Breeding Analytics User Release Notes

Management of single-occurrence analysis (SOA) requests is improved.

This version improves user experience in terms of managing SOA requests and results. Specifically, you can now:

1. Display the results of the first job with a READY status. From the ARM data browser, click the view icon () beside the request name. This redirects you to the analysis results viewer page, where the results of the first READY job is immediately displayed. If there are none, then the next job with a FINALIZED status is shown.

2. Navigate back to the ARM browser. A new Back button is enabled in the analysis results viewer page, so you can be redirected to the ARM data browser.

3. Finalize and continue to the next job. When you Finalize a job, the next READY job is automatically loaded. After finalizing all jobs in a request, you are prompted to stay in the analysis results viewer page or go back to the ARM data browser.

4. Easily manage your results. In the Table of Residuals tab, a new filter button () allows you to show a) possible outliers only, b) suppressed data only, or c) both. The new Edit button also lets you 1) suppress all possible outliers, or 2) suppress all selected data points.

Bug fixes

You can expect to encounter no errors when voiding a job in an analysis request.

Browse occurrences from the PDM data browser.

You can now access occurrences directly from the PDM data browser, so you can easily check the quality of your data. The occurrences listed in the browser is limited to Breeding Trial (BT) experiments with a status of TRAIT DATA COLLECTED, which are the same requirements when using the Experiment Manager as an entry point to PDM. In this version, only the first 100 records are shown in the browser. This version also excludes BT experiments using the On-Farm Trial stage and the Unspecified design.

Log in the Breeding Analytics domain using your institution credentials. Open the left navigation menu and choose PDM. From the browser, look for your experiment and click the expand icon (>). Then, select an occurrence and click Explore to begin assessing your trait data.

View the audit trail for trait data.

An audit trail is a list of changes made to the quality control (QC) code of the data. This lets you view an edit history containing details on who made the changes and when, provided that these changes were saved. This feature is available in the Trait Table. Simply right-click on a cell and choose to show edit history. The small pop-up window displays the most recent change to the data. It also shows how many changes have been made altogether. You can display each change using the page navigation icons (< and >).

Management and visualization of data is improved.

The following enhanced features are implemented for this version:

1. Change QC code by trait. This option lets you update the QC codes of trait data in bulk. From the Edit button, choose to change QC code by trait. This opens the modal window, where you can choose the Trait and then the QC code you want to apply to the dataset. A notification then confirms the changes applied in the Trait Table. Click the refresh icons () in both the Stats and Trait Tables to update the values.

2. Heatmaps now use planting arrangement (PA) X and Y values. When visualizing the magnitude of the occurrence’s plot and trait data in the Heatmaps tab, the PA X and PA Y values are now used in the graph. Previously, it used the Field X and Field Y values.

Bug fixes

Reported issues have been fixed. The following are now working as expected:

1. In the Trait Table, changes to QC codes are now immediately reflected onto the data and in terms of the cell background color.

2. In the Stats Table, bad values are now properly excluded in the computation for the No. of Valid Values.

A new download feature is enabled.

The Molecular Data Analysis (MDA) tool implements key analytical pipelines for molecular analyses supported within EBS. Following its launch in July 2023, the tool is improved with a new download icon () found in the toolbar of the MDA data browser. You have the option to:

1. Download current genotyping request data. This option allows you to export the data currently displayed in the browser. As such, you can customize the displayed data using filters and the page control button. After downloading, a CSV file is then saved in your device.

2. Download cleaned genotyping request data. This option lets you export only the cleaned genotyping data, which includes a) samples with missing data of less than or equal to 5%, and b) markers with a call rate of at least 95%. After downloading, a CSV file is then saved in your device.

3. Download all genotyping request data. This option allows you to export the complete genotyping data available for a request. An XLS file is then saved in your device.

Groundwork for sparse testing is being laid out.

Sparse testing allows test entries to be randomly distributed to different occurrences. Backend developments are in progress to enable and support sparse testing in Core Breeding’s Experiment Creation tool.

Page reloads automatically after selecting a new program.

A program filter is available in the domain’s menu bar. Selecting a program tells the domain that you want to view and access only the experiments, occurrences, and data under that program. When you want to switch to a different program, the page will now reload to refresh the browsers and display only the data under it. This feature is available for both the PDM and MDA tools.