BA 2024

Viewing analysis requests is improved.

To improve user experience, the following features are now implemented:

1. Filter by occurrence and trait. In the ARM data browser, you can now use the filter feature under the Occurrence and Trait columns. Simply supply keywords in the data fields under each column header and wait for the data browser to reload with the filtered results. The filters can also be used at the same time, allowing for more narrowed results. Lastly, click on the icon to remove the filters.

2. Scroll and navigate pages. When viewing () the results of your analysis requests, both the List of Jobs and Job Outputs panels now feature scrollbars and page navigation so you can easily move across results. This locks the position of both panels to view them at the same time. This feature is especially helpful for requests with more than 10 jobs.

Creating multi-occurrence analysis (MOA) requests is improved.

The following features can now be accessed as you create your MOA requests. Specifically, you can now:

1. Select latest finalized jobs. In the Experiments tab, you can now tick the checkbox beside the occurrence name to select all the recently finalized job IDs. You can still also select other job IDs for specific traits. Additionally, unselecting one job ID also unselects the checkbox beside the occurrence name.

2. Download BLUPs. In the Options tab, you can now add BLUPs to the list of data you can extract from the single occurrence analyses (SOA). The resulting zipped file thus contains the soa_result_predictions_BLUPs.csv file. Previously, the option to include BLUPs is disabled.

3. View improved file names. After downloading the result files from SOA and MOA requests, file names now contain a unique hash at the end, while downloaded MOA input files are also renamed. This allows for more descriptive file names that can be easily identified by users.

MOA reports are enhanced.

The following files from the downloaded () multi-occurrence analysis (MOA) results are now improved:

1. MOA report. This main CSV file’s worksheets now have improved relevance in terms of the datasets available.

   1. Request Info worksheet. The plot count column is now removed. It was decided that this data column does not contribute relevant information in the 2nd step-MOA.

       

   2. 2nd Step - BLUPs worksheet. The numbering in column A is now in ascending order.

2. Analysis input files. These files are now included in the folders created for each job in the request.

Bug fixes

You can expect to encounter no errors when:

1. downloading SOA reports through MOA, such that correct entry rows are reflected with no duplicates,

2. viewing requests with a void status where all buttons and checkboxes are disabled, and

3. viewing each job in a request, such that the occurrence name is accurately displayed.

Visualize data for traits with at least one good or questionable data point.

In the Box Plot, Histogram, Scatter Plot, and Heatmap tabs, the trait list box now only contains those traits with at least one plot trait data whose quality control (QC) code is good or questionable. Otherwise, the trait list box will be empty. This feature allows users to generate valid visualizations from their plot trait datasets. Previously, all traits are enabled for visualization by default.

Suppression of values in the Box Plot tab is enhanced.

The following improvements are featured:

1. Suppress values for traits with generated box plots. After generating the box plot graphs for some or all of the traits in your occurrence, the Suppress Values feature is enabled. Here, you can now select the trait whose data you want to suppress. Simply click the Trait drop-down menu to view the traits available for selection. Take note that only those traits with generated box plots can be seen in this list. Then, define the a) upper bound and/or b) lower bound trait values you want to suppress. Click Suppress to apply the changes to the box plot graph. These changes are also reflected in the Stats and Trait Table.

2. Suppress good and questionable data. Aside from outliers, you can now also suppress non-outliers, such as good (G) and questionable (Q) trait data. After clicking Apply, the box plot graph/s are also updated. This feature is also renamed to “Suppress Values”, to correctly indicate the full scope of its functionality.

Management of plot trait data is improved.

To improve user experience, the following improvements are featured:

1. View enhanced graph colors. A darker green shade now colors the graphs for all visualizations for better contrast. Previously, the graphs had a lighter green shade.

2. Optimized saving process. This enhancement is deployed to avoid timeout errors when saving multiple changes at once.

Bug fixes

Reported issues were resolved. You can now:

1. view the Trait Table’s plot data properly, such that the data remains visible even after filtering and navigating to other tabs,

2. view occurrences with the TRAIT DATA COLLECTED status in the PDM data browser based on the selected program data filter,

3. open an occurrence from the Experiment Manager and expect to see the same program data filter in PDM, and

4. generate heatmaps, such that:

   1. all suppressed, missing, and bad trait values are now gray in color, and

   2. occurrences with no block data will not have the block option in the drop-down menu.

Processes surrounding randomization and uploading of designs are improved.

Backend enhancements are now applied to Core Breeding’s Experiment Creation tool when generating randomizations for your Breeding Trial design. Specifically, you can now:

1. View error notification for uploaded RCBD design file with Rep and Block columns. In the upload modal window, an error message is now displayed when you upload RCBD design files containing both Rep and Block columns. This is because, for non-sparse and sparse testing, RCBD only requires either the Rep or Block values, but not both.

2. Use the updated P-Rep design. Changes to the design definition for the non-sparse Partially Replicated (P-Rep) design is now implemented in the Design tab of Core Breeding’s Experiment Creation tool, where the rep information is not required. This enhances both the front-facing interface and the backend validation.

Non-sparse designs are improved.

Updated definitions for the following non-sparse designs were enabled:

1. Alpha-Lattice,

2. Randomized Complete Block Design (RCBD),

3. Augmented RCBD, and

4. Partially Replicated (P-Rep).

This supports the new user interface implementation in Core Breeding’s Experiment Creation tool, specifically in the Design tab.

Bug fix

You can now encounter no errors when:

1. uploading randomization files even when the columns for field coordinates are empty, and

2. uploading and validating a P-Rep, Augmented, and Unspecified designs file with or without Reps.

Browse and view genotype requests and their data.

From the left navigation panel, select the MDA tool. This should open the newly-enabled data browser, which houses genotype requests and their basic information. The icon allows you to view the request’s data stored in the following tabs: Genotype Data, Excluded Germplasm, and Excluded Markers. An info panel also provides a summary of Germplasm and Markers, as well as the Call Rate Threshold. As of this version, the filter features in the tabs and buttons in the Call Rate Threshold are not yet working, while data on Excluded Markers is not yet available.

Bug fix

You can expect to encounter no errors when navigating to the MDA data browser and viewing genotype requests.

Accessing tools and programs is improved.

This version improves on the following:

1. Programs. On the program data filter, a scrollable drop-down menu is now featured when the available programs for selection is more than 10. This allows for an efficient display, preventing the list to occupy the entire screen.

2. Timeout. After an hour of inactivity, you will be logged out of BA. A notification will be displayed to inform you that you have been logged out due to inactivity. Simply log in again to resume your activities.

Bug fix

The program data filters are working as expected, such that the data from the selected program data filter is reflected.