT provides an optional genotyping/profiling service.


DNA Management

The DNA Management Page lists DNA plates that have been uploaded to KDDart.


Data Management Page (select to zoom)


Selecting the list-btn List Button for any plate will display a Plate Window which lists extracts that are associated with that plate (pictured below).


Plate Window (select to zoom)


Adding a DNA Plate

To add a new DNA plate, select the Add DNA Plate Button located on the DNA Management Page. This will display the Add DNA Plate Window as shown in the image below:


Add DNA Plate Window (select to zoom)


Field descriptions to assist with completing the form are displayed in the following table:

Add DNA Plate Fields
Field Mandatory? Description
Trial Name Mandatory Trial that this plate is associated with. Upon selecting an existing trial, this will display the relevant plates to this trial.
Creation Date Mandatory Date the genotyping service was created.
Plate Layout   CSV file containing plate name, row, column and genotype name columns.
Tissue Mandatory Tissue used in this plate.

Plates as in the following illustration may be removed using the Remove Plate button at the bottom left.

Also, individual cells may be edited or removed as required. The image and table below contain more information:


Add DNA Plate Window - Cells (select to zoom)


Add DNA Plate Fields - Individual Cells
Field Mandatory? Description
Plate 1 Name Mandatory Name for this iteration of plate.
Plate 1 Description   Description of the plate.
Plate 1 Storage Location   Location where the plate is stored.
Plate 1 Tissue   Tissue used in these plates.


Editing a Well Plate

Selecting a well will display the Edit Well Plate Window, as displayed in the following image, where the well may be edited or removed using the buttons on the window.


Editing Well Plate Window (select to zoom)


Note

Hovering the mouse above a well will display the trial unit position and the specimen name.


Marker Data Management

The Marker Data Management Page lists marker datasets that have been imported to KDDart and provides options for managing them including viewing, editing, and submitting samples.


Marker Data Management Page (select to zoom)


Adding Marker Data Management

To add a new marker data management genotyping/profiling entry, select the Add Marker Data Management Button located on the Marker Data Management Page to display the Add Marker Data Management Window:


Add Marker Data Management Window (select to zoom)


Field descriptions to assist with completing the form are displayed in the following table:

Field Mandatory? Description
Marker Data Management Name Mandatory Text string to describe the genotyping service.
Description   Additional description of the genotyping service.
Manager Name   A designated manager for the genotyping service who is defined in KDDart Contacts.
Selected plates Mandatory Plates from DNA management selected for this marker data. Drag and drop plates from the Plates List to add specific plates to this marker data.
Access Fields Mandatory Access and permissions. See the Access Settings and Permissions topic.

Each plate that is selected will be displayed in the window. See the image and table below for more information:


Plate Added to the Add Marker Data Management Window (select to zoom)


Add Marker Data Management Window - Plate Fields
Field Mandatory? Description
Plate 1 Name Mandatory Name for this iteration of plate.
Plate 1 Description   Description of the plate.
Plate 1 Storage Location   Location where the plate is stored.

Plates as in the following image may be removed using the Remove Plate button at the bottom left of Plates List

Note

Hovering the mouse above a well will display the trial Unit position and the specimen name.


Editing a Well Plate

Selecting a well will display the Edit Well Plate Window (as displayed in the following image) where the well may be edited or removed using the buttons on the window.


Edit Well Plate Window (select to zoom)


Upload Dataset File

To upload a new dataset to a marker data management group, select “Upload Dataset File” (under kdmanage-button-updateanalgroup dropdown) in the Actions Column for the required group. This will display the Upload Dataset File Window. The window and a table that describes the related fields can be found below:


Edit Well Plate Window (select to zoom)


Note

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

Tip

After selecting a file to upload, the file contents will be displayed underneath the form. This can be used to refer to the correct columns as required.

Field Description
CSV Data Set File Browse to locate and select the appropriate CSV file for import.
Plate Name Row The row that contains the plate names.
Well Row Position Row The row that contains the well row positions.
Well Column Position Row The row that contains the well column positions.
Header Row The row that contains the headers.
Marker Name Column The column that contains the marker names.
Sequence Column The column that contains the sequences.
Meta Data Start Column The first column in the CSV file containing meta data for import.
Meta Data End Column The last column in the CSV file containing meta data for import.
Data Start Column The first column in the CSV file containing data for import.
Data End Column The end column in the CSV file containing data for import.
Data Set Type The type of dataset, as defined in type definitions.


Collecting an Order

To collect a completed order and create relevant data points, select the Collect Order Button located on the Marker Data Management Page. This will display the Collect Order Window which is pictured below, along with a table that describes the relevant fields:


Collect Order Window (select to zoom)


Note

This feature requires system administrator set up, including the creation of relevant types and KDManage system configuration.

Field Mandatory? Description
BrAPI Genotyping Vendor Base URL Mandatory Select the vendor BrAPI URL.
Order ID Mandatory Full Order ID of completed order for import.
Authentication Token Mandatory Authentication token from genotyping vendor.
Source Field for Sample ID Mandatory KDDart entity that will be created or linked to sample ID.
Access Fields Mandatory Access and permissions. See the Access Settings and Permissions topic.


Printing Barcodes for Marker Data

To download a set of barcodes for the Marker Data Management group, select “Print Barcodes” (under kdmanage-button-listextract dropdown) in the Action Column for the required group in the Marker Data Management Page.


List Marker Datasets of Group

To list all datasets in a group, select kdmanage-button-listdataset List Datasets in the Actions Column for the required group in the Marker Data Management Page.


List Datasets Window (select to zoom)


Visualising a Dataset with a Heatmap

To visualise a dataset with a heatmap, select kdmanage-button-visualisedata Visualise Data in the Action Column of the List Datasets Window (for the required marker dataset of a group). This will open the Marker Data Window as seen in the image below:


Marker Data Window (select to zoom)


Data can be further filtered and sorted to retrieve more specific data. Visualised data can also be downloaded as an SVG file for further use.

Individual sample/marker squares can also be selected to reveal more information about a sample.


Downloading a Dataset

To download a dataset, select kdmanage-button-downloaddata Download Data in the Action Column of the List Datasets Window (for the required marker dataset of a group). This will open the Download Dataset Window as seen in the image below:


Download Dataset Window (select to zoom)


Download Dataset Fields
Field Description
Format Type The format that the dataset will be downloaded in. In standard installations, this will either be CSV or Flapjack. Extra formats can be added with extra development.
Marker Metadata Field List Chosen marker metadata fields to include in the download. Leave blank to include all.
List of DNA Extracts Chosen DNA Extracts to include in the download. Leave blank to include all.
List of Marker Chosen markers to include in the download. Leave blank to include all.
Marker list from CSV Upload a CSV of markers to filter from.
Extract list from CSV Upload a CSV of extracts to filter from. Use genotype names.

Data can be further filtered and sorted to retrieve more specific data.


Submitting Samples to a Genotyping Vendor

If KDManage has bee configured with a vendor ID, users will be able to submit samples to the vendor from analysis group plates. To submit, select kdmanage-button-submitsample Submit Samples in the Actions Column for the required analysis group. That will display the Sample Submissions Window which is shown below, along with a table that explains it’s fields:


Download Dataset Window (select to zoom)


Sample Submission to Genotyping Vendor Fields
Field Description
BrAPI Genotyping Vendor Base URL The URL for genotyping vendors. These must be configured by a system administrator.
Source Field for Sample ID How samples will be identified.
Authentication Token Authentication token from vendor.


Downloading Genotyping Results from a Vendor

If KDManage has bee configured with a vendor ID, users will be able to download genotyping results to the vendor for an analysis group. To submit, select “Download Genotyping result” (under kdmanage-button-submitsample dropdown) in the Action Column for the required analysis group.


Marker Maps

The Marker Maps Page lists marker maps that have been created within KDDart.


Marker Map Page (select to zoom)


Adding Marker Maps

To add a new marker map, select the Add Marker Map Button located in the Marker Map Page to open the Add Marker Map Window. An image of the window and a table explaining the related fields can be found below:


Add Marker Map Window (select to zoom)


Add Marker Map Fields
Field Mandatory Description
Map Name Mandatory Text string to describe the marker map.
Map type Mandatory The type of marker map, as defined in type definitions.
Map Software   Name of software used to create map.
Model Reference Information   Model reference information for physical maps.
Map Description   General description of the map.
Map Parameters Mandatory Map parameters (also software parameters) used for creation.


Importing a Marker Map Position

To add a new marker map position, select the kdmanage-button-importmarkermap Import Marker Map. This will open the Import Marker Map Position Window which is pictured below, along with a table that details related fields:


Import Marker Map Position Window (select to zoom)


Note

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

Import Marker Map Fields
Field Description
Marker Map Position File Browse to locate and select the appropriate CSV file for import.
Marker Name Column The column that contains the marker names. Markers must match the ones contained in the selected analysis group.
Contig Name Column The column that contains the contig names
Contig Position Column The column that contains the contig positions
Analysis Group The analysis group associated with uploaded marker map positions. The analysis group must have a least one dataset.

Tip

After selecting a file to upload, the file contents will be displayed underneath the form. This can be used to refer to the correct columns as required.